Cortical Neurophysiology Database Cortical Neurophysiology Database 2006-01-10T17:22:44 2006-03-10T13:26:56 lni http://neurodatabase.org Daniel Gardner dgardner@med.cornell.edu Adrian Robert arobert@med.cornell.edu CSV, XML, BrainML neurophysiology, spike train, membrane potential, time seriesContains spike trains, voltage time series, and some derived histograms from single cell and multiunit activity.cerebral cortex, neocortex, animal subjectsThe database focuses on in vivo somatosensory and visual activity during task performance. Access by XML over HTTP according to protocols defined in http://brainml.org/viewVersions.do?modelID=772 BrainML (http://brainml.org) cortex model: http://neurodatabase.org/dataserver/showModel.do?modelID=760 This resource contains only a few data sets, but they are of high quality and have been used for reanalysis by several parties. (Comments would occur here.) (Comments would occur here.) IATR Internet Analysis Tools Registry 2006-01-18T15:20:33 2006-03-10T13:31:51 nif http://www.cma.mgh.harvard.edu/iatr/ David Kennedy dave@cma.mgh.harvard.edu Christian Haselgrove ch@cma.mgh.harvard.edu analysis software, metadata The IATR provides a searchable listing of neuroscience analysis software. Users and developers alike should find it a useful resource for finding software suited to a particular task. No. We knew of no preexisting vocabulary for describing analysis software, so we have been evolving our own. Listings in IATR are user-maintained, and every attempt is made to make IATR known to software developers, but it is of course impossible to keep a definitive listing up to date. Descriptive fields have been chosen and may (rarely) change; keywords and platforms are a custom vocabulary which will evolve over time. L-Measure L-Measure 2006-01-15T20:49:25 2006-01-15T20:49:25 nif http://krasnow.gmu.edu/L-Neuron Giorgio A. Ascoli ascoli@gmu.edu Ruggero Scorcioni rscorcio@gmu.edu neuronal morphology, morphometric analysis, 3D reconstructions, neurolucida, dendritic trees Software for the extraction of quantitative measures from digital reconstructions of neuronal morphology. Reads all known formats, allows analysis and statistical comparison of groups of neurons, individual cells, and selected portions of the arborization. The tool can be used through a web browser as a Java applet, or it can be downloaded locally on any java-enabled machine (tested on Windows and Linux). The resource is most useful for owners and users of digital reconstructions and researchers interested in the quantitative analysis of neuronal morphology. ModelDB Modeldb Neuronal and Network Models 2006-01-26T16:28:15 2006-03-10T13:46:24 nif 2006-01-26T16:28:15 2006-03-10T13:46:24 nif http://senselab.med.yale.edu/senselab/modeldb Michael Hines michael.hines@yale.edu Tom Morse Tom.Morse@Yale.edu 203-785-5843 Yale SenseLab C or C++ program CSIM Catacomb CellML Chemesis FORTRAN Genesis IGOR Pro Java KInNeSS L-Neuron MATLAB MCell MVASpike NCS NEST (formerly BLISS/SYNOD) NEURONPM NSL Neosim NeuGen Neuron NeuronC Octave PDP++ PSpice QBasic/QuickBasic/Turbo Basic QuB SABER SNNAP SciLab Simulink Surf-Hippo Topographica Virtual Cell XML XPP computational model, simulation, neuronal, network, compartmental model ModelDB provides an accessible location for storing and efficiently retrieving computational neuroscience models. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models. disco We review requests from our contributors for new words in our currated hierarchical vocabulary. The definitions for our terms are available on the architecture pages. We have had very positive reviews from the computational neuroscience community on the utility of our resource. We have lists of attributes that can be assigned to the model entries for use in searching. ORDB Olfactory Receptor Database 2006-01-25T16:31:38 2006-03-10T13:45:59 nif http://senselab.med.yale.edu/ordb Chiquito Crasto chiquito.crasto@yale.edu Chiquito Crasto chiquito.crasto@yale.edu Yale SenseLab html,xml,owl(experimental) ORDB began as a database of vertebrate olfactory genes and proteins and continues to support sequencing and analysis of these receptors by providing a comprehensive archive with search tools for this expanding family. Because of the associated growth of interest in other chemsensory receptors, the database has grown over the years to include a broad range of chemosensory genes and proteins, that includes in addition to olfactory receptors, the taste papilla receptors, vomeronasal organ receptors, insect olfaction receptors, Caenorhabditis elegans chemosensory receptors, and fungal pheromone receptors. disco Internal use; mapped to UMLS concept ids. ORDB is the primary resource for information regarding olfactory and other chemosensory receptors Each Chemosensory receptor is represented by attributes and descriptors (values). ORDB is built on the EAV/CR (Entity-Attribute-Value with Classes and Relationships) schema. Chemosensory receptors are represented by an ORDB nomenclature and the common name (given by the laboratory that has cloned or otherwise identified the receptor). A consensus nomenclature represents receptors that have been identified from complete genome sequencing results. neuromorpho.org neuromorpho.org 2006-02-10T11:37:52 2006-02-10T11:37:52 nif http://neuromorpho.org/ Giorgio Ascoli ascoli@gmu.edu Giorgio Ascoli ascoli@gmu.edu Part of the L-Neuron resource suite, hosted by George Mason University. SWC (ASCII) files Digital reconstructions, neuronal morphology, dendrites, axons NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons. Each neuron in NeuroMorpho.Org is represented by a unique identifier, general information (metadata), the original and standardized ASCII files of the digital morphological reconstruction, and a set of morphometric features. disco Useful for researchers interested in modeling of dendritic and axonal structures. Also contains some of the most complete axonal arborizations digitally available in the community. Contains contributions from over two-dozen labs and is continuously updated as new morphological reconstructions are collected, published, and shared, with the goal of densely covering all available data. Cell Centered Database Cell Centered Database 2006-02-13T16:08:05 2006-02-13T16:08:05 nif http://ccdb.ucsd.edu Maryann Martone mmartone@ucsd.edu Joy Sargis jsargis@ncmir.ucsd.edu National Center for Microscopy and Imaging Research; Biomedical Informatics Research Network (BIRN) TIFF, Biorad PIC format, Analyze 7.5, some custom formats light microscopy, electron microscopy, 3D reconstruction, electron tomography, brain anatomy, glia The Cell Centered Database houses high resolution 2D, 3D and 4D datasets produced from reconstruction of light and electron microscopic images. The CCDB tracks the process of reconstruction from raw data, to reconstruction, to analysis products derived from the reconstruction and makes these datasets available to the scientific community. disco Data is cross referenced to shared ontologies/terminologies like the UMLS where possible; if a concept is not present in a shared terminology, then it is added to the Biomedical Informatics Research Network (BIRN) terminology database Bonfire. A CCDB dictionary contains terms and their ontological cross reference. The CCDB provides for dissemination of high resolution cell level data for visualization and re-analysis of structural and protein localization data derived from neurons, glia and other tissues. Many of the datasets include derived biological models, e.g. tree structures, surfaces, that can serve as the basis of mathematical models and simulations. CDT Cerebellar Development Transcriptome 2006-03-09T00:05:56 2006-03-10T13:43:37 BIRN http://www.cdtdb.brain.riken.jp/CDT/Top.jsp mol-neurogenesis@brain.riken.jp The Laboratory for Molecular Neurogenesis of RIKEN Brain Science Institute cerebellar development, gene expression, in situ hybridization, cDNA microarray, fluorescent differential display, RT-PCR mouse, cerebellar cortex, mRNA, brain Cerebellar Development Transcriptome (CDT) Database provides spatio-temporal gene expression profile information for deciphering the outline of the genetic blueprint of mouse cerebellar postnatal development. The CDT database includes a list of cerebellar developmental (CD) genes and their spatio-temporal expression profiles during postnatal cerebellar development. Spatio-temporal patterns of gene expression were determined during cerebellar post natal development (with some E18 data as well) using a multipronged approach. Techniques included cDNA microarray, Gene Chip, RT-PCR, in situ hybridization and fluroescence differential display. Gene names, gene descriptions, and alternative names to CD genes were defined according to the NCBI-Entrez Gene, the NCBI-UniGene, the Jackson Laboratory-Mouse Genome Informatics (MGI), and the Sanger Institute/EBI-Ensembl. This is a very impressive site which allows users to examine and query gene expression patterns according to temporal expression, spatial expression within cerebellar layers, brain distribution and brain specificity. This resource will be useful for both students and researchers. The interface is very mature and easy to use. It provides both text boxes and clickable diagrams to select regions. GenePaint GenePaint.org 2006-03-09T03:08:42 2006-03-16T11:18:46 BIRN http://www.genepaint.org gpscience@mpihan.mpg.de gptech@gsdg.de Max-Planck Institute for Biophysical Chemistry non radioactive in situ hybridization, gene expression, mouse, atlas; annotated, mRNA, C57Bl6, mouse embryo, adult mouse, transmitted light microscopy GenePaint.org is a digital atlas of gene expression patterns in the developing and adult mouse. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections. Sections were labeled using non radioactive in situ hybridization with riboprobes and annotated for level of gene expression (not detected, weak, medium, strong) and pattern (ubiquitous, regional, scattered). Sections are available from several developmental ages: E10.5, E14.5 (whole embryos), E15.5, P7 and P56 (brains only). Annotation of gene expression level and pattern is mapped to a standard set of terms that are defined in the documentation. Anatomical structures and hierarchies are derived from several sources and are published in the documentation. In some cases, the characterization of the resource can be more than one term: e.g., atlas and database. Five key words aren't always enough. Atlas of Adult C57BL/6J Mouse Brain Atlas of Adult C57BL/6J Mouse Brain 2006-03-15T00:35:34 2006-03-16T11:12:06 BIRN http://www.bnl.gov/CTN/mouse/ Leonard Slatest slatest@bnl.gov Center for Translational Neuroimaging, Brookhaven National Laboratories Analyze 7.5 3D brain atlas, magnetic resonance microscopy, probabilistic atlas, mouse, adult male C57BL/6J mouse, T2 weighted magnetic resonance microscopy, average shape atlas, autosegmentation This site provides access to several 3D brain atlases based on magnetic resonance microscopy, including a probabilistic atlas based on 10 brains and an average shape atlas. Twenty structures were segmented from each brain using Amira. Perfused brains were obtained from male C57BL/6J mice aged 12-15 weeks. Twenty structures were segmented manually using Amira, followed by autosegmentation of additional brains using AIR. Twenty high level brain regions were labeled according to Paxinos and Franklin (1997) and Hof (2000). This is a very nice website which has multiple segmented MRI data sets available. The probilistic and average shape atlas will be useful. The segmentation is very coarse, but appears to be of high quality. We should probably be able to select multiple resource types, e.g., the site I just reviewed is both a database and an atlas. Also, can you provide definitions of the different types of resources (forgive me if I've asked that question already. Also, we'll need the capacity to edit this form; sometimes all of the information is not available when I first fill it in. Gene Expression Profiling in Spinal Cord Injury Gene Expression Profiling in Spinal Cord Injury 2006-03-15T01:40:43 2006-03-15T01:40:43 BIRN http://spine.rutgers.edu/microarray/ Ronald P. Hart rhart@rci.rutgers.edu The W.M. Keck Center for Collaborative Neuroscience, Spinal Cord Injury Project, Rutgers University PDF, database is downloadable according to the site, but the link wasn't working at this time. microarray, rat, spinal cord injury, contusion; Affymetrix, Rat Neuro U34 chip, Long Evans rat This database provides on-line search of microarray datasets generated from rat spinal cord after contusion injury. Both the primary injury site and a site 5 mm distal to the injury site were assayed. Tissue was obtained from 24 Long Evans rats subject to spinal cord contusion injury using the MASCIS impactor (formerly known as the NYU impactor). RNA expression was assayed at the site of injury and distal to the site of injury using the Affymetrix Rat Neuro U34 chip. Looks like it uses the Genbank ID This site houses microarray data that was published in a 2001 article in Physiol. Genomics (Camel et al., 7:201, 2001). Access to newer data is provided by a link to the PEPR site. Looks like the site was recently updated and some of the broken links were fixed. We should probably have a description of whether the site is actively maintained or not. SCIgenes Spinal Cord Injury-Related Gene Database 2006-03-16T00:53:44 2006-03-16T00:53:44 BIRN http://scigenes.uky.edu/ Tim McClintock, Ph.D. mcclint@uky.edu Jolanta W. Jaromczyk jolanta@pop.uky.edu University of Kentucky spinal cord injury, gene expression, neuron, glia, regneration This database has the gene expression profiles of over 1200 genes at various time points after spinal cord injury. The database may be searched using a variety of criteria including gene name, type of injury, treatment, organism, temporal response and cell type. The data are derived mostly from rodent, but there are also a few results from chicken and monkey. Swiss Prot, Locus Link, GeneBank accession numbers provided. Other fields such as cell type and organism did not reference a standard terminology. This resource has compiled the results of gene expression studies after spinal cord injury from the literature. It is easy to search along multiple axes and contains links back to the primary literature. Neuroanatomy and Neuropathology on the Internet Neuroanatomy and Neuropathology on the Internet 2006-03-17T02:25:28 2006-03-17T02:25:28 BIRN http://www.neuropat.dote.hu/ Katalin Hegedus, MD, Ph. D. hegedus@jaguar.dote.hu Neuropathology Laboratory, Department of Neurology, University of Debreen, Hungary JPEGs available for download brain atlas, histology, neuropathology, functional neuroanatomy This site serves as a gateway to a set of human neuroanatomical resources developed at the University of Hungary. Resources include an on-line brain atlas, a neuropathology atlas, functional neuroanatomy for neurologists and an extensive series of links to other neuroanatomy and neurological resources on the web. The original resources developed by this site include a set of neuropathological slides covering many neurological conditions, e.g., Alzheimer's disease, an atlas of normal human neuroanatomy based on unstained brain slices, along with histological images of brainstem and spinal cord. On-line quizzes are also provided. The site uses standard anatomical names with their Latin translations. The exact terminology employed was not specified. This is an excellent educational site and gateway to neurological resources on the web. Comparative Mammalian Brain Collections Comparative Mammalian Brain Collections 2006-03-18T01:50:53 2006-03-18T01:50:53 BIRN http://www.brainmuseum.org/ Wally Welker welker@neurophys.wisc.edu http://www.brainmuseum.org/feedback.html The University of Wisconsin, Michigan State University, National Museum of Health and Medicine Images can be downloaded as JPEGs. comparative anatomy, brain atlas, brain collections, mammalian brain, histology, brain sections, mammals, educational resources, Nissl stain, myelin stain, whole brain, animations This site contains a large collection of digitized histological sections from a large number of mammalian brains, including exotic species like anteaters. This is just a subset of sections from large comparative collections at the University of Wisconsin and Michigan State University. Brains were embedded in celloidin, sectioned in the coronal plane and stained for Nissl or myelin. Views of the whole brain are available for most species as are descriptions of the animal and its habitat. Anatomical regions are not delineated. The terminology used for taxonomy wasn't specified. This site is an important resource for those interested in comparative anatomy, beyond the usual model organisms. The sections and images are of generally high quality although most are not annotated. PEPR Public Expression Profiling Resource 2006-03-21T01:13:54 2006-03-21T01:13:54 BIRN http://pepr.cnmcresearch.org/ Eric Hoffman PEPR@cnmcresearch.org Josephine Chen jchen@cnmcresearch.org Children's National Medical Center dat, chp or cel files available for download A database of microarray gene expression studies conducted through the Children's National Medical Center. Projects involve multiple tissues, including brain and spinal cord and several models of brain/spinal cord injury or pathologies. An online query interface is provided and data can be downloaded in a variety of formats or ported to some tools available through the site. No description of terminology was provided. This resource is not in my field so I can't comment too much on the utility but it appears to have a lot of data available. I was unable to get many of the visualization functions to work. The data appear to be publicly available without registration but access to the analysis and visualization tools requires an account. We should put a field to check if the resource will accept outside data. Atlas of the Human Brain Stem Atlas of the Human Brain Stem 2006-03-22T03:13:38 2006-03-22T03:13:38 BIRN http://www.msu.edu/~brains/brains/human/brainstem/index.html John I. Johnson johnij@aol.com Brain Biodiversity Bank: Michigan State University Images are available for download as JPEGs. atlas, brainstem, human, cell stain, fiber stain, human, brain section This site contains a series of axial sections stained for cell bodies or fibers at six rostro-caudal levels of the human brain stem. Sections are labeled for approximately 50 structures and are searchable through a web interface. For each level, a fiber and cell stain is provided. Labels may be turned on or off. Standard anatomical terms are used, although there is no reference to a particular terminology. The creators of the site encourage the use of the data and it is available freely, but ask that they be contacted before any use. Perhaps a "use with permission" category should be added to the license list. SumsDB Surface Management Systems Database 2006-06-26T12:58:07 2006-03-24T17:52:50 nif NDG 28494 http://sumsdb.wustl.edu/sums/ David van Essen vanessen@brainvis.wustl.edu Ping Gu ping@brainvis.wustl.edu Neuroimaging standard formats as well as surface-based file formats. architecture; morphology; anatomy; atlas; cortex; mri; olfactory; map; fmri; volume; talairach; connections; 3d models; cerebellum; segmentation; white matter; gray matter; warping; imaging; data management; data storage Surface-based atlases of primate and rodent cortex. To view most data user must use Caret or Java-enabled WebCaret software package. transform.py; supporting agencies: NIMH; NASA; NSF; NLM; NPACI; NCI; HBP SenseLab The SenseLab Project 2006-06-26T12:58:07 2006-03-24T17:54:41 nif NDG 28498 http://senselab.med.yale.edu Gordon Shepherd gordon.shepherd@yale.edu Gordon Shepherd gordon.shepherd@yale.edu HTML, XML SenseLab contains seven related databases that support experimental and theoretical research on the membrane properties: CellPropDB, NeuronDB, ModelDB, ORDB, OdorDB, OdorMapDB, BrainPharm A pilot Web portal that sucessfully integrates multidisciplinary neurocience data transform.py; Supporting agencies: NIH; NIMH; NINDS; NASA; NSF; NLM; NCI; HBP; NIDCD; NIA [Resource Type].[Educational] BAMS Brain Architecture Management System 2006-06-26T12:58:07 2006-03-24T17:56:22 nif NDG 28586 http://brancusi.usc.edu/bkms Larry Swanson lswanson@usc.edu Mihail Bota mbota@usc.edu HTML, XML architecture; anatomy; ontology; atlas; cortex; cellular/molecular; connections; cerebellum; nissl; neuroinformatics; data managementa repository of information about brain structures from different species which has a set of inference engines for processing the neurobiological data at different levels of organization of the cns. disco transform.py; supporting agencies: NIH; NIMH BrainInfo BrainInfo 2006-06-26T12:58:07 2006-03-24T17:57:48 nif NDG 28605 http://braininfo.rprc.washington.edu Douglas Bowden dmbowden@u.washington.edu Douglas Bowden dmbowden@u.washington.edu HTML architecture; morphology; anatomy; ontology; histology; atlas; cortex; mri; map; talairach; connections; brainstem; cerebellum; subcortical; segmentation; NeuroNames; portal BrainInfo is a web portal to information about human, macaque, rat and mouse neuroanatomy and a repository for original data on the macaque brain. Descriptions and illustrations of some 2000 brain structures are accessible by more than 12,000 names in seven languages. disco XML NIF entry generated by program transform.py; supporting agencies: ncrr; nimh; nlm; other species: human; macaque; mouse; rat; other mammalian; other non human primate; monkey BrainWeb Simulated Brain Database 2006-06-26T12:58:07 2006-03-24T17:59:04 nif NDG 28608 http://www.bic.mni.mcgill.ca/brainweb/ Alan Evans alan@bic.mni.mcgill.ca Robert Vincent bert+bw@bic.mni.mcgill.ca mri; simulation; imaging; neuroinformatics A database of human brain images derived from a realistic phantom and generated using a sophisticated MRI simulator. Custom simulations may be generated to match a user's selected parameters. The goal is to aid validation of computer-aided quantitative analysis of medical image data. transform.py Schramm Lab Spinal Cord Atlases Schramm Lab Spinal Cord Atlases 2006-03-25T12:34:45 2006-03-25T12:34:45 BIRN http://www.jhu.edu/lschramm/spinalindex.htm Lawrence S. Schramm lschramm@bme.jhu.edu Lawrence P. Schramm, Ph.D., Johns Hopkins University JPEG serial tissue section, histological section, rat, thoracic spinal cord, lumbar spinal cord This site contains serial histological sections of rat spinal cord at the lumbar and thoracic levels. Serial sections of rat spinal cord cut in the horizontal and sagittal planes. No terminology employed The quality of the sections is reasonable, if at low resolution. The site works nicely, but there are no annotations on the images which limits their utility as an atlas. Because of the nature of the site, it is difficult to comment on the coverage; it is what it is. We should probably have degrees of atlases; e.g., series of slices, annotated slices, coordinate systems etc. CoCoMac Collations of Connectivity Data on the Macaque Brain 2006-06-26T12:58:07 2006-03-27T13:51:05 nif NDG 28634 http://cocomac.org/ Kotter Rolf rk@hirn.uni-duesseldorf.de Kotter Rolf rk@hirn.uni-duesseldorf.de XML architecture; anatomy; histology; cortex; map; connections; subcortical; segmentation; white matter; imaging; neuroinformatics; somatosensory; brain mapping Systematic collation of connectivity and mapping data from published experimental reports in macaque monkeys. Data integration based on fully documented routines. Interfaces for automated database query by extended URL and XML formatted output. The interface can be queried automatically using extended URL strings, whose vocabulary and syntax are documented in a separate document. Output is either textual in the browser or XML-formatted according to the CoCoMac XML schema. Supporting Agencies: German Research Council, Henrich Heine University, Wellcome Trust transform.py ver 0.5 Neuroshare Neuroshare 2006-06-26T12:58:07 2006-03-27T13:55:50 nif NDG 28773 http://neuroshare.sf.net Kirk Korver kkorver@cyberkineticsinc.com Kirk Korver kkorver@cyberkineticsinc.com development; data management; software Neuroshare aims to develop a standard for accessing neurophysiological data from any vendor's acquisition device or software. An API is defined, and vendors and communities are encouraged to provide implementations of a library of functions that can read data files collected with that vendor's instrument or software. Supporting Agencies: NINDS transform.py ver 0.5 Neuroguide Neurosciences on the Internet 2006-06-26T12:58:07 2006-03-27T13:57:00 nif NDG 28775 http://www.neuroguide.com/ Neil Busis nab@neuroguide.com Neil Busis nab@neuroguide.com A searchable and browsable index of neuroscience resources available on the internet including neurobiology, neurology, neurosurgery, psychiatry, psychology, cognitive science sites and information on human neurological diseases. transform.py ver 0.5 FMRIDC The fMRI Data Center 2006-06-26T12:58:07 2006-03-27T14:01:45 nif NDG 28777 http://www.fmridc.org John Van Horn john.d.van.horn@dartmouth.edu Jeffrey Woodward jeffrey.b.woodward@dartmouth.edu Analyze 7.5, NIFTI anatomy; ontology; atlas; cortex; mri; fmri; volume; talairach; brainstem; cerebellum; white matter; gray matter; neuroinformatics; data management; data storage; portal; software; neuroimaging; brain mapping; cognitive The fMRI data center (fMRIDC) is a curated respository of neuroimaging data obtained in published studies of cognitive function. these data sets typically include raw fMRI timecourse volumes, the timecourses after data preprocessing, statistical result images, and high-resolution anatomical image volumes. All studies also contain study meta-data describing the scanner, experimental, and subject protocols. Platform independent fMRI study data management tools are openly available for researchers to use in maintaining their own study databases and that facilitate data sharing within and between labs as well as with archives like the fMRIDC. This data respository seeks to encourage researchers to perform novel analyses of previously published study data to broaden the scope of original study conclusions. All data are provided free for use in research and education and are distributed on media or via download. http://www.fmridc.org/harvester/fmristudy.xsd.html Supporting Agencies: HBP transform.py ver 0.5 Synapse Web SynapseWeb 2006-06-26T12:58:07 2006-03-27T14:02:57 nif NDG 28778 http://synapses.clm.utexas.edu Bitao Shi bshi@mail.utexas.edu 512-471-3965 Bitao Shi bshi@mail.utexas.edu 512-471-3965 Has raw images, reconstructions, and quantitative data along with tutorial instructions and numerous tools for investigating the functional structure of objects that have been serial thin sectioned for electron microscopy.Species: rats Synapse Web Supporting Agencies: NIBIB; HBP transform.py ver 0.5 BIRN Biomedical Informatics Research Network 2006-06-26T12:58:07 2006-03-27T14:36:07 nif NDG 28779 http://www.nbirn.net/index.htm Greg Farber farberg@mail.nih.gov Jeffrey Grethe jgrethe@ucsd.edu neurinformatics infrastructure The Biomedical Informatics Research Network (BIRN), a National Institutes of Health (NIH) National Center for Research Resources (NCRR)-sponsored initiative, is establishing a distributed information technology infrastructure to improve biomedical research. This evolving "cyberinfrastructure" will enable researchers throughout the United States to collaborate on large-scale studies of human disease with unique, multi-resolution databases and tools. BIRN has developed the BIRNLex, a lexicon of terms covering BIRN activities. The BIRNLex in turn is built using community standards and other community terminologies where possible. Supporting Agencies: NIH; NCRR; DOHHS transform.py ver 0.5 Neurosys Hierarchical Database Project 2006-06-26T12:58:07 2006-03-27T14:36:59 nif NDG 28781 http://neurosys.cns.montana.edu Gwen Jacobs gwen@montana.edu 406 994-7334 Ivan Judson ivan.judson@montana.edu 406 994-6090 data management; data storage; software Interactive software to create and query data entry screens for a web database describing meta-data about experimental protocols, procedures and results. Supporting Agencies: NIH; HBP transform.py ver 0.5 HBP Human Brain Project 2006-06-26T12:58:07 2006-03-27T14:37:34 nif NDG 28782 http://www.nimh.nih.gov/neuroinformatics/ Stephen H. Koslow koz@helix.nih.gov Alesa Teague ateague@mail.nih.gov The Human Brain Project was an NIH funding initiative launched in 1993 to devcelop and support a new science: neuroinformatics. It provided grants and sponsored workshops, conferences, and other initiatives. Supporting Agencies: NIH transform.py ver 0.5 MBL The Mouse Brain Library 2006-06-26T12:58:07 2006-03-27T14:38:24 nif NDG 28783 http://mbl.org Robert Williams rwilliam@nb.utmem.edu Glenn Rosen grosen@bidmc.harvard.edu A collection of high resolution histologic images of over 2000 mice representing over 120 strains. The site includes genetic databases, brain atlases, and iScope, a microscope that can be controlled over the internet. An absolute must for mouse brain anatomy, knock out, and gene expression. Supporting Agencies: NIMH; NSF; HBP; NIDA transform.py ver 0.5 FlyBrain FlyBrain: An Online Atlas and Database of the Drosophila Nervous System 2006-06-26T12:58:07 2006-03-27T14:42:58 nif NDG 28786 http://www.flybrain.org/ Nicholas Strausfeld flybrain@neurobio.arizona.edu Nicholas Strausfeld flybrain@neurobio.arizona.edu architecture; morphology; anatomy; histology; atlas; map; development; 3d models; golgi Interactive database of the drosophila brain, used by the drosophila neuroscience community and by other researchers studying arthropod brain structure. An excellent, wide-ranging, well-designed resource for the Drosophila community (D. Van Essen) transform.py ver 0.5 IBSR Internet Brain Segmentation Repository 2006-06-26T12:58:07 2006-03-27T14:45:20 nif NDG 28805 http://www.cma.mgh.harvard.edu/ibsr/ David Kennedy dave@cma.mgh.harvard.edu Andrew Worth andy@cma.mgh.harvard.edu morphology; anatomy; atlas; cortex; mri; volume; 3d models; brainstem; cerebellum; segmentation; white matter; gray matter; imaging The IBSR provides manually-guided expert segmentation results along with magnetic resonance brain image data. Its purpose is to encourage the evaluation and development of segmentation methods.Species: Human Supporting Agencies: NIMH; NINDS; HBP transform.py ver 0.5 IBVD Internet Brain Volume Database 2006-06-26T12:58:07 2006-03-27T14:46:26 nif NDG 28806 2006-06-26T12:58:07 2006-03-27T14:46:26 nif NDG 28806 http://www.cma.mgh.harvard.edu/ibvd/ David Kennedy dave@cma.mgh.harvard.edu Christian Haselgrove ch@cma.mgh.harvard.edu anatomy; volume The Internet Brain Volume Database is a searchable database of neuroanatomic volume measurements spanning various species, diagnoses, and structures for both individual and group results. disco Supporting Agencies: NIMH; NINDS; HBP transform.py ver 0.5 NIP The Neuroinformatics Portal Pilot 2006-06-26T12:58:07 2006-03-27T14:47:07 nif NDG 28811 http://www.neuroinf.de Andreas Herz a.herz@biologie.hu-berlin.de Raphael Ritz r.ritz@biologie.hu-berlin.de ontology; neuroinformatics; portal; software; metadata; literature Portal and listing of available neuroinformatics resources (databases, software, journals, institutions). Supporting Agencies: bmbf.de transform.py ver 0.5 Nervenet Neurogenetics Online 2006-06-26T12:58:07 2006-03-27T14:49:04 nif NDG 28830 http://www.nervenet.org Robert W. Williams rwilliam@nb.utmem.edu Robert W. Williams rwilliam@nb.utmem.edu Mouse Brain Library; MBL Portal to neurogenetic resources: the mouse brain library, digital atlases of the mouse brain, extensive brain microarray data in WebQTL, and internet access to microscopes and stereology tools. transform.py ver 0.5 BayGenomics BayGenomics 2006-06-26T12:58:07 2006-03-27T14:49:40 nif NDG 28833 http://baygenomics.ucsf.edu/ Tom Ferrin tef@cgl.ucsf.edu Tom Ferrin tef@cgl.ucsf.edu The major goal of BayGenomics is to identify genes relevant to cardiovascular and pulmonary disease. We are using gene-trap vectors to inactivate thousands of genes in mouse embryonic stem (ES) cells for the purpose of generating knockout mice. We make all of our ES cell lines readily available to the scientific research community. Supporting Agencies: NIH transform.py ver 0.5 LGICdb Ligand Gated Ion Channel Database (LGICdb) 2006-06-26T12:58:07 2006-03-27T14:50:32 nif NDG 28835 http://www.ebi.ac.uk/compneur-srv/LGICdb/ Nicolas Le Novere lenov@ebi.ac.uk Nicolas Le Novere lenov@ebi.ac.uk cellular/molecular; receptor; genetics; 3d models; neuroinformatics; ion channel; sequence data Curated DNA and protein sequences of ionotropic receptor subunits, a unique database entry per gene. Multiple sequence alignments, phylogenetic analysis and atomic coordinates are also provided. transform.py ver 0.5 MAP Mouse Atlas Project 2006-06-26T12:58:07 2006-03-27T14:53:57 nif NDG 28836 http://www.loni.ucla.edu/MAP/ Arthur Toga toga@loni.ucla.ed Karen Crawford kcrawford@loni.ucla.edu The goal of the Mouse Atlas Project (MAP) is to empower researchers with the ability to compare gene expression patterns with a conveniently accessible inventory of digital brain maps. It aims to produce a powerful imaging framework to house and correlate gene expression with anatomic and molecular information drawn from traditional and novel imaging technologies. Supporting Agencies: NINDS; NIBIB; NIDA; NIDCD; NIA transform.py ver 0.5 MBAT Mouse BIRN Atlasing Toolkit 2006-06-26T12:58:07 2006-03-27T14:55:45 nif NDG 28837 http://nbirn.net/downloads/mbat/index.shtm Jyl Boline jyl.boline@loni.ucla.edu Steve Anderson sanderso@loni.ucla.edu Biomedical Informatics Research Network (BIRN); Mouse BIRN architecture; morphology; anatomy; ontology; histology; atlas; cortex; mri; cellular/molecular; glia; dendrites; volume; connections; subcortical; segmentation; white matter; gray matter; warping; imaging; neuroinformatics; data management; data storage; portal; software The Mouse BIRN test bed is helping scientists study neurodegenerative diseases by marshaling multi-modal data from the mouse, as an animal model, to investigate neurological disorders. Researchers across six groups are pooling and analyzing multi-scale structural and functional data and integrating it with genomic and gene expression data acquired from the mouse brain. MBAT is mapping to the nomenclature developed by the BIRN project: BIRNLex, which in turn imports from multiple shared ontologies, e.g., NCBI taxonomy, NeuroNames The MBAT tool provides a 3D image-based interface for accessing and mapping gene expression data from microarray experiments, histological, cellular and subcellular data from light and electron microscopy and volummetric data from MRI imaging. Supporting Agencies: NIH; NCRR; DOHHS transform.py ver 0.5 INDP Identified Neuron Database Project 2006-06-26T12:58:07 2006-03-27T14:56:31 nif NDG 28839 http://n002bsel.bios.uic.edu/ Christopher Comer ccomer@uic.edu John Dowd jdowd7@yahoo.com anatomy; neuroinformatics; physiologyThis website hosts a searchable database of uniquely identifiable insect neurons.Species: Other Invertebrate INDP transform.py ver 0.5 LONI Database LONI Image Database 2006-06-26T12:58:07 2006-03-27T14:57:14 nif NDG 28842 http://www.loni.ucla.edu/Research/Databases/ Arthur Toga toga@loni.ucla.edu Karen Crawford kcrawford@loni.ucla.edu Laboratory of Neuroimaging (LONI), UCLA histology; mri; volume; data storage The LONI Image Database has been constructed to provide an effective means for archival and protection of collaborator collected image data. Supporting Agencies: NCRR transform.py ver 0.5 ICBM Subject Database ICBM Subject Database 2006-06-26T12:58:07 2006-03-27T14:57:49 nif NDG 28843 http://www.loni.ucla.edu/ICBM/Databases/ John Mazziotta mazziotta@loni.ucla.edu Karen Crawford kcrawford@loni.ucla.edu International Consortium for Brain Mapping (ICBM) MRI; volume; data storage The ICBM Subject Database is a web-based database infrastructure that simplifies image dataset collection, organization and dissemination. transform.py ver 0.5 Talairach Daemon Talairach Daemon 2006-06-26T12:58:07 2006-03-27T14:58:17 nif NDG 28844 http://ric.uthscsa.edu/TDinfo/ Jack Lancaster jlancaster@uthscsa.edu Mick Fox foxm@uthscsa.edu 210-567-8100 International Consortium for BrainMapping (ICBM) anatomy; atlas; map; talairach; neuroinformatics; software Provides 5 level hierarchy of label names created for the 1988 Talairach atlas. labels can be accessed using talairach corodinates. Java Applet and/or Web Talairach and Tournoux Atlas Useful for identifying standardized locations for empirically determined functional MRI and/or PET activation foci from studies of cognition processes. transform.py ver 0.5 Angela Uecker (uecker@uthscsa.edu) ZFIN Zebrafish Information Network 2006-06-26T12:58:07 2006-03-27T14:59:04 nif NDG 28845 http://zfin.org Jonathan Knight zfinadmn@zfin.org Dave Clements clements@cs.uoregon.edu anatomy; ontology; atlas; cellular/molecular; map; genetics; development; sequence data ZFIN serves as the zebrafish model organism database. The long term goals for XFIN are: a) to be the community database resource for the laboratory use of zebrafish, b) to develop and support integrated zebrafish genetic, genomic and developmental information, c) to maintain the definitive reference data sets of zebrafish research information, d) to link this information extensively to corresponding data in other model organism and human databases, e) to facilitate the use of zebrafish as a model for human biology, and f) to serve the needs of the research community. Supporting Agencies: NIH transform.py ver 0.5 XANAT XANAT Graphical Anatomical Database 2006-06-26T12:58:07 2006-03-27T14:59:49 nif NDG 28847 http://redwood.ucdavis.edu/bruno/xanat Bruno Olshausen baolshausen@ucdavis.edu Bruno Olshausen baolshausen@ucdavis.edu anatomy; atlas; cortex; subcortical; neuroinformatics; data storage; software A graphical tool for storing and searching information on neuroanatomical connections. Injection and label sites are drawn onto cross-sections or flattened representations of the brain. Searches are performed by querying an anatomical region of interest (e.g., pointing or drawing onto the brain with the mouse, or entering a keyword), and a color-coded heatmap is returned showing the net evidence for connections between the queried region and other regions of the brain. At present the database contains information on cortical-pulvinar connections in the macaque monkey. transform.py ver 0.5 July 3, 2007: I could not access their website, and thus could not re-evaluate it. L-Neuron L-Neuron 2006-06-26T12:58:07 2006-03-27T15:00:29 nif NDG 28855 http://krasnow.gmu.edu/L-Neuron/ Giorgio Ascoli ascoli@gmu.edu Ruggero Scorcioni rscorcio@gmu.edu Computational Neuroanatomy Group; Center for Neural Informatics, Structures, and Plasticity; Krasnow Institute for Advanced Study; George Mason University morphology; 3d models; cerebellum; neuroinformatics; model; software L-Neuron is a tool to generate visualizable 3-D reconstructions of neurons based on anatomical parameters. Supported platforms: Linux and Windows Moderately annotated, expert-usage tool to synthesize neural arbors from simple statistical distributions. Postdocs or grad-students can get up to speed within a day of work, and email support from the authors is available. Supporting Agencies: HBP transform.py ver 0.5 MBA Mouse Brain Atlases 2006-06-26T12:58:07 2006-03-27T15:03:34 nif NDG 28861 http://www.mbl.org/mbl_main/atlas.html Robert W. Williams rwilliam@nb.utmem.edu Robert W. Williams rwilliam@nb.utmem.edu morphology; anatomy; atlas; volume; genetics; cerebellum; subcortical High-resolution electronic atlases for mouse strains c57bl/6j, a/j, and dba/2j in either coronal or horizontal section. Supporting Agencies: NIMH; NSF; HBP; NIDA transform.py ver 0.5 MMRRC Mutant Mouse Regional Resource Centers 2006-06-26T12:58:07 2006-03-27T15:04:12 nif NDG 28863 http://www.mmrrc.org/ Rick Palazola rpp@jax.org Rick Palazola rpp@jax.org genetics; model Mutant mouse regional resource centers: accepts suitable mouse strains from the research community for maintenance, cryopreservation and distribution to researchers. MMRRC offers requesting investigators a catalog of mice available and an interest registration list of strains undergoing importation into the MMRRC. The individual centers offer numerous other services, including additional characterization of accepted strains, rederivation into specific pathogen free colonies, and microinjection. Supporting Agencies: NIH; NCRR transform.py ver 0.5 Neuromice Neuromice.org Consortium 2006-06-26T12:58:07 2006-03-27T15:04:41 nif NDG 28864 http://www.neuromice.org Joseph Takahashi j-takahashi@northwestern.edu Jeana Yates cjs@northwestern.edu Three mutagenesis and phenotypic screening facilities, focused on identifying alterations in nervous system function and behavior, were established by NIH. These three sites have come together as the Neuromice.org consortium to maintain and distribute the resources generated -- the new lines of mutant mice. Supporting Agencies: NIH transform.py ver 0.5 DOQCS Database of Quantitative Cellular Signaling 2006-06-26T12:58:07 2006-03-27T15:05:49 nif NDG 28866 http://doqcs.ncbs.res.in Upinder Bhalla bhalla@ncbs.res.in Upinder Bhalla bhalla@ncbs.res.in simulation; cellular/molecular; model The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. DOQCS Supporting Agencies: other transform.py ver 0.5 Visiome Visiome Platform 2006-06-26T12:58:07 2006-03-27T15:06:21 nif NDG 28869 http://platform.visiome.org/ Shiro Usui usuishiro@riken.jp Shiro Usui usuishiro@riken.jp RIKEN Brain Science Institute neuroinformatics; visual system Visiome Platform is the Neuroinformatics Search Service that provides access to mathematical models, experimental data, analysis libraries and related resources. transform.py ver 0.5 NTSA NTSA Workbench 2006-06-26T12:58:07 2006-03-27T15:08:07 nif NDG 28894 http://soma.npa.uiuc.edu/ntsa/ Michael Gabriel mgabriel@uiuc.edu Rongkai Zhao rongkai@uiuc.edu anatomy; histology; atlas; volume; 3d models; imaging; neuroinformatics; data management; data storage; sequence data; software The neuronal time series analysis (NTSA) workbench is a set of tools, techniques and standards designed to meet the needs of neuroscientists who work with neuronal time series data. The goal is to develop an information handling system that will make routine the storage, organization, retrieval, analysis and sharing of experimental and simulated neuronal data. Defines a data format, "Time Series Data Protocol" (TSDP), and provides an open source software library for processing it. transform.py ver 0.5 BrainMap BrainMap: A Functional Neuroimaging Database 2006-06-26T12:58:07 2006-03-27T15:09:12 nif NDG 28895 http://brainmap.org/ Peter Fox fox@uthscsa.edu Angela Laird lairda@uthscsa.edu Research Imaging Center of the University of Texas Health Science Center San Antonio atlas; map; fmri; pet; talairach; 3d models; warping; imaging; neuroinformatics; data management; software Brainmap is an online database of published functional neuroimaging experiments (fMRI, PET, MEG) with activation locations in Talairach space. the goal of BrainMap is to provide a vehicle to share methods and results of brain functional imaging studies. It is a tool to rapidly retrieve and understand studies in specific research domains, such as language, memory, attention, reasoning, emotion, and perception, and to perform meta-analyses of like studies. transform.py ver 0.5 CoCoDat Collation of Cortical Data 2006-06-26T12:58:07 2006-03-27T15:10:11 nif NDG 28896 http://www.cocomac.org/cocodat Rolf K?tter rk@hirn.uni-duesseldorf.de Rolf K?tter rk@hirn.uni-duesseldorf.de Microsoft Access 2000 database file architecture; morphology; anatomy; histology; cortex; cellular/molecular; dendrites; connections; gray matter; neuroinformatics; physiology; somatosensory; ion channel; model; metadata Cocodat contains data on morphology, firing properties, ionic currents, ionic conductances, synaptic currents, and connectivity from published experimental reports along with brain structures, methods, bibliographic references and pubmed ids. The data is available online, as well as for download as a Microsoft Access file including a search board with powerful data retrieval and display options. disco Supporting Agencies: other transform.py ver 0.5 FlyTrap FlyTrap 2006-06-26T12:58:07 2006-03-27T15:10:35 nif NDG 28897 http://www.fly-trap.org/ Douglas Armstrong da@dai.ed.ac.uk Douglas Armstrong da@dai.ed.ac.uk anatomy; genetics; 3d models Database of P{GAL4} expression patterns in the drosophila brain. A useful source of information regarding expression patterns, but only limited descriptions of the labeled anatomical cells and structures. transform.py ver 0.5 NeSys Neurao Systems and Graphics Computing Laboratory 2006-06-26T12:58:07 2006-03-27T15:13:55 nif NDG 28899 http://www.nesys.uio.no Jan G. Bjaalie j.g.bjaalie@basalmed.uio.no Pettersen Christian christian.pettersen@basalmed.uio.no architecture; morphology; anatomy; atlas; cortex; map; connections; 3d models; brainstem; cerebellum; imaging; neuroinformatics; somatosensory; data storage This database contains axonal tracing data from the cerebro-ponto-cerebellar system in rats. Data are presented as 3-D coordinates in a common coordinate system for the pontine nuclei. transform.py ver 0.5 Wormbase WormBase 2006-06-26T12:58:07 2006-03-27T15:14:28 nif NDG 28901 http://www.wormbase.org Paul Sternberg pws@caltech.edu Lincoln Stein lstein@cshl.org anatomy; connections; genetics; development; sequence data Public database of information about the genome and biology of c. elegans and closely related nematodes. transform.py ver 0.5 BrainML BrainML 2006-06-26T12:58:07 2006-03-27T15:14:53 nif NDG 28902 http://brainml.org Daniel Gardner dan@aplysia.med.cornell.edu Daniel Gardner dan@aplysia.med.cornell.edu Laboratory of Neuroinformatics (LNI), Cornell University Medical College XML Schema, XML architecture; ontology; neuroinformatics; data management; metadata; software BrainML is a developing initiative to provide a standard XML metaformat for exchanging neuroscience data. It focuses on layered definitions built over a common core in order to support community-driven extension. Schemas and vocabulary files are provided at well-defined, permanent URLs suitable for machine access. BrainML is a framework for defining and utilizing neuroscience data model descriptions and terminology. Supporting Agencies: NIMH; NINDS; HBP transform.py ver 0.5 NeuronDB Database of membrane properties in neuronal compartments 2006-06-26T12:58:07 2006-03-27T15:15:39 nif NDG 28903 http://senselab.med.yale.edu/senselab/neurondb/default.asp Gordon Shepherd gordon.shepherd@yale.edu Luis Marenco lnm7@email.med.yale.edu text, neuron hoc files cortex; cellular/molecular; receptor; dendrites; olfactory; cerebellum; neuroinformatics; physiology; ion channel; retina A database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substancesSpecies: Human; Mouse; Rat; Other Invertebrate disco Supporting Agencies: NIH; NIMH; NINDS; NLM; HBP; NIDCD; NIA transform.py ver 0.5 CellPropDB Cell Properties Database 2006-06-26T12:58:07 2006-03-27T15:16:09 nif NDG 28904 http://senselab.med.yale.edu/senselab/cellpropdb Gordon Shepherd gordon.shepherd@yale.edu Luis Marenco lnm7@email.med.yale.edu Senselab (Yale) cortex; cellular/molecular; receptor; olfactory; genetics; cerebellum; neuroinformatics; physiology; ion channel; retina CellPropDB provides a simple repository for data regarding membrane channels, receptor and neurotransmitters that are expressed in specific types of cells Species: Cat; Human; Mouse; Rat; Other Mammalian; Other Invertebrate Supporting Agencies: NIH; NIMH; NINDS; NLM; HBP; NIDCD; NIA transform.py ver 0.5 OdorDB Odor Molecules Database 2006-06-26T12:58:07 2006-03-27T15:17:05 nif NDG 28906 http://senselab.med.yale.edu/odordb Gordon Shepherd gordon.shepherd@yale.edu Chiquito Crasto chiquito.crasto@yale.edu Yale SenseLab HTML, XML, images(gif,jpeg,...) cellular/molecular; receptor; olfactory; genetics Functional studies of olfactory receptors involve their interactions with odor molecules. OdorDB contains a list of odors that have been identified as binding to olfactory receptors. OdorDB Supporting Agencies: nih; nimh; ninds; nlm; hbp; nida; nidcd transform.py ver 0.5 OdorMapDB Odor Maps Database 2006-06-26T12:58:07 2006-03-27T15:17:33 nif NDG 28907 http://senselab.med.yale.edu/odormapdb Gordon Shepherd gordon.shepherd@yale.edu Nian Liu nian.liu@yale.edu Yale SenseLab HTML,XML,IMAGES anatomy; mri; olfactory; map; fmri; warping; imaging; neuroinformatics; data storage; software; neuroimaging; brain mapping It is primarily concerned with archiving, searching and analysing maps of the olfactory bulb generated by different methods. The first aim is to facilitate comparison of activity patterns elicited by odor stimulation in the glomerular layer obtained by different methods in different species. It is further aimed at facilitating comparison of these maps with molecular maps of the projections of olfactory receptor neuron subsets to different glomeruli, especially for gene targeted animals and for antibody staining. Supporting Agencies: NIH; NIMH; NINDS; NLM; HBP; NIDCD; NIA transform.py ver 0.5 Olfactory Bulb needs to be added to neural structure under Forebrain. PPID Protein-Protein Interaction Database 2006-06-26T12:58:07 2006-03-27T15:19:14 nif NDG 28909 http://www.ppid.org Seth Grant sg3@sanger.ac.uk Mark Cumiskey mcumiske@inf.ed.ac.uk Mammalian protein protein interaction database focussing on synaptic proteins. transform.py ver 0.5 BCDB Brain Collection Database 2006-06-26T12:58:07 2006-03-27T15:21:01 nif NDG 28912 http://www.brains.rad.msu.edu John I. Johnson johnij@aol.com John I. Johnson johnij@aol.com morphology; anatomy; histology; atlas; cortex; mri; brainstem; cerebellum; nissl; subcortical; white matter; imaging Online access to histology and MRI images from the brain collections of the National Museum of Health and Medicine, Michigan State University, and the University of Wisconsin. Access Supporting Agencies: nsf transform.py ver 0.5 Brain Atlases Brain atlases 2006-06-26T12:58:07 2006-03-27T15:21:28 nif NDG 28913 http://brainatlases.ucdavis.edu Edward Jones ejones@ucdavis.edu James Stone jmstone@ucdavis.edu atlas; nissl High resolution digital images of nissl-stained, serial sections of monkey, cat, and pidgeon brains cut in standard planes. Supporting Agencies: nimh; hbp transform.py ver 0.5 DataSharing Datasharing.net 2006-06-26T12:58:07 2006-03-27T15:23:18 nif NDG 28914 http://datasharing.net Daniel Gardner dan@aplysia.med.cornell.edu Daniel Gardner dan@aplysia.med.cornell.edu neuroinformatics; data management; portal A source of, and portal to, tools and proposals supporting the informed exchange of neuroscience data. Supporting Agencies: nimh; ninds transform.py ver 0.5 MOFBR Model Organisms for Biomedical Research 2006-06-26T12:58:07 2006-03-27T15:24:09 nif NDG 28915 http://www.nih.gov/science/models/ Bettie Graham bettie_graham@nih.gov Bettie Graham bettie_graham@nih.gov genetics; sequence data This web site provides information about national and international activities and major resources that are being developed to facilitate biomedical research using the animal models listed here. For organisms not listed, web pages may be developed in the future.Drosophila; Zebrafish; Non Mammalian Vertebrate Supporting Agencies: nih transform.py ver 0.5 LONI Software LONI Software 2006-06-26T12:58:07 2006-03-27T15:25:33 nif NDG 28916 http://www.loni.ucla.edu/Software/ Arthur Toga toga@loni.ucla.edu Karen Crawford kcrawford@loni.ucla.edu volume; segmentation; warping; imaging; software Neuroimaging analysis and processing software distribution. The LONI Pipeline is available under the LONI software license. This license is an open source license, similar to the Apache software license, with an additional restriction of non-redistribution. This restriction is a result from stipulations of our funding resources to track downloads and usage. Supporting Agencies: ncrr; nimh; ninds; nibib transform.py ver 0.5 Brede Brede database 2006-06-26T12:58:07 2006-03-27T15:26:10 nif NDG 28917 http://hendrix.imm.dtu.dk/services/jerne/brede/ Finn ?rup Nielsen fn@imm.dtu.dk Finn ?rup Nielsen fn@imm.dtu.dk text, VRML fMRI; talairach; neuroinformatics Data from functional neuroimaging scientific articles containing Talairach coordinates. As of 2006/11, 186 papers with 586 experiments. transform.py ver 0.5 Language Map EMS Language Map Experiment Management System 2006-06-26T12:58:07 2006-03-27T15:28:21 nif NDG 28929 http://tela.biostr.washington.edu/cgi-bin/repos/bmap_repo/main-menu.pl Jim Brinkley brinkley@u.washington.edu Kevin Hinshaw khinshaw@u.washington.edu anatomy; cortex; mri; fmri; volume; 3d models; segmentation; imaging; data management An experiment management system for researchers studying language organization in the brain. Data from thirteen patients are available as a public demo. As of 2006/11 data from 110 patients in repository. Language Map EMS Supporting Agencies: nimh; nidcd; nia transform.py ver 0.5 FMA Foundational Model of Anatomy 2006-06-26T12:58:07 2006-03-27T15:28:58 nif NDG 28930 http://sig.biostr.washington.edu/projects/fm/ Cornelius Rosse rosse@u.washington.edu Todd Detwiler det@u.washington.edu Protege 3.0 anatomy; ontology; model An evolving representation of concepts and relationships necessary for the symbolic modeling of the structure of the human body. http://sig.biostr.washington.edu/projects/oqafma/ Project to define terminology for anatomy. The Foundational Model of Anatomy ontology contains approximately 75,000 classes and over 120,000 terms; over 2.1 million relationship instances from 168 relationship types link the FMA?s classes into a coherent symbolic model. The FMA is one of the largest computer-based knowledge sources in the biomedical sciences. FMA Supporting Agencies: nlm transform.py ver 0.5 NeuroScholar NeuroScholar 2006-06-26T12:58:07 2006-03-27T15:29:24 nif NDG 28931 http://www.neuroscholar.org Gully Burns gully@usc.edu Shyam Kapadia kapadia@usc.edu neuroinformatics; data storage; metadata Neuroscholar is a framework for knowledge management of the neuroscientific literature. It is not a single database but a methodology for creating knowledge models that answer specific questions with direct links to the literature. Supporting Agencies: nlm transform.py ver 0.5 BIRN-CC BIRN Coordinating Center 2006-06-26T12:58:07 2006-03-27T15:29:51 nif NDG 28932 http://www.nbirn.net/testbeds/coordinatingcenter/index.htm Michael Marron marronm@mail.nih.gov Jeffrey Grethe jgrethe@ucsd.edu Biomedical Informatics Research Network (BIRN) architecture; anatomy; ontology; atlas; mri; map; fmri; talairach; 3d models; warping; imaging; neuroinformatics; data management; data storage; model; portal; software The BIRN coordinating center (BIRN-CC) was established to develop, implement and support the information infrastructure necessary to achieve large-scale data sharing among the test bed participants (function, morphometry and mouse birn). The BIRN-CC consists of a unique and well-established partnership between computer scientists, neuroscientists and engineers. this partnership addresses a large array of technical, policy, and architectural issues to fundamentally enable a new suite of information technology supported database and analysis tools that allow scientists to analyze and interpret significantly larger sets of data than is possible in the traditional single-institution study paradigm. Supporting Agencies: nih; ncrr; dohhs transform.py ver 0.5 MorphBIRN Morphometry BIRN 2006-06-26T12:58:07 2006-03-27T15:30:33 nif NDG 28933 http://www.nbirn.net/research/testbeds/morphometry/index.shtm Michael Marron marronm@mail.nih.gov Jeffrey Grethe jgrethe@ucsd.edu Bioinformatics Research Network (BIRN) architecture; morphology; anatomy; ontology; atlas; cortex; mri; volume; talairach; 3d models; subcortical; segmentation; white matter; gray matter; warping; neuroinformatics; data management; data storage; portal; software Focuses on pooling and analyzing data across neuroimaging sites for potential relationships between anatomical differences and specific memory dysfunctions, such as depression, mild Alzheimer?s disease, and mild cognitive impairment. Ten groups currently participate. Supporting Agencies: nih; ncrr; dohhs transform.py ver 0.5 FBIRN Function BIRN 2006-06-26T12:58:07 2006-03-27T15:30:59 nif NDG 28934 http://nbirn.net/research/testbeds/function/index.shtm Steve Potkin sgpotkin@uci.edu Jessica Turner turnerj@uci.edu Bioinformatics Research Network (BIRN) architecture; morphology; anatomy; ontology; atlas; cortex; mri; map; fmri; volume; talairach; genetics; 3d models; subcortical; segmentation; white matter; gray matter; warping; imaging; neuroinformatics; data management; data storage; portal; sequence data; software A team of researchers at eleven institutions is studying regional brain dysfunctions related to the progression and treatment of schizophrenia. the research is enabled by the federation of large databases of functional imaging data at the participating sites, the design and execution of new cooperative functional neuroimaging studies across sites, and the use of new techniques to create grid-based workflows from their current analysis tools. BIRNLex The function BIRN makes available many tools for calibration and montoring of fMRI scanners and protocols for standardized imaging across sites. More data will likely be added in the future. Supporting Agencies: nih; ncrr; dohhs transform.py ver 0.5 NDB National Brain Databank 2006-06-26T12:58:07 2006-03-27T15:31:28 nif NDG 28940 http://national_databank.mclean.org Francine M. Benes, M.D., Ph.D. benesf@mclean.harvard.edu David Ennulat, Ph.D. dennulat@mclean.harvard.edu cortex; cellular/molecular; genetics; sequence data The databank collects and disseminates gene expression data from microarray experiments on brain tissue samples, along with diagnostic results from postmortem studies of neurological and psychiatric disorders. Supporting Agencies: nih; nimh; ninds transform.py ver 0.5 Nclamp Nclamp 2006-06-26T12:58:07 2006-03-27T15:32:45 nif NDG 28942 http://www.physiol.ucl.ac.uk/research/silver_a/nclamp/ Angus Silver a.silver@ucl.ac.uk Jason Rothman jason@thinkrandom.com Data acquisition software that runs in conjunction with neuromatic. configured to work with Igor Pro on PC or Mac, instrutech or national instrument acquisition devices. Supporting Agencies: MRC transform.py ver 0.5 NeuroMatic NeuroMatic 2006-06-26T12:58:07 2006-03-27T15:33:17 nif NDG 28943 http://www.neuromatic.thinkrandom.com/ Jason Rothman jason@thinkrandom.com Jason Rothman jason@thinkrandom.com data management; software NeuroMatic is a collection of Igor Pro functions for analyzing electrophysiological data. By allowing users to organize their data into sets or groups, NeuroMatic makes it a relatively straight forward process of performing any number of transformations and statistical analyses on their data sets, including scaling, alignment averaging, baseline subtraction, spike detection, stationarity analysis, and rise-time computations. Being open source and of modular design, NeuroMatic also allows users to develop their own analysis functions that can be easily incorporated into NeuroMatic's framework. Supporting Agencies: MRC, Wellcome Trust transform.py ver 0.5 NIH Neuroscience Microarray Consortium NIH Neuroscience Microarray Consortium 2006-06-26T12:58:07 2006-03-27T15:35:05 nif NDG 28945 http://arrayconsortium.tgen.org Dietrich Stephan dstephan@tgen.org Sarah Brautigam sbrautigam@tgen.org NIH Neuroscience Blueprint genetics; sequence data The NIH Microarray Consortium provides for-fee services to a community of NIH grantees, together with a more limited set of services to the public. There is also a repository containing raw microarray data files from microarray experiments performed on the following platforms: Agilent, Spotted cDNA, Operon Oligo, and Affymetrix. All data files are associated with complete sample annotation information in compliance with miame standards. Web-based data analysis tools are also available. Scientists can analyze microarray data from the consortium repository or investigators can upload outside data for analysis. See http://arrayconsortium.tgen.org/np2/public/eligibility.jsp for access information. Many services are for-fee. Supporting Agencies: nimh; ninds transform.py ver 0.5 Hereditary Hearing Loss Homepage Hereditary Hearing Loss Homepage 2006-06-26T12:58:07 2006-03-27T15:35:35 nif NDG 28946 http://webh01.ua.ac.be/hhh/ Guy Van Camp guy.vancamp@ua.ac.be Richard Smith richard-smith@uiowa.edu cellular/molecular; genetics The hereditary hearing loss homepage provides an up-to-date overview of the genetics of hereditary hearing impairment for researchers and clinicians. This site lists data and references for all known gene localizations and identifications for nonsyndromic hearing impairment, and several for syndromic hearing loss. This site lists data and links for all known gene localizations and identifications for nonsyndromic hearing impairment. For syndromic hearing impairment, only a few of the most frequent forms are covered. Supporting Agencies: other transform.py ver 0.5 NeuroHomology Database Data on Interspecies Similarities 2006-06-26T12:58:07 2006-03-27T15:36:43 nif NDG 28947 http://brancusi.usc.edu/scripts/webmerger.exe?/database/homologies-main.html Michael Arbib arbib@pollux.usc.edu Mihail Bota mbota@usc.edu cortex; connections; brain mappingThe neurohomology database handles brain regions, fiber tracts, and neural similarities data across different species. it allows to evaluate the reliability of connectivity data, and how similar are brain regions across different species.Species: Human; Rat; Monkey NeuroHomology Database Supporting Agencies: nih; nimh transform.py ver 0.5 EEGLab EEE Lab 2006-06-26T12:58:07 2006-03-27T15:37:43 nif NDG 28949 http://sccn.ucsd.edu/eeglab/ Scott Makeig smakeig@ucsd.edu Arnaud Delorme arno@sccn.ucsd.edu Swartz Center for Computational Neuroscience (SCCN), Institute for Neural Computation (INC), UC San Diego data management; software Extensive open-source toolset for EEG data analysis under Matlab. Design allows easy transition from gui-based to script-based analyses, and easy creation of new plug-in tools. Currently supported functions include independent component analysis, time/frequency analysis, source dipole fitting and 2-d/3-d vizualization. Supporting Agencies: NIMH transform.py ver 0.5 FMR Lab Independent Component Analysis Software 2006-06-26T12:58:07 2006-03-27T15:38:08 nif NDG 28950 http://sccn.ucsd.edu/fmrlab/index.html Scott Makeig smakeig@ucsd.edu Jen-Renn Duann duann@sccn.ucsd.edu Swartz Center for Computational Neuroscience, UCSD anatomy; fmri; software; brain mapping Software for performing independent component analysis (ICA) on imaging data and evaluating the resulting components, running under Matlab. Several image formats are supported. Supporting Agencies: NIH transform.py ver 0.5 Washington University Inner Ear Protein Database Inner Ear Proteins in Health and Disease 2006-06-26T12:58:07 2006-03-27T15:38:47 nif NDG 28951 http://oto.wustl.edu/thc/innerear2d.htm Isolde Thalmann thalmanni@wustl.edu Isolde Thalmann thalmanni@wustl.edu cellular/molecular; sequence data The fully federated database provides information on proteins identified in inner ear structures and fluids in health and disease. in addition, protein maps derived from 2d electrophoresis/mass spectrometry are displayed. Supporting Agencies: other transform.py ver 0.5 Whole Brain Atlas The Whole Brain Atlas 2006-06-26T12:58:07 2006-03-27T15:39:43 nif NDG 28952 http://www.med.harvard.edu/aanlib/home.html Keith A. Johnson keith@bwh.harvard.edu John A. Becker kajohnson@partners.org Harvard Medical School anatomy; atlas Database of normal and abnormal brain images. Supporting Agencies: other transform.py ver 0.5 Catacomb Modeling Software for Neuroscience 2006-06-26T12:58:07 2006-03-27T15:40:13 nif NDG 28953 http://www.catcmb.org/ Robert Cannon robert@catcmb.org Robert Cannon robert@catcmb.org simulation; ion channel; model; software Software system for modeling in neuroscience, covering scales from ion channels to behavioral experiments. Developed by Mike Hasselmo (Boston University) and Robert Cannon (Edinburgh) Supporting Agencies: nih transform.py ver 0.5 EMAGE EMAGE Gene Expression Database 2006-06-26T12:58:07 2006-03-27T15:40:46 nif NDG 28955 http://genex.hgu.mrc.ac.uk/Emage/database/emageIntro.html Jeff Christiansen jeffc@hgu.mrc.ac.uk Peter Stevenson p.stevenson@hgu.mrc.ac.uk Edinburgh Mouse Atlas Project (EMAP) morphology; anatomy; genetics; development; 3d models EMAGE is a database of spatially mapped 2d and 3d gene expression data in the developing mouse embryo. All emage data is housed in a standard framework: a series of 3d virtual embryo models at different stages of development which have accompanying lists of standardized terms for the anatomical structures present. emage expression data is incorporated into this framework both using text and space. searching emage data can therefore be performed by either text based methods or by spatial based approaches where 2d or 3d query domains are defined by the user or by regions already housed in the public database. further emage search capabilities are currently being developed to automatically identify groups of genes with similar expression patterns in large datasets.Species: Mouse Supporting Agencies: MRC transform.py ver 0.5 NEURON NEURON Simulation Environment 2006-06-26T12:58:07 2006-03-27T15:41:36 nif NDG 28956 http://www.neuron.yale.edu Michael Hines michael.hines@yale.edu Michael Hines michael.hines@yale.edu architecture; simulation; dendrites; ion channel; model; software Simulation of individual neurons and networks of neurons whose properties include, but are not limited to, complex branching morphology, multiple channel types, inhomogeneous channel distribution, ionic diffusion, extracellular fields, electronic instrumentation, single channels, and artificial spiking neurons. NEURON has long been a standard in single-cell neural modeling, and recently added network features as well. transform.py ver 0.5 Chronux Chronux 2006-06-26T12:58:07 2006-03-27T15:42:08 nif NDG 28996 http://chronux.org Partha Mitra mitra@cshl.edu Peter Andrews paa@drpa.us fmri; software; brain mapping Chronux is a software platform for the analysis of neurobiological time series data. It is meant to be applicable broadly, from electrophysiological time series (spikes, lfp), to eeg, meg, fmri and optical imaging data. we focus specifically on the time series or signal processing aspects of these data sets. the goal is to create a high quality set of tools implementing standardised metrics on time series along with error estimates where appropriate. Species: Human Chronux Supporting Agencies: nimh transform.py ver 0.5 The World-Wide Web Virtual Library:Neurosciences Neuroscience Link List 2006-06-26T12:58:07 2006-03-27T15:43:20 nif NDG 28998 http://neuro.med.cornell.edu/ Daniel Gardner dan@aplysia.med.cornell.edu The world-wide web virtual library:neurosciences provides links to many neuroscience resources on the web as well as links to university neuroscience and neurobiology program home-pages. The World-Wide Web Virtual Library:Neurosciences transform.py ver 0.5 SynDB Synapse Database 2006-06-26T12:58:07 2006-03-27T15:44:12 nif NDG 29001 http://syndb.cbi.pku.edu.cn Liping Wei weilp@mail.cbi.pku.edu.cn Yong Zhang zhangy@mail.cbi.pku.edu.cn SynDB is an online resource of proteins known or predicted to be related to the synapse or synaptic activity, and extensive information on the proteins' functions, sequences, structures, expression, pathways, interactions, and disease associations. It is intended to be a repository of current knowledge and data as well as a starting point for future proteomics research in neurobiology. transform.py ver 0.5 Conditioned Taste Aversion Bibliography Conditioned Taste Aversion: An Annotated Bibliography 2006-06-26T12:58:07 2006-03-27T15:45:16 nif NDG 29004 http://www.ctalearning.com Anthony Riley alriley@american.edu Anthony Riley alriley@american.edu A searchable, keyword-indexed bibliography on conditioned taste aversion learning, the avoidance of fluids and foods previously associated with the aversive effects of a variety of drugs. The database includes articles as early as 1955, and papers just published given that the database is ongoing and constantly updated. transform.py ver 0.5 SNNAP Simulator for Neural Networks and Action Potentials 2006-06-26T12:58:07 2006-03-27T15:46:12 nif NDG 29005 http://snnap.uth.tmc.edu/ Douglas Baxter douglas.baxter@uth.tmc.edu Douglas Baxter douglas.baxter@uth.tmc.edu SNNAP is a neurosimulator for developing and simulating conductance-based model of neurons and neural networks. Supporting Agencies: NCRR transform.py ver 0.5 Mouse Brain Atlas High Resolution Mouse Brain Atlas 2006-06-26T12:58:07 2006-03-27T15:47:41 nif NDG 29007 http://www.hms.harvard.edu/research/brain/atlas.html Richard Sidman richard_sidman@hms.harvard.edu Richard Sidman richard_sidman@hms.harvard.edu Coronal nissl- and myelin-stained sections with labels; a few 3D images of hippocampal formation and other brain structures; detailed methods section. Supporting Agencies: NIH; HBP transform.py ver 0.5 The Navigable Atlas of the Human Brain Human Brain Atlas 2006-06-26T12:58:07 2006-03-27T15:49:13 nif NDG 29009 http://www.msu.edu/user/brains/humanatlas/ John I. Johnson johnij@aol.com John I. Johnson johnij@aol.com Images of a series of 100 coronal, 50 sagittal and 50 horizontal (axial) sections through the human brain, alternate sections stained for cell bodies and for myelinated fibers. For each level of stained sections a corresponding level of MRI images is included. nuclei and tracts are labeled, labels can be applied and removed and progressive sections viewed with electronic controls. A search feature allows electronic searching through all images for specific labels of structures. Supporting Agencies: NSF transform.py ver 0.5 The Navigable Atlas of the Dolphin Brain The Navigable Atlas of the Dolphin Brain 2006-06-26T12:58:07 2006-03-27T15:49:49 nif NDG 29010 http://www.msu.edu/~brains/brains/dolphin/index.html John I. Johnson johnij@aol.com John I. Johnson johnij@aol.com Brain Biodiversity Bank http://www.msu.edu/~brains/ online images Images of a series of 50 sagittal sections through the bottlenosed dolphin brain, alternate sections stained for cell bodies and for myelinated fibers. For each level of stained sections a corresponding level of MRI images is included. Nuclei and tracts are labeled, labels can be applied and removed and progressive sections viewed with electronic controls. Permission required Currently only web based images: All of the images on this site are copyrighted. They were produced with the support of public funds, and we wish to keep them available for public use. You may use them for any purpose which will not interfere with their use by others. We do ask that you SECURE OUR PERMISSION, so that we can track the uses being made. Supporting Agencies: NSFBrain Biodiversity Bank transform.py ver 0.5 Virtual Atlas of the Honeybee Brain Virtual Atlas of the Honeybee Brain 2006-06-26T12:58:07 2006-03-27T15:50:34 nif NDG 29011 http://www.neurobiologie.fu-berlin.de/beebrain Randolf Menzel menzel@neurobiologie.fu-berlin.de Sabine Krofczik sabine@krofczik.de VRML Integrates functional and anatomical information to produce a virtual atlas of the honeybee brain. VRML technology is used to present the atlas. transform.py ver 0.5 DD-Database Drug Discrimination Bibliographic Database 2006-06-26T12:58:07 2006-03-27T15:51:31 nif NDG 29012 http://dd-database.org Ian Stolerman i.stolerman@iop.kcl.ac.uk Jonathan Kamien jkamien@biopsych.com The bibliography is a list of references published between 1951 and and the present, and includes abstracts, journal articles, book chapters and books. Each reference is followed by a list of standardized keywords that were used to index the bibliography. Most of the keywords are generic drug names but they also include methodological terms, species studied and drug classes. This index makes it possible to selectively retrieve references according to the drugs used as the training stimuli, drugs used as test stimuli, drugs used as pretreatments, species, etc. by entering your own terms or by using our comprehensive lists of search terms. Supporting Agencies: NIDA transform.py ver 0.5 GENESIS Simulator GEneral NEural SImulation System 2006-06-26T12:58:07 2006-03-27T15:51:59 nif NDG 29013 http://genesis-sim.org/ James Bower bower@uthscsa.edu David Beeman dbeeman@dogstar.colorado.edu GENESIS is used for constructing, running, visualizing, and analyzing biologically accurate models of neurons, networks, and biochemical kinetics. Supporting Agencies: NIH transform.py ver 0.5 Atlases of the Brain Atlases of the Brain 2006-06-26T12:58:07 2006-03-27T15:52:44 nif NDG 29024 http://library.med.utah.edu/kw/brain_atlas/ Suzanne Stensaas suzanne.stensaas@hsc.utah.edu Suzanne Stensaas suzanne.stensaas@hsc.utah.edu Brain atlas in sagittal, coronal, and axial planes some from myelin stained sections, others from MRI. The structures are outlined and labeled on the zoomable images in the coronal series. The labels can also be used in quiz mode. Designed as part of of program for second year medical students studying neuroanatomy. transform.py ver 0.5 BrainMaps.org High Resolution Primate Brain Atlases 2006-06-26T12:58:07 2006-03-27T15:54:37 nif NDG 29028 http://brainmaps.org Ted Jones ejones@ucdavis.edu Shawn Mikula samikula@ucdavis.edu Atlases integrated with database and search features. BrainMaps.org is an interactive zoomable high-resolution digital brain atlas and virtual microscope that is based on more than 12 million (and counting) megapixels of scanned images of serial sections of both primate and non-primate brains and that is integrated with a high-speed database for querying and retrieving data about brain structure and function over the internet. Currently featured are complete brain atlas datasets for 9 mammalian and 1 avian species. Connectivity data also available. Very extensive and highly-detailed image collection. Supporting Agencies: NIMH; HBP transform.py ver 0.5 ASTD Audimotor Spike Train Database 2006-06-26T12:58:07 2006-03-27T15:55:21 nif NDG 29029 http://repositories.cdlib.org/mrrc/1 Charles Woody cwoody@mednet.ucla.edu Charles Woody cwoody@mednet.ucla.edu cerebellum; neuroinformatics; cognitive; conditioning; cochear nucleus; dentate; inferior colliculus; medial geniculate; auditory cortex; thalamus; motor cortex; lemniscal nucleus; caudate A database of recordings of spike activity from about 5000 neurons along the auditorimotor pathway from the cochlear nuclei to the neocortex, cerebellum, and elsewhere. No search interface; distribution consists of a collection of Microsoft Office and Windows executable files. The data can be downloaded or borrowed on CD from the UCLA Biomedical Library. Also available is an analysis program that averages histograms of spike activity and concurrent electromyographic (EMG) activity before and after conditioning of a Pavlovian blink response to an acoustic CS. Note: no search interface is available. Index and data files can be downloaded for use with Microsoft Office on Windows. Supporting Agencies: NIH, UCLA, DRF transform.py ver 0.5 ALZForum Alzheimer Research Forum 2006-06-26T12:58:07 2006-03-27T15:56:01 nif NDG 29043 http://www.alzforum.org/ Species: Human; Mouse transform.py ver 0.5 MGI Mouse Genome Informatics 2006-06-26T12:58:07 2006-03-27T16:26:43 nif NDG 28829 http://www.informatics.jax.org mgi-help@informatics.jax.org (207) 288-6445 Jackson Laboratory anatomy; ontology; cellular/molecular; map; genetics; development; neuroinformatics; data management; data storage; sequence data; software The primary mission of the Mouse Genome Informatics database (MGI) is to facilitate the use of the mouse as a model system for understanding human biology and disease. To achieve this objective we: 1) create and maintain an integrated representation of mouse genetic, genomic, expression, and phenotype data; 2) develop definitive reference data sets and consensus data views; 3) synthesize comparative genomic data between mouse and other mammals; 4) maintain a rich set of links and collaborations with other bioinformatics resources; 5) develop and support analysis and data submission tools; 6) develop user-friendly interfaces for public access to mouse genomic data; 7) provide extensive technical support for our community of database users; 8) actively participate in and coordinate with the global research community. Supporting Agencies: NIH (NHGRI, NICHD, NCI) transform.py ver 0.5.1 NEIBank National Eye Institute Bank 2006-06-26T12:58:07 2006-03-27T16:28:24 nif NDG 28944 http://neibank.nei.nih.gov Graeme Wistow graeme@helix.nih.gov Patee Buchoff buchoffp@nei.nih.gov genetics; retina; sequence data Neibank is a database of assembled expressed sequence tag (EST) data from eye tissue libraries. Supporting Agencies: NIH transform.py ver 0.5.1 WormAtlas A Database of Behavioral and Structural Anatomy of C. elegans 2006-06-26T12:58:07 2006-03-27T16:29:38 nif NDG 29027 http://wormatlas.org hall@aecom.yu.edu http://wormatlas.org/contactus.htm zaltun@aecom.yu.edu HTML Collection of resources on C elegans anatomy: - Worm anatomy handbook; - Methods for cell identification, staining, etc.; - Individual neuron gazetteer; - Discussion forum - Full texts of selected literature articles Supporting Agencies: NIH transform.py ver 0.5.1 there were several staining methods that listed at http://wormatlas.org/anatmeth/anatmeth.htm that had no terms to select. Maybe this is OK that they do not exist. UKU Neuroscience Links UKU Neuroscience and Neurology Links 2006-06-26T12:58:07 2006-03-27T16:30:45 nif NDG 29026 http://www.uku.fi/neuro/links2.htm Mikko Laakso mikko.laakso@uku.fi Mikko Laakso mikko.laakso@uku.fi University of Kuopio Department of Neuroscience and Neurology Simple list of links to neurology and neuroscience journals on the net, as well as some other relevant sites of the neurosciences. transform.py ver 0.5.1 Neurological Disorzder Resources Neurological Disorzder Resources 2006-06-26T12:58:07 2006-03-27T16:31:53 nif NDG 29025 http://faculty.washington.edu/chudler/disorders.html Eric H. Chudler chudler@u.washington.edu Eric H. Chudler chudler@u.washington.edu Hierarchically-organized list of links to web resources concerning neurological disorders. transform.py ver 0.5.1 EarLab A Digital Warehouse of Auditory Models and Data 2006-06-26T12:58:07 2006-03-27T16:32:40 nif NDG 29017 http://earlab.bu.edu/ David C. Mountain dcm@bu.edu dvajda@bu.edu HTML, text, matlab Earlab contains extensive online, freely-accessable auditory databases as well as custom designed modeling and data analysis software tools. A fully functional online auditory modeling environment is also available, as well as downloadable models in several languages. EarLab also provides custom cross-platform software for creating your own distributed auditory modeling environment, as well as software for analyzing the results from experimentation. A database of auditory modules is available for online use or download for the distributed auditory modeling environment, as well as instructions and specifications for creating your own modules. This unique resource provides a wealth of information on auditory processing in humans and other animals. Mathematical models are also provided. Supporting Agencies: NIMH; NIDCD transform.py ver 0.5.1 Sheep Brain Atlas The Navigable Atlas of the Sheep Brain 2006-06-26T12:58:07 2006-03-27T16:36:33 nif NDG 29008 http://www.msu.edu/~brains/brains/sheep/index.html John I. Johnson johnij@aol.com John I. Johnson johnij@aol.com Brain Biodiversity Bank (http://www.msu.edu/~brains/) Online images anatomy; atlas Images of a series of 100 coronal sections through the sheep brain, alternate sections stained for cell bodies and for myelinated fibers. Nuclei and tracts are labeled, labels can be applied and removed and progressive sections viewed with electronic controls. Data only available as online images. All of the images on this site are copyrighted. They were produced with the support of public funds, and we wish to keep them available for public use. You may use them for any purpose which will not interfere with their use by others. We do ask that you SECURE OUR PERMISSION, so that we can track the uses being made. Supporting Agencies: NSF transform.py ver 0.5.1 ICBM International Consortium for Brain Mapping 2006-06-26T12:58:07 2006-03-27T17:11:20 nif NDG 28918 http://www.loni.ucla.edu/ICBM/ John Mazziotta mazz@loni.ucla.edu architecture; morphology; anatomy; histology; atlas; cortex; mri; receptor; map; fmri; pet; volume; genetics; brainstem; cerebellum; subcortical; segmentation; white matter; gray matter; warping; imaging; neuroinformatics; software The primary goal of the ICBM project is the continuing development of a probabilistic reference system for the human brain. As part of this effort, data from 7,000 normal human subjects including demographic data, general and neurological exams, multi-pulse sequence MRI, handedness and neuropsychological data, and banked DNA (n=5,800) has been assembled in multiple databases. Supporting Agencies: NIMH; NINDS; NIBIB; HBP transform.py ver 0.5.1 Conexus Conexus 2006-06-26T12:58:07 2006-03-27T17:20:15 nif NDG 28910 http://mallorn.ucdavis.edu/ Isaac Trotts ijtrotts@ucdavis.edu Isaac Trotts ijtrotts@ucdavis.edu Center for Neuroscience, University of California Davis Conexus is a collection of software tools for computational neuroanatomy, written by Issac Trotts <ijtrotts@ucdavis> with principal investigator Edward G. Jones. They include graphical tools for OS X as well as command-line tools for OS X and Linux. - seg removes the background of an image, using statistics from an example provided by the user. - match-colors changes the colors in one image to match the colors in another image. - alignrows aligns adjacent rows of pixels in an image. - CnxSegment.app and CnxWarp.app provide segmentation and warping facilities via a graphical interface. transform.py ver 0.5.1 ChannelDB ChannelDB 2006-06-26T12:58:07 2006-03-27T17:23:18 nif NDG 28908 http://www.modelersworkspace.org/channeldb/ChannelDB.html James Bower bower@uthscsa.edu David Beeman dbeeman@dogstar.colorado.edu Modelers Workspace NeuroML ChannelDB is an implementation of a database of ionic conductance models stored in simulator-independent NeuroML format. transform.py ver 0.5.1 neuroConstruct neuroConstruct: Biophysical Neural Network Modeling Software 2006-03-29T13:52:25 2006-03-29T13:52:25 nif http://www.physiol.ucl.ac.uk/research/silver_a/neuroConstruct/ Padraig Gleeson p.gleeson@ucl.ac.uk Padraig Gleeson p.gleeson@ucl.ac.uk neuroConstruct is cross-platform Java software for simulating complex networks of biologically realistic neurons. Some of the key features of neuroConstruct are: Creation of networks of biologically realistic neurons, positioned in 3D space. Complex connectivity patterns between cell groups can be specified for the networks. neuroConstruct can import morphology files in GENESIS, NEURON, Neurolucida, SWC and MorphML format for inclusion in network models. Simulations can be run on the NEURON or GENESIS platforms. Cellular processes (synapses/channel mechanisms) can be imported from native script files or created in ChannelML. Recording of simulation data generated by the simulation and visualisation/analysis of data in neuroConstruct. Stored simulation runs can be viewed and managed through the Simulation Browser interface. As of 2006/11 the software has not yet been released. Target of this tool is the computational neuroscience community. In particular anybody interested in creating and visualizing large neuronal networks with NEURON. NEURON is required to actually perform the simulations. Neuron_Morpho Neuron_Morpho 2006-03-29T13:53:50 2006-03-29T13:53:50 nif http://www.maths.soton.ac.uk/staff/D'Alessandro/morpho/ Giampaolo D'Alessandro dales@soton.ac.uk Neuron_Morpho is a plugin for ImageJ that allows one to trace image stacks loaded into ImageJ. Tracing provides morphological data in the form of a digital reconstruction. NeuronJ provides the necessary neuronal data required to analyze a comprehenive battery of morphological parameters Computational Neuroscience on the Web Computational Neuroscience on the Web 2006-03-29T13:53:58 2006-03-29T13:53:58 nif http://home.earthlink.net/~perlewitz/ Jim Perlewitz perlewitz@earthlink.net Hierarchical link list. NeuronJ NeuronJ: A Java Program for Neurite Tracing and Quantification 2006-03-29T13:56:47 2006-03-29T13:56:47 nif http://imagescience.bigr.nl/meijering/software/neuronj/ Erik Meijering meijering@imagescience.org Erik Meijering meijering@imagescience.org NeuronJ is a plugin for ImageJ that can semi-automatically trace a structure confined to two-dimensional image. Cvapp Cvapp 2006-03-29T14:00:19 2006-03-29T14:00:19 nif http://www.compneuro.org/CDROM/docs/cvapp.html Erik De Schutter erik@tnb.ua.ac.be Robert Canon Computation Neuroscience Journal .swc .asc Java-based cross-platform digital reconstruction visualization and editor. Can load .swc or .asc reconstruction files for visualization, editing, or conversion. This is one of several tools for converting 3D reconstructions into formats for modeling and for correcting errors in morphology. MicroBrightfield MicroBrightfield, Inc. 2006-03-29T14:03:55 2006-03-29T14:03:55 nif http://www.mbfbioscience.com/ Neuronal morphology, neuronal stereology, Neurolucida Commercial products for analyzing neuronal morphology, stereology, etc.. This is a website used to market and provide information about the company's software and other tools. HubMed HubMed 2006-03-29T14:05:13 2006-03-29T14:05:13 nif http://www.hubmed.org/ alf@hubmed.org Export citations in RIS, BibTeX, RDF and MODS formats, or directly to RefWorks or EndNote. Provides interface to PubMed. The Mauk Lab Cerebellar PDF Library The Mauk Lab Cerebellar PDF Library 2006-03-29T14:06:47 2006-03-29T14:06:47 nif http://nba.uth.tmc.edu/homepage/mmauk/pdf.htm Mike Mauk m.mauk@uth.tmc.edu PDF Provides an extensive list of journal article citations that relate to the cerebellum. Poor utility for users outside of the Mauk Lab. Only citation details available to public. Full-text PDF documents available to lab members. Neuroscience For Kids Neuroscience For Kids 2006-03-29T14:08:07 2006-03-29T14:08:07 nif http://staff.washington.edu/chudler/neurok.html Eric H. Chudler chudler@u.washington.edu Eric H. Chudler chudler@u.washington.edu Provides an illustrative resource for kids or beginners to learn about neuroscience and the brain. Support: NCRR Neuroscience Tutorial Washington University School of Medicine Neuroscience Tutorial 2006-03-29T16:35:08 2006-03-29T16:35:08 nif http://thalamus.wustl.edu/course Diana Weedman Molavi susan@pulvinar.wustl.edu The Washington University School of Medicine An illustrated guide to the essential basics of clinical neuroscience created in conjunction with the first-year course for medical students. An illustrated guide to the essential basics of clinical neuroscience ANDP The Association of Neuroscience Departments and Programs (ANDP) 2006-03-29T16:38:15 2006-03-29T16:38:15 nif http://www.andp.org/ andp@andp.org andp@andp.org The Association of Neuroscience Departments and Programs (ANDP) is an organization of more than 250 member departments and programs from academic institutions in North America. ANDP's goal is to advance education and research training in academic neuroscience programs by disseminating information about neuroscience education and providing a forum for discussion of issues in training and research at both the institutional and national levels. The Association of Neuroscience Departments and Programs (ANDP) is an organization of more than 250 member departments and programs from academic institutions in North America. ANDP's goal is to advance education and research training in academic neuroscience programs by disseminating information about neuroscience education and providing a forum for discussion of issues in training and research at both the institutional and national levels. The ANDP is an independent, nonprofit, academically oriented organization which shares many interests with the Society for Neuroscience and works closely with the Society to advance common goals. The Association of Neuroscience Departments and Programs (ANDP) is an organization of more than 250 member departments and programs from academic institutions in North America. ANDP's goal is to advance education and research training in academic neuroscience programs by disseminating information about neuroscience education and providing a forum for discussion of issues in training and research at both the institutional and national levels. The ANDP is an independent, nonprofit, academically oriented organization which shares many interests with the Society for Neuroscience and works closely with the Society to advance common goals NeuraLinksPlus NeuraLinksPlus 2006-03-29T16:47:37 2006-03-29T16:47:37 nif http://spot.colorado.edu/~dubin/bookmarks Mark Dubin dubin@colorado.edu http://spot.colorado.edu/~dubin/bookmarks/index.html Hierarchically-organized annotated list of approximately 2,500 neuroscience-related web resources. Last update August 2005. All you need to know for understanding the synapse machinery The Basics of MRI The Basics of MRI 2006-03-29T16:54:46 2006-03-29T16:54:46 nif http://www.cis.rit.edu/htbooks/mri/ Joseph P. Hornak jphsch@rit.edu MRI, tutorial, FMRI Online book on principles and practice of magnetic resonance imaging. Instructional on the basics of MR imaging and data acquisition (e.g. the purpose and use of various MR contrast methods) An interesting and exhaustive explanation of how the technology works and is applied. NDG Neuroscience Database Gateway 2006-03-29T17:01:30 2006-03-29T17:01:30 nif http://ndg.sfn.org/ SfN Neuroscience Database Gateway The Neuroscience Database Gateway is a resource aimed at promoting awareness and facilitating access to online neuroscience databases. Neuroscience Course: Atlas Images Neuroscience Course: Atlas Images 2006-03-31T02:05:28 2006-03-31T02:05:28 BIRN http://anatomy.uams.edu/anatomyhtml/neuro_atlas.html Parthenon Publishing Group University of Arkansas for Medical Sciences Can save images one at a time in JPEG format. brain anatomy, eye, eye anatomy, spinal cord; gross dissection, atlas, tissue slice This site contains a comprehensive set of images of human brain and spinal cord slices, surface views and gross dissections along with dissections of the eye. Major structures are labeled on each slice. Standard anatomical terms are used, although no mention of terminology is given. This site is primarily aimed at medical students. In terms of labeled slices, the level of annotation is very coarse. However, it does provide a comprehensive set of dissections, many of which are very valuable. With respect to the license, there isn't any specific usage policy stated, although the copyright notice at the bottom states that "Unauthorized use prohibited". Estima: Bee Honey Bee Brain EST Project 2006-03-31T02:42:29 2006-03-31T02:42:29 BIRN http://titan.biotec.uiuc.edu/bee/honeybee_project.htm Gene E. Robinson, Ph. D. generobi@uiuc.edu Dr. Lei Liu leiliu@uiuc.edu The W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign Output can be exported as a text file. cDNA clones are available from Clemson Universitiy Genomics Institute www.genome.clemson.edu/orders/ expressed sequence tag, bee brain, cDNA clone The University of Illinois Bee-ESTdb integrates data from the bee brain EST sequencing project with data from sequencing and gene research projects from other organisms, primarily the fruit fly Drosophila melanogaster. The goal of Bee-ESTdb is to provide updated information on the genes of the honey bee, currently using annotation primarily from flies to suggest cellular roles, biological functions, and evolutionary relationships. The site allows searches by sequence ID, EST annotations, Gene Ontology terms, Contig ID and using BLAST. Site utilizes NCBI gene accession ID's and annotations based on Gene Ontology. Very nice resource for those interested in comparative genomics of brain. The Visible Mouse Project The Visible Mouse Project 2006-04-01T01:02:09 2006-04-01T01:02:09 BIRN 2006-04-01T01:02:09 2006-04-01T01:02:09 BIRN http://tvmouse.compmed.ucdavis.edu/index.html Dr. Jose Galvez jjgalvez@ucdavis.edu Dr. Jose Galvez jjgalvez@ucdavis.edu University of California, Davis Images can be downloaded individually as JPEGs. Some movies are available for download in Quicktime format. histology, CNS, pathology, magnetic resonance imaging, neoplasms; animation, virtual histology, mouse, correlated imaging, necropsy, whole mouse This site is intended as an educational resource to introduce users to the anatomy, physiology, histology, and pathology of the laboratory mouse, with an emphasis on the Genetically Engineered Mouse (GEM). It provides access to histological images, scanned at high resolution and browsable through Zoomify, movie loops and animations derived from MRI, correlated MRI and histology. It has CNS data but is focused on the whole body, e.g., physiological data is available for the heart in the form of wave patterns. None employed. This site still appears to be under construction. It may be useful to neuroscientists by relating brain anatomy to the rest of the body. There is a movie illustrating necropsy of the mouse. A link to a compendium of histological slices of brain neoplasms is provided under the "Image Archive" link. There is a "CNS" link under construction for anatomical system, whic presumably will include detailed CT imaging. Permission is required to link to any material on the site. This site employs Macromedia Flash to view the content. Should this information be noted anywhere? IHC World Online Information Center for Immunohistochemistry 2006-04-01T01:43:35 2006-04-01T01:43:35 BIRN http://www.ihcworld.com/ info@ihcworld.com Life Span Biosciences On-line text immunocytochemistry protocol, immunohistochemical protocol, neuroscience methods and techniques, neurohistology protocol This site provides access to a very wide variety of histological protocols either directly or through links. An entire section is devoted to neuroscience, including neurohistology and cell culture protocols.protocol, experimental technique. This resource is a comprehensive source for experimental techniques and protocols. The links are of varying quality and the site is not database driven, so there is a lot of information to sort through. But this site has to be one of the largest repostories of this type of information. Some neuroscience specific protocols are available, either contributed to the site or as links. Many of the links are broken, however. Neuroanatomy Atlas Neuroanatomy Atlas 2006-04-21T00:59:19 2006-04-21T00:59:19 BIRN http://www.sph.sc.edu/comd/rorden/anatomy/home.html Chris Rorden rorden@gwm.sc.edu Chris Rorden rorden@gwm.sc.edu University of South Carolina Atlas images are downloadable as GIFs. A viewer for MRI images (MRicro) is available and is described in a separate entry. brain atlas, magnetic resonance images, normalized brain scans, imaging tutorial, sulci, gyri This site provides sets of annotated magnetic resonance brain images, both slices and surface views, normalized to Talairach space, along with annotations and a nice tutorial on image normalization. A viewer for MRI images (MRicro) is available and is described in a separate entry. Series of coronal, axial and sagittal brain slices along with some rendered volumes with major brain structures delineated. Slices are presented as static series with partial overlap of slices, so they are not suitable for 3d reconstruction. Standard neuroanatomical nomenclature is used, but the source of the nomenclature is not identified. Some data from the Duvernoy (1991) atlas: The Human Brain: Structure, Three-dimensional Sectional Anatomy and MRI, New York: Springer-Verlag, are included on the page so this may be the source. This is a nice introductory site for researchers and students interested in learning about processing of MRI images and basic brain anatomy. This site dates from 2002 and many of the links are no longer current. Very clear, well-laid out site with lots of explanatory material. MRIcron MRIcron 2006-04-21T01:06:23 2006-04-21T01:06:23 BIRN http://www.sph.sc.edu/comd/rorden/mricro.html Chris Rorden rorden@gwm.sc.edu Works on Windows and Linux. Can read Analyze, Nifti and other medical imaging formats. magnetic resonance imaging, viewer, software tool, medical image viewer MRIcro allows Windows and Linux computers view medical images. It is a standalone program, but includes tools to complement SPM (software that allows neuroimagers to analyse MRI, fMRI and PET images). MRIcron allows efficient viewing and exporting of brain images. In addition, it allows neuropsychologists to identify regions of interest (ROIs, e.g. lesions). MRIcron can create Analyze format headers for exporting brain images to other platforms. NA Could not evaluate because it doesn't run on Macintosh. Citation: Rorden, C., Brett, M. (2000). Stereotaxic display of brain lesions. Behavioural Neurology, 12, 191-200. We should probably include a citation link so that users can read more about a tool/site or use it for acknowledgement. Also, for software tools, where should we put platform dependencies? PDSP Ki Database Pyschoactive Drug Screening Program Ki Database 2006-04-22T03:32:37 2006-04-22T03:45:59 KSkinner http://pdsp.med.unc.edu/pdsp.php Jamie Driscoll, B.S. jdrisco1@mail.nih.gov (301) 443-5288 Bryan L. Roth MD, PhD at Case Western Reserve University in Cleveland OH and Project Officer Jamie Driscol at NIMH, Bethesda MD, USA. Contract # NO1MH32004. bryan_roth@med.unc.edu 919-966-7535 Part of the NIMH sponsored Pyschoactive Drug Screening Program Ki,drug target affinity values, affinity binding, transporters, G-protein coupled receptors, enzymes, drug targets, G-protein coupled receptors, ion channels, transporters, enzymes, ligand, species, biological source, hot ligand, test ligand, publication reference, Ki value The Ki database serves as a data warehouse for published and internally-derived Ki, or affinity, values for a large number of drugs and drug candidates at an expanding number of G-protein coupled receptors, ion channels, transporters and enzymes. The flexible user interface provides for customized data mining. Includes drug molecular targets derived from and relevant to neuronal tissues. Offers more than 40,000 values for searching. Search via web interface or download tab delimited text file. CAS and NSC numbers for searching PubChem substances and compounds respectively. Sponsored by NIMH, this database is highly useful to those exploring the binding of drugs to a variety of targets. See Nat Rev Drug Discov. 2005 Dec;4(12):1005-14. Drop down keyword list for molecular targets and othe search parameters. Neuropad Neuropad 2006-04-22T04:11:24 2006-04-22T04:11:24 BIRN http://n002bsel.bios.uic.edu/ Chris Comer ccomer@uic.edu John Dowd biff@uic.edu Comer Laboratory, University of Illinois at Chicago identified neuron, neuron morphology, connectivity, physiology; insect, ganglion, anatomy, cricket, cockroach. This website hosts a database of about 40 uniquely identifiable insect neurons from 5 different species. NEUROPAD allows structural information about nerve cells to be mapped onto an idealized plan of the central nervous system [CNS] and it stores that information along with physiological observations and a reproduction of the original anatomical description of each cell. NEUROPAD was designed with orthopteroid insects (such as crickets and cockroaches) in mind. However, it contains information on cells from a number of different insect species, with slightly different CNS organizational schemes, such as differing numbers of ganglia. Unknown In most cases (exceptions will be noted on the appropriate record) in this database, the orientation scheme recommended by Strausfeld et al. (1984) has been adopted. In the living animal, the brain (supraesophageal ganglion, Sa) is oriented at approximately a right angle to the rest of the CNS, i.e. the ventral nerve cord, and the nerve cord is parallel to the long axis of the body. The CNS will be viewed as though Sa wererotated downward and into the same plane as the cord. Therefore, the posterior surface of Sa in the intact animal is considered here its dorsal surface. Standard abbreviations for all ganglia are employed and are listed on the website. Provides a nice summary of the anatomy and physiology of identified neurons in the insect nervous system. Will grow in value as more neurons are added. The site doesn't provide datafiles but does provide links to the literature. Neocortical Microcircuit Database Neocortical Microcircuit Database 2006-04-22T19:15:21 2006-04-22T19:15:21 BIRN http://microcircuit.epfl.ch/ Henry Markram henry.markram@epfl.ch Brain Mind Institute,EPFL, Lausanne, Switzerland Cell profiles are available in Neurolucida .asc format. neuron morphology, analysis tools, connectivity, microcircuit, cortical neuron, gene expression, synaptic connectivity, rat, microcircuitry, intracellular injection, intracellular recording, microscopy, 3D reconstruction, Neurolucida, electrophysiology Neurons are characterized in terms of their morphological, physiological and gene expression profiles. Synaptic connections are characterized in terms of their physiological and anatomical profiles.Neuron morphology profiles are obtained from detailed morphometric breakdown of 3D reconstructed neurons (m-Profiles), neuron physiology profiles are obtained from detailed measurement of the electrophysiological responses to a series of stimulus protocols (e-Profiles), and neuron gene expression profiles are obtained from single cell RT-PCR data (g-Profiles) and in the near future from gene-chips. Synaptic connections are characterized by the identity of the pre and postsynaptic neurons (sn-Profile), the anatomy of synaptic connections as characterized by the axonal and dendritic location of light microscopically identified putative synapses (sm-Profile), and the physiology of synaptic connections as characterized by a profile of electrophysiological parameters obtained from a series of stimulation protocols applied to the presynaptic neuron (se-Profile). unknown A list of terms and their definitions for describing neuronal morphology and electrophysiological characterizations is provided on the site. The origin of the terms were not specified. This site will provide a major resource for those interested in cortical microcircuitry once it is complete. It currently has almost 300 neuronal reconstructions and 176 connections mapped. Stereotaxic MRI Brain Atlas of Monkey Stereotaxic MRI Brain Atlas of Monkey 2006-04-24T22:34:58 2006-04-24T22:34:58 BIRN http://www.med.nihon-u.ac.jp/department/physiol1/ Masato Taira masato@med.nihon-u.ac.jp Nihon University, School of Medeicine, Laboratory for Magnetic Resonance, Imaging and Spectroscopy, National Institutes for Phsyiological Sciences JPEG magnetic resonance imaging, stereotaxic brain atlas, monkey Series of MRI slices from 3 male Japanese snow monkeys (Macaca fuscata). Slices are presented according to distance from interaural line. No annotations are provided. Images are provided of 2 mm MRI slices of male monkey brain in the coronal (N = 5), horizontal (N =1) and sagittal (N =1) planes. No terminology used The slices are low resolution and no annotations are provided which decrease the utility of this site. Would be suitable for low resolution 3D reconstruction of monkey brain, however. Also, there are datasets provided for 5 monkeys total, 3 m.fuscata and 2 m. mulatta. Vervet Monkey Brain Atlas Vervet Monkey Brain Atlas 2006-04-24T22:49:13 2006-04-24T22:49:13 BIRN http://labs.pharmacology.ucla.edu/mellab/vervet_atlas/ Dan Rubins drubins@mednet.ucla.edu Crump Institute for Biological Imaging, Department of Molecular and Medical Pharmacology, UCLA School of Medicine. Slices may be saved as JPEGs. It doesn't appear that the entire atlas can be downloaded. brain atlas, vervet monkey, 3D brain atlas, head An unannotated digital brain atlas of the vervet monkey has been developed using images obtained by cryosectioning. High quality images of the vervet monkey brain may be viewed from three orthogonal planes.cryosection, 3D reconstruction, male, 8 year old monkey, 300 um slice, 1.073 mm resolution. A male, eight year old, vervet monkey was sacrificed by an overdose of pentobarbital. The monkey was decapitated, and the head frozen in isopentane chilled with liquid nitrogen. The frozen head was blocked in distilled water for cryosectioning, and placed with the rostral extent of the head facing downward. The 2-D images were read into Interactive Data Language (Research Systems, Inc., Denver, CO, USA), where they were assembled into a 3-D volume, and rotated into a standardized orientation. No terminology utilized for anatomical structures. Orientation of the brain relative to external landmarks and laterality are clearly described but rely on an arbitrary reference point in the center of the volume. The images are of good quality and are available in each of the 3 orthogonal planes. Because the atlas cannot be downloaded, it cannot be easily used for 3D reconstruction or segmentation. No anatomical annotations are provided. We should divide the atlas designation into "annotated" and "unannotated". I'm coming across a lot of unlabeled image stacks that call themselves atlases. Arrowsmith Arrowsmith 2006-05-10T12:27:12 2006-05-10T12:43:53 BIRN http://arrowsmith.psych.uic.edu/arrowsmith_uic/ Neil Smalheiser neils@uic.edu Vetle Torvik vtorvik@uic.edu University of Illinois at Chicago Web-based software tool The Arrowsmith project is developing text mining tools to operate on the scientific literature. The "Arrowsmith" tool is designed to identify implicit links between two sets of Medline articles; the "Author-ity" tool is designed foridentifying Medline articles written by a particular author; "Anne O'Tate" tool provides multiple ways of summarizing the results of a PubMed query. Web service Not really relevant, but the Arrowsmith uses medline records which include MESH terms. The Arrowsmith tool suite is designed to assist scientists in mining the scientific literature to help assess and prioritize new hypotheses and find information that cannot be found using more traditional searches. This tool is not specific to Neuroscience, but is certainly very relevant and has been field tested specifically by neuroscientists. This tool is listed as using web services, but I don't know that this is true. The Brain from Top to Bottom The Brain from Top to Bottom 2006-05-11T21:38:18 2006-05-11T21:38:18 nif www.thebrain.mcgill.ca Bruno Dubuc bruno.dubuc@videotron.ca Text, images, HTML, and Flash training, education, high school, college, graduate level, brain function, synapse, brain evolution, drug abuse, sensory systems, physiological psychology A highly effective educational resource and review for training in neuroscience and cognitive science. Requires Flash plugin. Flash Material on the site is open under the Copyleft agreement. Copyleft The content of the site The Brain from Top to Bottom is under copyleft. The concept of "copyleft" is a method of providing free access to the results of original work and of encouraging people to reproduce and even modify this work on an equally free basis. Copyleft is thus diametrically opposed to the traditional concept of copyright, which nowadays people seem to be trying to use to cover absolutely everything, from genes to intellectual property. In the libertarian spirit, the concept of copyleft promotes freedom of expression and staunchly opposes the idea that knowledge can be the private property of a small elite. Introductory and education neuroscience material for independent or class room use. FMRIDC The fMRI Data Center 2006-05-11T21:53:38 2006-05-11T21:53:38 nif http://www.fmridc.org/ John Van Horn jvanhorn@loni.ucla.edu John Van Horn jvanhorn@loni.ucla.edu Analyze 7.5, NIFTI anatomy; ontology; atlas; cortex; mri; fmri; volume; talairach; brainstem; cerebellum; white matter; gray matter; neuroinformatics; data management; data storage; portal; software; neuroimaging; brain mapping; cognitive The fMRI data center (fMRIDC) is a curated respository of neuroimaging data obtained in published studies of cognitive function. these data sets typically include raw fMRI timecourse volumes, the timecourses after data preprocessing, statistical result images, and high-resolution anatomical image volumes. All studies also contain study meta-data describing the scanner, experimental, and subject protocols. Platform independent fMRI study data management tools are openly available for researchers to use in maintaining their own study databases and that facilitate data sharing within and between labs as well as with archives like the fMRIDC. This data respository seeks to encourage researchers to perform novel analyses of previously published study data to broaden the scope of original study conclusions. All data are provided free for use in research and education and are distributed on media or via download. Scriptable interface is described at http://www.genenetwork.org/CGIDoc.html http://www.fmridc.org/harvester... /fmristudy.xsd.html Major effort to archive the complete raw, processed and results data from functional/structural MRI data from published studies of cognitive function. Now based at UC Santa Barbara. Supporting Agencies: HBP transform.py ver 0.5 AlzGene AlzGene - Published AD Candidate Genes 2006-05-14T00:41:29 2006-05-14T00:41:29 nif http://www.alzforum.org/res/com/gen/alzgene/ Lars Bertram http://www.alzforum.org/contact.asp Alzheimer Research Forum forum genetic analysis, human populations, association study, gene, allele, neurodegeneration, Alzheimer An excellent summary of large numbers of human genetic studies of Alzheimer's disease. This database provides a summary of the association between allelic variants and disease susceptibility and progression. An excellent summary of large numbers of human genetic studies of Alzheimer's disease. This database provides a summary of the association between allelic variants and disease susceptibility and progression. The alzGene web site has drugs that are approved for Alzheimers with various attributes stored. There was no appropriate "Data Type" for that. We suggest "Drugs" or "Therapeutics". Antibody Directory for Alzheimer Research Antibody Directory for Alzheimer Research 2006-05-14T00:47:50 2006-05-14T00:47:50 nif http://www.alzforum.org/res/com/ant/ Alzheimer Research Forum antibody, neurodegeneration, Alzheimer A database of providers of antibodies directed against several hundred molecules and proteins of relevant to research on Alzheimer and other neurodegenerative diseases. Gensat NINDS Gensat BAC Transgenic Project 2006-05-24T10:12:34 2006-05-24T10:12:34 nif NDG 29051 http://www.gensat.org/ Nathaniel Heintz heintz@rockefeller.edu gensat@mail.rockefeller.edu The Gensat database contains a gene expression atlas of the central nervous system of the mouse based on bacterial artificial chromosomes (BACs). Supporting Agencies: NINDS transform.py ver 0.5.2 BGED Brain Gene Expression Database 2006-05-24T10:56:04 2006-05-24T10:56:04 nif NDG 29044 http://genome.mc.pref.osaka.jp/BGED/ Kikuya Kato katou-ki@mc.pref.osaka.jp Kikuya Kato katou-ki@mc.pref.osaka.jp cortex; genetics; cerebellum; data management; metadata This database contains gene expression data for various physiological and pathological processes in mouse brain. All the data have been obtained by adaptor-tagged competitive PCR, an advanced version of quantitative PCR. transform.py ver 0.5.2 SymAtlas SymAtlas 2006-05-24T11:16:42 2006-05-24T11:16:42 nif NDG 29066 http://symatlas.gnf.org hilmar lapp Hilmar Lapp symatlas@gnf.org Genomics Institute of the Novartis Research Foundation cortex; olfactory; genetics; cerebellum; somatosensory; retina Symatlas is a web-application for publishing experimental gene functionalization datasets integrated with a flexibly searchable gene-centric database of public and proprietary annotations. transform.py ver 0.5.2 RAD RNA Abundance Database 2006-05-24T11:20:35 2006-05-24T11:20:35 nif NDG 29072 http://www.cbil.upenn.edu/RAD rad3@pcbi.upenn.edu rad3@pcbi.upenn.edu ontology; genetics; microarrays The RNA Abundance Database (RAD) provides a comprehensive MIAME-supportive infrastructure for gene expression data management and makes extensive use of ontologies. Specific details on protocols, biomaterials, study designs, etc., are collected through a user-friendly suite of web annotation forms. Software has been developed to generate MAGE-ML documents to enable easy export of studies stored in RAD to any other database accepting data in this format. RAD is part of a more general Genomics Unified Schema (http://gusdb.org), which includes a richly annotated gene index (http://allgenes.org), thus providing a platform that integrates genomic and transcriptomic data from multiple organisms. transform.py ver 0.5.2 RGD Rat Genome Database 2006-05-24T11:21:35 2006-05-24T11:21:35 nif NDG 29074 http://rgd.mcw.edu/ Simon Twigger simont@mcw.edu Jiali Chen jlchen@mcw.edu The Rat Genome Database (RGD) curates and integrates rat genetic and genomic data and provides access to this data to support research using the rat as a genetic model for the study of human disease. Supporting Agencies: NHLBI transform.py ver 0.5.2 UniProt Universal Protein Resource 2006-05-24T11:22:32 2006-05-24T11:22:32 nif NDG 29076 http://www.pir.uniprot.org/ http://www.pir.uniprot.org/support/helpdesk.shtml help@uniprot.org http://www.pir.uniprot.org/support/helpdesk.shtml help@uniprot.org Hosted by SWISSPROT, EMBL and Georgetown university genetics; proteomics UniProt (Universal Protein Resource) is the world's most comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-prot, TREMBL, and PIR. the terminology is as is used in EXPAZY-SWISSPROT, TREMBL and PIR transform.py ver 0.5.2 PDB RCSB Protein Data Bank 2006-05-24T11:23:26 2006-05-24T11:23:26 nif NDG 29077 http://www.rcsb.org/pdb/ Dr. Helen M. Berman berman@rcsb.rutgers.edu http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/contact/index.html info@rcsb.org Research Collaboratory for Structural Bioinformatics (RCSB) The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease. It is the single worldwide repository of information about the three-dimensional structures of large biological molecules, including proteins and nucleic acids. Supporting Agencies: NCRR; NINDS; NSF; NLM; NIBIB transform.py ver 0.5.2 PEP Predictions for Entire Proteomes 2006-05-24T11:25:02 2006-05-24T11:25:02 nif NDG 29079 http://cubic.bioc.columbia.edu/pep/ Burkhard Rost rost@columbia.edu carter@cubic.bioc.columbia.edu PEP is a database of Predictions for Entire Proteomes, including ORFs (Open Reading Frames), sequences, and putative structural domains (self-sufficient folding units). transform.py ver 0.5.2 HPRD Human Protein Reference Database 2006-05-24T11:25:49 2006-05-24T11:25:49 nif NDG 29080 http://hprd.org/ Akhilesh Pandey pandey@jhmi.edu http://www.hprd.org/help The human protein reference database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. transform.py ver 0.5.2 PANTHER Protein ANalysis THrough Evolutionary Relationships Classification System 2006-05-24T11:26:41 2006-05-24T11:26:41 nif NDG 29082 http://www.pantherdb.org/ http://www.pantherdb.org/feedback.jsp http://www.pantherdb.org/feedback.jsp feedback@pantherdb.org The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. Proteins are classified by expert biologists into families and subfamilies of shared function, which are then categorized by molecular function and biological process ontology terms. For an increasing number of proteins, detailed biochemical interactions in canonical pathways are captured and can be viewed interactively. transform.py ver 0.5.2 NCBI National Center for Biotechnology Information 2006-05-24T11:28:21 2006-05-24T11:28:21 nif NDG 29087 http://www.ncbi.nih.gov/ http://www.ncbi.nih.gov/about/glance/contact_info.html info@ncbi.nlm.nih.gov Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease. Supporting Agencies: NIH; NLM; NCBI transform.py ver 0.5.2 SOURCE SOURCE at Stanford University 2006-05-24T11:33:34 2006-05-24T11:33:34 nif NDG 29094 http://source.stanford.edu array@genome.stanford.edu array@genome.stanford.edu genetics SOURCE is a unification tool which dynamically collects and compiles data from many scientific databases, and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of homo sapiens, mus musculus, rattus norvegicus into easy to navigate genereports. Supporting Agencies: NIH transform.py ver 0.5.2 a7db Alpha-7 Database 2006-05-24T11:35:04 2006-05-24T11:35:04 nif NDG 29101 http://www.lgics.org/a7db/ Philip C. Biggin phil@biop.ox.ac.uk Steven Buckingham HTML The α7 database (or a7db) provides physiological, pharmacological and structural data pertaining to the α7 subunit of the nicotinic acetylcholine receptor. transform.py ver 0.5.2 GEO Gene Expression Omnibus 2006-05-24T13:24:23 2006-05-24T13:24:23 nif NDG 29070 http://www.ncbi.nlm.nih.gov/geo/ geo@ncbi.nlm.nih.gov geo@ncbi.nlm.nih.gov anatomy; genetics; brain mapping; microarrays A gene expression/molecular abundance repository supporting MIAME compliant data submissions, and a curated, online resource for gene expression data browsing, query and retrieval. GEO is the largest fully public repository for high-throughput molecular abundance data, primarily gene expression data. these data include microarray-based experiments measuring the abundance of mRNA, genomic DNA and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Supporting Agencies: NIH; NLM; NCBI transform.py ver 0.5.3 PIR Protein Information Resource 2006-05-24T13:25:31 2006-05-24T13:25:31 nif NDG 29078 http://pir.georgetown.edu/ pirmail@georgetown.edu pirmail@georgetown.edu UniProt Consortium The Protein Information Resource (PIR), located at Georgetown University Medical Center (GUMC), is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies. Supporting Agencies: NIH; NSF transform.py ver 0.5.3 Array Express - EBI Array Express at the European Bioinformatics Institute 2006-05-24T13:27:01 2006-05-24T13:27:01 nif NDG 29089 http://www.ebi.ac.uk/arrayexpress/ arrayexpress@ebi.ac.uk http://www.ebi.ac.uk/support/ microarrays Arrayexpress is a public repository for microarray data, which is aimed at storing well annotated data in accordance with MGED (Microarray Gene Expression Data society) recommendations. transform.py ver 0.5.3 SMD Stanford Microarray Database 2006-05-24T13:28:28 2006-05-24T13:28:28 nif NDG 29091 http://smd.stanford.edu/ Catherine Ball ball@genome.stanford.edu Michael Nitzberg nitz@genome.stanford.edu Comforms to MIAME standard. microarray SMD is a private database system for Stanford investigators and their collaborators, in which a portion of the data is released to the public (with registration), and a portion is also available on a for-fee basis. It stores raw and normalized data, as well as the corresponding image files, from microarray experiments. SMD provides interfaces for data retrieval, analysis and visualization. It also allows public access to data already published by smd users. Data may be exported to ArrayExpress and GEO. MIAME standard meta-data Useful for anyone wishing to examine gene expression microarray data. Supporting Agencies: NIH; NCI transform.py ver 0.5.3 ABA Allen Brain Atlas 2006-05-25T12:49:20 2006-05-25T12:49:20 nif NDG 29096 http://www.brain-map.org info@brainatlas.org info@brainatlas.org Allen Brain Institute HTML anatomy; atlas; map; genetics; 3d models; data management; data storage; neuroimaging The goal of the Allen Brain Atlas is to create a detailed cellular-resolution, genome-wide map of gene expression in the mouse brain. The completion of the sequencing of the mouse brain and the availability of techniques to probe gene expression amenable to scale-up and automation have made this an achievable, albeit ambitious, goal. The Allen Brain Atlas has created an automated platform for high-throughput in situ hybridization that allows a highly systematic approach for analyzing gene expression in the brain. transform.py ver 0.5.3 Cys-Loop Ligand Gated Channels None 2006-05-25T13:25:00 2006-05-25T13:25:00 nif NDG 29100 http://www.gwumc.edu/pharm/cys-loop.htm Timothy Hales phmtgh@gwumc.edu Erica Steinman This resource contains two dendrograms indicating the relatedness of human subunits that form cys-loop receptors specific for cations and anions, respectively. The dendrograms contain links to the receptors and their individual subunits. These pages give brief information about the subunits and links to their gene and amino acid sequences in Genbank. There are also diagrams of the subunit topology. transform.py ver 0.5.3 Dolphin Brain Atlas None 2006-05-25T13:25:53 2006-05-25T13:25:53 nif NDG 29102 http://www.msu.edu/user/brains/turs/ John L. Johnsonn johnij@aol.com John L. Johnsonn johnij@aol.com anatomy; atlas; map; MRI The Dolphin Brain Atlas consists of electronic anatomically labeled 3D atlas of the dolphin brain created from MRI images. in conjunction is also presented, anatomically labeled stained sections that correspond to the 3D MRI images. Supporting Agencies: NSF transform.py ver 0.5.3 Neuron at Duke Neuron at Duke 2006-05-25T13:27:46 2006-05-25T13:27:46 nif NDG 29104 http://neuron.duke.edu/ John W. Moore moore@neuro.duke.edu Ted Carnevale ted.carnevale@yale.edu NEURON is a simulation environment for developing and exercising models of neurons and networks of neurons. it is particularly well-suited to problems where cable properties of cells play an important role, possibly including extracellular potential close to the membrane), and where cell membrane properties are complex, involving many ion-specific channels, ion accumulation, and second messengers. transform.py ver 0.5.3 Brain Architecture Center None 2006-05-25T13:28:58 2006-05-25T13:28:58 nif NDG 29105 http://brancusi.usc.edu/ Larry Swanson lswanson@usc.edu Mihail Bota mbota@usc.edu anatomy; atlas; map; 3d models; neuroimaging; brain mapping The goal of the Center is to clarify the basic structural plan of the human brain. To reach this goal, the Center catalyzes research on the wiring diagram of this supremely important biological computer, which mediates our thoughts and feelings-good and bad, painful and pleasurable, normal and pathological. Special emphasis is placed on gaining insights into human brain organization from the vast amounts of neuroanatomical information obtained from research on lower animals in the last three decades. The Center sponsors symposia, lectures, and workshops; promotes undergraduate and graduate training in structural neuroscience; and is implementing a Brain Architecture Workbench? on the web. transform.py ver 0.5.3 ImageBank ImageBank 2006-05-25T13:29:52 2006-05-25T13:29:52 nif NDG 29106 http://bio.ltsn.ac.uk/imagebank/ imagebank@ltsnbio.leeds.ac.uk imagebank@ltsnbio.leeds.ac.uk Centre for Bioscience, the Higher Education Academy, ImageBank Imagebank consists of freely available images contributed by academics, researchers, Learned Societies, industry and individuals with rights cleared for educational purposes. Users are able to search for images based on keywords or browse within a wide range of bioscience subject areas. Images are then ?downloadable? along with informative descriptive text provided by the contributor. All images undergo a validation process by Centre for Bioscience staff with good subject knowledge. ImageBank also offers reviews of, and links to existing bioscience image databases. transform.py ver 0.5.3 gpDB gpDB: a database of G-proteins and their interaction with GPCRs 2006-05-25T14:24:16 2006-05-25T14:24:16 nif NDG 29108 http://biophysics.biol.uoa.gr/gpDB/ Stavros Chamodrakas biodb@biol.uoa.gr cellular/molecular; genetics; G-protein gpDB is a publicly accessible, relational database of G-proteins and their interactions with GPCRs. The sequences are classified according to a hierarchy of different classes, families and sub-families, based on extensive literature search. The main innovation besides the classification of both G-proteins and GPCRs is the relational model of the database, describing the known coupling specificity of the GPCRs to their respective alpha subunit of G-proteins, a unique feature not available in any other database. There is full sequence information with cross-references to publicly available databases, and the user may submit advanced queries for text search. Furthermore there is an interface for running BLAST against the database and a pattern search tool. transform.py ver 0.5.3 NeuroTerrain Laboratory for Bioimaging and Anatomical Informatics 2006-05-25T14:25:04 2006-05-25T14:25:04 nif NDG 29109 http://neuroterrain.org/ Jonathan Nissanov nissanov@drexel.edu William Bug william.bug@drexel.edu architecture; anatomy; atlas; map; neuroinformatics; software; neuroimaging The Laboratory for Bioimaging and Anatomical Informatics develops and distributes software tools for neuroinformatics and neurocartography. Supporting Agencies: HBP transform.py ver 0.5.3 HDBase HDBase - A Community Website for Huntington's Disease Research 2006-05-25T14:26:04 2006-05-25T14:26:04 nif NDG 29110 http://hdbase.org/ Nathan Goodman natg@shore.net hdbase@systemsbiology.org cellular/molecular; development; data management; metadata; microarrays HDBase is a community website for Huntington's disease research. Presently, we have Y2H and Mass Spec. protein-protein interaction data centered around the HD protein (huntingtin) and information on therapeutic studies in mouse. We also have Human and Mouse Affymetrix Microarray data from Strand et al.. transform.py ver 0.5.3 Schziophrenia Research Forum Schizophrenia Research Forum 2006-05-25T14:27:42 2006-05-25T14:27:42 nif NDG 29111 http://www.schizophreniaforum.org/ Hakon Heimer Elizabeth Wu http://www.schizophreniaforum.org/contact.asp Schizophrenia research forum is involved in dissemination of biomedical information related to schizophrenia, including research papers, news, and discussion. Supporting Agencies: NIMH transform.py ver 0.5.3 Lowe Syndrome Mutation Database Lowes Syndrome Mutation Database 2006-05-25T14:28:54 2006-05-25T14:28:54 nif NDG 29112 http://research.nhgri.nih.gov/lowe/ bioinformatics@nhgri.nih.gov bioinformatics@nhgri.nih.gov genetics Lowe oculocerebrorenal syndrome is an X-linked disorder caused by mutations in the OCRL1 gene, which encodes a 105-kDa Golgi protein with phosphatidylinositol (4,5) bisphosphate 5-phosphatase activity. A database of mutations causing Lowe syndrome has been established. Information on new mutations may be submitted online. Supporting Agencies: NHGRI transform.py ver 0.5.3 RettBase RettBASE: IRSA MECP2 Variation Database 2006-05-25T14:29:39 2006-05-25T14:29:39 nif NDG 29113 http://mecp2.chw.edu.au/ John Christodolou johnc@chw.edu.au Andrew Grimm andrewg3@chw.edu.au Western Sydney Genetics Program genetics; metadata This database has been constructed by merging mutation and polymorphism data from the published literature pertaining to Rett syndrome and related clinical disorders, and by incorporating unpublished mutation and polymorphism data that have been submitted directly to us. RettBase is updated on a very frequent basis manually by our curators to ensure the validity of the data being sent to us. transform.py ver 0.5.3 Lafora The Lafora Progressive Myoclonus Epilepsy 2006-05-25T14:30:29 2006-05-25T14:30:29 nif NDG 29114 http://projects.tcag.ca/lafora/ jzhang@sickkids.ca jzhang@sickkids.ca genetics The lafora database is a respository of information related to progressive myoclonus epilepsy mutation and polymorphism data. transform.py ver 0.5.3 Neuromuscular Disease Center Neuromuscular Disease Center 2006-05-25T14:31:12 2006-05-25T14:31:12 nif NDG 29115 http://www.neuro.wustl.edu/neuromuscular/ Alan Pestronk pestronka@neuro.wustl.edu Alan Pestronk pestronka@neuro.wustl.edu neuromuscular disease; cerebellum; motor cortex; spinal cord The Neuromuscular Disease Center is an institute at Washington University in St. Louis. The web site acts as a portal for the neuromuscular disease community and contains a comprehensive listing of biological and clinical aspects of neuromuscular disorders. transform.py ver 0.5.3 FlexPROT None 2006-05-25T14:31:52 2006-05-25T14:31:52 nif NDG 29116 http://bioinfo3d.cs.tau.ac.il/FlexProt/ Maxim Shatsky maxshats@tau.ac.il Maxim Shatsky maxshats@tau.ac.il protein alignment; software FlexProt detects the optimal flexible structural alignment of a pair of protein structures. The first structure is assumed to be rigid, while in the second structure potential flexible regions are automatically detected. transform.py ver 0.5.3 MCell MCell: A Monte Carlo Simulator of Cellular Microphysiology 2006-05-25T14:32:29 2006-05-25T14:32:29 nif NDG 29117 http://www.mcell.cnl.salk.edu/ MCell Team mcell@salk.edu 858-453-4100 ext 1420 MCell Team mcell@salk.edu 858-453-4100 ext 1420 simulation; signaling MCell is a modeling tool for realistic simulation of cellular signaling in the complex 3-D subcellular microenvironment in and around living cells -- what we call cellular microphysiology. At such small subcellular scales the familiar macroscopic concept of concentration is not useful and stochastic behavior dominates. MCell uses highly optimized Monte Carlo algorithms to track the stochastic behavior of discrete molecules in space and time as they diffuse and interact with other discrete effector molecules (e.g. ion channels, enzymes, transporters) heterogeneously distributed within the 3-D geometry of the subcellular environment. Supporting Agencies: NIH; NSF; NPACI transform.py ver 0.5.3 Virtual Cell Virtual Cell Modeling and Simulation Framework 2006-05-25T14:55:39 2006-05-25T14:55:39 nif NDG 29118 http://vcell.org/ Les Loew les@volt.uchc.edu Frank Morgan frm@neuron.uchc.edu National Resource for Cell Analysis and Modelling (NCRAM) anatomy; simulation; cellular/molecular; 3d models; imaging; neuroinformatics; software; brain mapping NCRAM, the National Resource for Cell Analysis and Modeling is developing a unique software modeling environment, the virtual cell, for quantitative cell biological research. Supporting Agencies: NI; NCRR transform.py ver 0.5.3 NEOSIM Neural Open Simulation 2006-05-25T14:56:37 2006-05-25T14:56:37 nif NDG 29119 http://www.neurogems.org/neosim2/ Nigel Goddard nigel.goddard@ed.ac.uk Nigel Goddard nigel.goddard@ed.ac.uk systems modeling; simulation; software; model The original NEOSIM project developed tools for large scale systems modelling of the nervous system, integrating computational models ranging from the sub-cellular to the whole brain level. The NEOSIM framework is based on parallel discrete event simulation techniques, whereby simulation components are distributed across a parallel machine or network and communicate using timestamped events. The successor NEOSIM2 project under the NeuroGems umbrella at Edinburgh University (http://www.neurogems.org) continues to distribute the software. Documentation is still available at http://neosim.org . Supporting Agencies: NIH; HBP; UK MRC, BBSRC transform.py ver 0.5.3 NEST The Neural Simulation Technology Initiative 2006-05-25T14:58:03 2006-05-25T14:58:03 nif NDG 29121 http://www.nest-initiative.org/ simulation; development; neuroinformatics; physiology; software The Neural Simulation Technology (NEST) initiative is a collaborative effort to advance simulation technology for of large, biologically realistic networks of spiking neurons. transform.py ver 0.5.3 DsTool DsTool 2006-05-25T14:58:49 2006-05-25T14:58:49 nif NDG 29123 http://www.cam.cornell.edu/~gucken/dstool/ John Guckenheimer gucken@cam.cornell.edu John Guckenheimer gucken@cam.cornell.edu simulation; 3d models; software DsTool is a computer program for the interactive investigation of dynamical systems on computers using Unix and the X window system. transform.py ver 0.5.3 NSL Neural Simulation Language 2006-05-25T14:59:34 2006-05-25T14:59:34 nif NDG 29124 http://www.neuralsimulationlanguage.org/about.html Michael Arbib Alfredo Weitzenfeld alfredo@itam.mx simulation; software NSL, Neural Simulation Language, is a simulation system for large-scale general neural networks. NSL provides a simulation environment simplifying the task of modeling neural networks. In particular, NSL supports neural models having as basic data structure neural layers with similar properties and similar connection patterns, where neurons are modeled as leaky integrators with connections subject to diverse learning rules. Development of NSL has gone hand in hand with modeling of neural mechanisms underlying visuomotor coordination, with special emphasis on the analysis of data from anurans, monkeys, and humans. NSL follows an object-oriented design, providing higher level programming abstraction corresponding to neural elements. NSL provides system development tools, such as visualization capabilities and a run-time interpreter, which give the user powerful tools in developing and analyzing models. NSL has been widely used throughout the world for both teaching and research. transform.py ver 0.5.3 MATCONT MATCONT and CL_MATCONT: Continuation Software in Matlab 2006-05-25T15:00:19 2006-05-25T15:00:19 nif NDG 29125 http://users.ugent.be/~ajdhooge/research.html Willy Govaerts willy.govaerts@ugent.be Annick Dhooge annick.dhooge@ugent.be simulation; neuroinformatics; software MATCONT is a graphical MATLAB package for the interactive numerical study of dynamical systems. It is developed in parallel with the command line continuation toolbox CL_MATCONT. Both MATCONT and CL_MATCONT allow to compute curves of equilibria, limit points, Hopf points, limit cycles and bifurcation points of limit cycles. transform.py ver 0.5.3 ARC Alzheimer's Research Center (ARC) 2006-05-25T15:02:15 2006-05-25T15:02:15 nif NDG 29127 http://www.mcg.edu/centers/alz/ Jerry J. Buccafusco jbuccafu@mcg.edu Jerry J. Buccafusco jbuccafu@mcg.edu HTML The Alzheimer's Research Center was developed to support collaborative basic and clinical research in the area of Alzheimer's disease and related neurodegenerative disorders, by (1) promoting interdisciplinary approaches to answering research questions, (2) providing a venue for regular meetings of its members for the purpose of sharing members' research findings, the latest published works in the field, and supporting visits to this campus by outside experts, (3) providing course materials and lectures related to Alzheimer's disease for undergraduate, graduate, and postgraduate student instruction , and (4) supporting two core facilities, the Neurological Disorder Database Registry, and the Animal Behavior Center. Supporting Agencies: NIH transform.py ver 0.5.3 NINDS National Institute of Neurological Disorders and Stroke 2006-05-25T15:03:05 2006-05-25T15:03:05 nif NDG 29128 http://www.ninds.nih.gov/ http://www.ninds.nih.gov/about_ninds/addresses.htm http://www.ninds.nih.gov/about_ninds/addresses.htm National Institutes of Health (NIH) The mission of NINDS is to reduce the burden of neurological disease - a burden borne by every age group, by every segment of society, by people all over the world. transform.py ver 0.5.3 BrainPharm Brain Pharmacological Database 2006-05-25T15:03:41 2006-05-25T15:03:41 nif NDG 29129 http://senselab.med.yale.edu/brainpharm/ Gordon Shepherd gordon.shepherd@yale.edu Chiquito Crasto chiquito.crasto@yale.edu Yale Senselab anatomy; simulation; cellular/molecular; connections; development; neuroinformatics; ion channel; data management; data storage; model; software; brain mapping; cognitive; motor cortex BrainPharm is a database under development to support research on drugs for the treatment of different neurological disorders. It contains agents that act on neuronal receptors and signal transduction pathways in the normal brain and in nervous disorders. It enables searches for drug actions at the level of key molecular constituents, cell compartments and individual cells, with links to models of these actions. Supporting Agencies: NIH; NIDCD transform.py ver 0.5.3 Coriell Cell Repositories Coriell Cell Repositories 2006-05-25T15:04:15 2006-05-25T15:04:15 nif NDG 29130 http://ccr.coriell.org/ccr/ David Beck Christine M. Beiswanger cbeiswan@coriell.org cellular/molecular; genetics; cell lines; cultures The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cells, cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world. Supporting Agencies: NIH; NIDA; NIA transform.py ver 0.5.3 Surf-Hippo The Surf-Hippo Neuron Simulation System 2006-05-25T16:23:27 2006-05-25T16:23:27 nif NDG 29120 http://www.neurophys.biomedicale.univ-paris5.fr/~graham/surf-hippo.html Lyle J. Graham lyle@biomedicale.univ-paris5.fr surf-hippo@ai.mit.edu The Surf-Hippo neuron simulator is used to investigate morphologically and biophysically detailed compartmental models of single neurons and networks of neurons. Surf-Hippo allows ready construction of cells and networks using built-in functions and various anatomical file formats (Neurolucida, NTS and others). Surf-Hippo is a public domain package, written in Lisp, and runs under Unix and Linux. transform.py ver 0.5.3 mAdb Micro-array Database at the National Cancer Institute 2006-05-25T16:45:04 2006-05-25T16:45:04 nif NDG 29092 http://nciarray.nci.nih.gov/ madb-support@bimas.cit.nih.gov madb-support@bimas.cit.nih.gov CIT/BIMAS is collaborating with NCI/CCR in the development of the BioInformatics to manage, access and analyze cDNA Microarray data generated by the NCI/CCR Microarray Center. Supporting Agencies: NIH; NCI transform.py ver 0.5.3 PDP++ None 2006-05-25T16:47:41 2006-05-25T16:47:41 nif NDG 29126 http://www.cnbc.cmu.edu/Resources/PDP%2B%2B/PDP%2B%2B.html Randall C. O'Reilly randall c. o pdpadmin@cnbc.cmu.edu neural network; model; simulation; backpropagation; feedforward; software; metadata The PDP++ software is a neural-network simulation system written in C++. It represents the next generation of the PDP software originally released with the McClelland and Rumelhart "Explorations in Parallel Distributed Processing Handbook", MIT Press, 1987. transform.py ver 0.5.3 HUPO BPP HUPO Brain Proteome Project 2006-05-26T11:08:50 2006-05-26T11:08:50 nif NDG 29083 http://www.hbpp.org/ Helmut E. Meyer helmut.e.meyer@ruhr-uni-bochum.de http://www.hbpp.org/6087/index.html Human Proteome Organisation (HUPO) HUPO BPP is an open international project under the patronage of the Human Proteome Organisation (HUPO) that aims: ? To analyze the brain proteome of human as well as mouse models in healthy, neurodiseased and aged status with focus on Alzheimer's and Parkinson's Disease; ? To perform quantitative proteomics as well as complemantary gene expression profiling on disease-related brain areas and bodily fluids; ? To advance knowledge of neurodiseases and aging in order to push new diagnostic approaches and medications; ? To exchange knowledge and data with other HUPO projects and national / international initiatives in the neuroproteomic field; ? To make neuroproteomic research and its results available in the scientific community and society. transform.py ver 0.5.3 CSD Cambridge Structural Data Base 2006-10-24T18:10:00 2006-10-24T18:10:00 KSkinner 2006-10-24T18:10:00 2006-10-24T18:10:00 KSkinner http://www.ccdc.cam.ac.uk/products/csd/ Cambridge Crystallographic Data Center admin@ccdc.cam.ac.uk +44 1223 336408 This is part of the CSD system having many international affiliated Centers CIF (Crystallography Information File)or .txt The Cambridge Structural Database System (CSDS) is a single product that comprises the following components: The Cambridge Structural Database (CSD) CSDS Software: search and information retrieval (ConQuest), structure visualisation (Mercury), statistical analysis of retrieved data (VISTA), and software for database creation (PreQuest) Knowledge bases derived from the CSD: Mogul (intramolecular geometry) and IsoStar (intermolecular interactions, including data from the PDB) ConQuest - The Interface for the CSD System ConQuest is the primary program for searching and retrieving information from the Cambridge Structural Database (CSD). ConQuest provides a full range of text/numeric database search options, in addition to more complex search functionality including: Each entry in the Cambridge Structural Database (CSD) corresponds to an individual determination of a specific crystal structure. Each database entry is identified by a CSD reference code, comprising: six alphabetic characters (e.g. BENZEN) to identify the chemical compound a possible two-digit number (as in BENZEN05, FERROC14, etc.) to identify a specific experimental determination of the crystal structure of BENZEN, FERROC, perhaps by different authors, using a different radiation, at a different temperature, etc. TCambridge Structural Database (CSD) is the world repository of small-molecule crystal structures. For example, the crystal structures supported by the National Institute on Drug Abuse are deposited here. The crystal structures supported by the National Institute on Drug Abuse are deposited here. NeuroMab UC Davis/NINDS/NIMH NeuroMab Facility 2006-11-16T02:17:15 2006-11-16T02:17:15 KSkinner http://www.neuromab.org/index.htm Antibodies Inc. antibodyco@antibodiesinc.com 800) 824-8540 NeuroMab Pharm/SOM neuromab@ucdavis.edu (530) 756-4420 cooperative venture among the University of California at Davis, the National Institute for Neurological Disorders and Stroke, the National Institute for Mental Health, and Antibodies Inc. monoclonal antibodies; membrane proteins;receptors channels transporters, synaptic proteins, neuronal signaling molecules, disease-related proteins K channel subunits, transporters scaffold proteins protein targets link to NCBI through accession numbers 80 antibodies in catalog The NeuroMab facility serves as a resource to the entire neuroscience community by providing high quality reagents that will serve as critical links between information emerging from genomic efforts and future proteomic approaches to brain function. Moreover, the unique neuroscience-based approach that the NeuroMab facility will yield reliable antibodies that might not otherwise be available, and the comprehensive biochemical and immunohistochemical verification will save countless investigators the time, money and effort of attempting to use expensive yet suboptimal reagents in their research. The Mouse Transcriptome Project The Mouse Transcriptome Project 2006-11-16T03:46:07 2006-11-16T03:46:07 KSkinner http://www.ncbi.nlm.nih.gov/genome/guide/mouse/MouseTranscriptome.html trans-NIH project with Lynx MPSS? technology html, xml, text The focus of this project is the generation of a reference RNA transcriptome expression database for the C57BL/6J mouse. The current dataset will consist of 90 samples, primarily from adult tissue, and was analyzed using a technique known as Massively Parallel Signature Sequencing (MPSS) Genes identified by NCBI GSM Accession The focus of this project is the generation of a reference expression database for the C57BL/6J mouse. The current dataset will consist of 90 samples, primarily from adult tissue, and was analyzed using a technique known as Massively Parallel Signature Sequencing (MPSS). The data are stored in the Gene Expression Omnibus (GEO). need to add "SAGE" and "MPSS" under gene/protein expression analysis techniques; Knockout Mice and Phenotypic Data Deltagen and Lexicon Knockout Mice and Phenotypic Data Resource 2006-11-16T14:10:47 2006-11-16T14:10:47 KSkinner http://www.nih.gov/science/models/mouse/deltagenlexicon/theresource.html Colin Fletcher, Ph. D. nhgrikoquestions@mail.nih.gov This resource is offered by the trans-NIH Mouse Initiative genes listed in html table The phenotypic data on all 251 mouse lines will be made available on the Mouse Genome Informatics website at The Jackson Laboratory (http://www.informatics.jax.org ), through weblinks to the phenotypic data reports on each line, available at http://www.informatics.jax.org/external/ko/. MGI controlled phenotypic terms to the mutant strains with links to the phenotypic data reports (see http://www.informatics.jax.org/searches/allele_form.shtml Deltagen, Lexicon, mouse phenotyping, gene knockouts, mouse line, gene deletion, appearance, health, fitness, behavior, reproductive ability, radiological data, microscopic data Abca12 Acvrl1 Adamts4 Adamts5 Adcy3 Adcy4 Adcy7 Adcy9 Adfp Adipor1 Adipor2 Agpat5 Aldh7a1 Apobec2 Arts1 Atp1a1 Avpr1a Avpr1b Axl B3galt2 B3galt3 B3galt5 B3gnt1 B3gnt3 B4galt5 B4galt6 Bai2 Bdkrb1 Birc1a Bmp6 Cacna1c Cacna2d3 Cacng3 Cacng4 Cacng6 Calcr Capn5 Capn7 Casp12 Cck Ccr6 Ccr7 Ccrl1 Ccrl2 Ccr1l1 Cd97 Cdc25a Cds2 Celsr2 Cer1 Cfl1 Chrna2 Chst3 Clca5 Cnr2 Ctsc Cxcr3 Ddc Defb3 Dgat2 Dnmt2 Dpagt1 Drd5 Edg6 Efemp1 Efemp2 Esrra Esrrg Ext1 Faah Faim2 Fkbp11 Frzb Fzd1 Fzd6 Fzd8 Fzd9 Fzd10 Gabarap Gabbr1 Gabra3 Gabra4 Gabrp Gabrq Galnt10 Galr1 Galr2 Gdf6 Glra3 Glt8d1 Gng7 Gpm6a Gpr3 Gpr6 Gpr19 Gpr37 Gpr37l1 Gpr82 Gpr151 Gprk5 Gria3 Gria4 Grik5 Grin3a Grm1 Grm3 Grm7 Gsk3b Gsr Gsta4 Gstt2 Hcrtr1 Hs6st2 Htr1d Htr1f Htr2b Htr4 Htr5a Htr5b Htr6 Htr7 Ide Igfbp2 Igf2bp1 Ihpk1 Il4i1 Il8ra Il21 Il21r Il23a Inpp5a Insl5 Itk Kcna6 Kcnh5 Kcnmb4 Kcnq2 Kcns2 Kl Lats2 Ldb2 Lgals8 Lias Lmbr1 Lmbr1l Lrp5 Lu Mapkapk2 Mmp10 Mmp16 Mmp17 Mtmr1 Mtmr2 Mtmr3 Nagk Ncam2 Ndrg3 Nedd4 Npl Npm1 Nrg1 Nrg4 Ntsr1 Nucb2 Olr1 Omd Oprd1 Oprl1 Oprs1 P2rx7 Pde1b Pdgfc Pdpk1 Phb Pik3cb Pik3cd Pip5k1b Pkd2l2 Pknox1 Pofut2 Pomt1 Ppard Ppm1f Ppm1g Ppp1cb Ppp5c Prdm16 Prkcn Prss12 Psenen Ptch2 Ptger1 Ptpro Pzp Rab6b Rgs2 Rgs4 Rgs5 Rgs7 Rgs10 Rgs11 Rgs14 2210013K02Rik 4932417H02Rik Rtn4rl1 Rtn4rl2 Rya3 S100a1 Sacy Scn3a Scn9a Scn11a Sema3e Sema5a Sema6c Serpinc1 Shc1 Sirt3 Slamf6 Slc6a9 Slc6a11 Slc7a8 Slc9a6 Slc12a6 Slc12a8 Slc17a5 Slc17a7 Slc22a6 Slc22a12 Slc27a4 Slc35a1 Slc40a1 Slco1a5 Srd5a2l Sstr1 Stub1 Stx4a Tgfbr1 Thbs4 Tlr2 Tmprss11a Tpp1 Trpc2 Trpm5 Twsg1 Txndc2 Uchl1 Ulk2 Vcp Wasf2 Xcr1 MGI controlled phenotypic terms This resource will give researchers unprecedented access to two private collections of knockout mice, providing valuable models for the study of human disease and laying the groundwork for a public, genome-wide library of knockout mice.Under the license agreements with Deltagen and Lexicon, researchers who receive the knockout mice lines through NIH are free to publish any results from research involving the line and also to seek patent or other intellectual property protection for any of the inventions or discoveries resulting from such research. need entry for "mutants" in resource type; need entry for knockout in data type; need term "knockout" for techniques; need term "phenotypic assay" for techniques; in "stage" need term for NCRAD National Cell Repository for Alzheimer's Disease 2006-11-17T13:40:25 2006-11-17T13:40:25 dshurtle http://ncrad.iu.edu/ NIA alzstudy@iupui.edu The National Cell Repository for Alzheimer's Disease is supported by the National Institute on Agiing and is housed at Indiana University Medical Center in Indianapolis, Indiana. Even though located in Indiana, it works with families nationwide. Researchers seeking to identify the genes contributing to the risk for Alzheimer's disease and other related diseases may be limited in their attempts to obtain large, well-characterized families with Alzheimer's disease (AD). The National Cell Repository for Alzheimer's Disease (NCRAD) was established to provide the research community with DNA and cell lines from large numbers of informative families with multiple individuals affected with Alzheimer's Disease or related diseases. NCRAD samples are available for qualified researchers who are interested in expanding the understanding of the etiology, pathogenesis, diagnosis, treatment and prevention of diseases like AD. The NIA Alzheimer?s Disease Genetics Study seeks to enroll 1,000 families in which a pair of living siblings (brothers or sisters) has Alzheimer?s disease. Families will often be seen at one of the 29 Alzheimer?s Disease Centers located throughout the country NIAGADS NIA Genetics of Alzheimer's Disease Data Storage 2006-11-17T13:48:16 2006-11-17T13:48:16 dshurtle http://zork.wustl.edu/nia/ Scott F. Saccone, Ph.D. ssaccone@wustl.edu Sue Winkeler sue@bacchus.wustl.edu The National Institute on Aging (NIA) has established the National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site at Washington University, St. Louis All Genetic Data derived from NIA funded studies for the genetics of late-onset Alzheimer's disease be deposited at NIAGADS or another NIA approved site or both whenever possible. Such Genetic Data shall be made available as soon as possible, but no later than upon acceptance of a subset of data for publication or public disclosure of a submitted patent application, whichever is earlier. For example, after publication of preliminary reports of the work, a subset of phenotypic Access requests will be considered based on experience and qualifications of the investigators in conducting genetic research on complex disorders Data avaialable for Caribbean Hispanic AD Study, Genomic Search for Susceptibility to Alzheimer's disease,Genetic Epidemiological Studies of Alzheimer's Disease, Urokinase-type Plasminogen Activator and Alzheimer's Disease, An Integrated Genomic Approach to Alzheimer Disease, Alzheimer's Disease and Gene Discovery on Chromosome 9, Genetics Consortium for Late Onset of Alzheimers (LOAD CIDR Project) COGA Collaborative Study on the Genetics of Alcoholism 2006-11-17T13:55:12 2006-11-17T13:55:12 dshurtle http://zork.wustl.edu/niaaa/ John Rice, Ph.D. john@zork.wustl.edu Sue Winkeler sue@bacchus.wustl.edu 314-286-2569 Blaise software used for data collection The Collaborative Study on the Genetics of Alcoholism (COGA) is a multi-site, multi-disciplinary undertaking with the overall goals of characterizing the familial transmission of alcoholism and related phenotypes and identifying susceptibility genes using genetic linkage. The study is being coordinated by the SUNY Health Science Center at Brooklyn (HSCB) under the leadership of Henri Begleiter. The study was initially funded by the National Institute of Alcohol Abuse and Alcoholism (NIAAA) in 1989. Uses Blaise system for data entry Additional useful information at http://www.niaaa.nih.gov/ResearchInformation/ExtramuralResearch/SharedResources/projcoga.htm National Institute on Drug Abuse Center National Institute on Drug Abuse Center for Genetic Studies 2006-11-17T14:01:43 2006-11-17T14:01:43 dshurtle http://zork.wustl.edu/nida/ John Rice, Ph.D john@zork.wustl.edu Sue Winkeler sue@bacchus.wustl.edu The National Institute on Drug Abuse (NIDA), in collaboration with The NIH, has established the Center for Genetic Studies, under a contract to Rutgers University and its subcontractor, Washington University Banks DNA samples and cell lines from individuals diagnosed with substance abuse disorders. Over 22,000 samples are currently available. Information on 14 studies. Includes Genome Wide Association of Nicotine Dependence Currently 23 ongoing studies. Information on 14 studies. Includes Genome Wide Association of Nicotine Dependence CCR NIGMS Human Genetic Cell Repository 2006-11-17T14:11:23 2006-11-17T14:11:23 dshurtle http://ccr.coriell.org/nigms/ Christine M. Beiswanger, Ph.D. cbeiswan@coriell.org 856-757-9694 Barbara Frederick bfrederi@coriell.org 856-757-9690 Sponsored by the National Institute of General Medical Sciences (NIGMS) and housed at the Coriell Institute for Medical Research Banks more than 9400 unique cell lines and over 4000 DNA samples. Over 700 different diseases. Samples from the DNA Polymorphism Discovery Research, the CEPH collections, and International HapMap Project. The NIGMS Human Genetic Cell Repository is collaborating with the Centers for Disease Control and Prevention's (CDC) Genetic Testing Reference Material Coordination Program (GeT-RM) to distribute reference materials to the genetics community. These reference materials contain mutations of clinical importance that have been confirmed by multiple volunteer laboratories using different testing platforms Samples from the collection have been used in more than 5,000 publications and are distributed to scientists in more than 50 countries. MMFADR MOUSE MODELS FOR ALZHEIMER?S DISEASE RESEARCH 2006-11-17T14:25:59 2006-11-17T14:25:59 KSkinner 2006-11-17T14:25:59 2006-11-17T14:25:59 KSkinner 2006-11-17T14:25:59 2006-11-17T14:25:59 KSkinner http://jaxmice.jax.org/library/models/ad.pdf The Jackson Laboratory http://jaxmice.jax.org/orderquest/index.html 207-288-6000 JAX? Mice and Services http://jaxmice.jax.org/micetech/index.html 800-422-MICE (800-422-6423) www.jax.org/jaxmice/models/alzheimers Aged Alzheimer's Disease Models The Jackson Laboratory's Alzheimer's Disease Mouse Model Repository offers several models that develop Alzheimer's-related characteristics as they age. Aged mice are available from JAX? Services for the following strains: B6C3-Tg(APPswe,PSEN1dE9)85Dbo/J STOCK Mapttm1(EGFP)Klt Tg(MAPT)8cPdav/J B6.Cg-Tg(PDGFB-APPSwInd)20Lms/2J B6.Cg-Mapttm1(EGFP)KitTg(MAPT)8cPdav/J B6.Cg-Tg(APPswe,PSEN1dE9)85Dbo/J Supporting Agencies: NIH; ARRC Aging-Related Rodent Colonies 2006-11-17T14:54:56 2006-11-17T14:54:56 KSkinner http://www.nia.nih.gov/ResearchInformation/ScientificResources/default.htm Heidi Brogdon obrrd_order_desk@nia.nih.gov 301-496-0181 Heidi Brogdon obrrd_order_desk@nia.nih.gov 301-496-0181 http://www.nia.nih.gov Mice and rats of varying ages (1-36 months) and genetic backgrounds are available to researchers. NIA maintains colonies of aged rats and mice for use by the scientific community for research directly related to aging and age-related diseases. The animals are housed behind specific pathogen-free barriers and monitored for genetic purity and health status, and a health report accompanies each shipment of animals. In addition, NIA supports a tissue bank of flash frozen tissues from mice and rats from the aged rodent colonies and tissue arrays containing punches of multiple ages and multiple tissues per slide. Click here for the new restrictions on eligibility to use the NIA aged rodent colonies. 1)Aged Rodent Colonies Handbook 2)Aged Rodent Tissue Bank Handbook; 3)Oldest Ages Available in NIA Aged Rodent Colonies; 4)Rodent and Tissue Bank Resources Information Supporting Agencies: NIH; KOMP Knockout Mouse Project 2006-11-17T15:13:07 2006-11-17T15:13:07 KSkinner http://www.nih.gov/science/models/mouse/knockout/index.html NIH knockout mouse project nhgrikoquestions@mail.nih.gov 301-496-7531 NIH knockout mouse project nhgrikoquestions@mail.nih.gov 301-496-7531 The Knockout Mouse Project is a trans-NIH initiative that aims to generate a comprehensive and public resource comprised of mouse embryonic stem (ES) cells containing a null mutation in every gene in the mouse genome Seeks to generate a comprehensive and public resource comprised of mice containing a null mutation in every gene in the mouse genome. Several RFAs were issued in early FY 2006 and FY 2007 Standard Mouse Nomenclature Facilitates making Knockouts and shorten time to make a knockout. Supporting Agencies: NIH; Under technique there is no field for mutation or induced mutation. Under resource content body should be maintained. Neural structure: under cell list also other so other cell types can be included. A general resource may be useful for neurobiology but it does necessarily have a neurobiological focus NIMH Human Genetics Initiative Center for Collaborative Genetic Studies 2006-11-17T15:16:39 2006-11-17T15:16:39 dshurtle http://nimhgenetics.org/ John P. Rice, Ph.D. john@zork.wustl.edu Sue Winkeler sue@bacchus.wustl.edu The National Institute of Mental Health (NIMH) has established the Center for Collaborative Genetic Studies with a grant to Rutgers University and a sub-contract to Washington University, to produce, store, and distribute clinical data and biomaterials (DNA samples and cell lines) The National Institute of Mental Health (NIMH) has established the Center for Collaborative Genetic Studies with a grant to Rutgers University and a sub-contract to Washington University, to produce, store, and distribute clinical data and biomaterials (DNA samples and cell lines) available in the NIMH Human Genetics Initiative. This center produces, stores, and distributes clinical data and biomaterials (DNA samples and cell lines) available in the NIMH Human Genetics Initiative. Repository of over 50,000 subjects. Collection of affected individuals and their relatives (including Caucasian, African American, Asian and Hispanic individuals) Over 5,000 control subjects (including Caucasian, African American and Hispanic individuals) for case-control and other genetic studies on mental disorders and mental functioning Sixty two ongoing studies PDmice NINDS/UCLA Repository for Parkinson's Disease Mouse Models 2006-11-17T15:51:29 2006-11-17T15:51:29 KSkinner 2006-11-17T15:51:29 2006-11-17T15:51:29 KSkinner 2006-11-17T15:51:29 2006-11-17T15:51:29 KSkinner http://www.ninds.nih.gov/funding/research/parkinsonsweb/amr/amr_mice_ucla_repository.htm NIH Neurological Institute http://www.ninds.nih.gov/contact_us.htm (800) 352-9424 or (301) 496-5751 Dr. Lorenzo Refolo PDMice@ninds.nih.gov (800) 352-9424 or (301) 496-5751 This is part of the Parkinsons Web Gene Strain Creator Comments DJ-1 Knockout BL6 Gerfen Lab, NIMH Re-derived mt human alpha synuclein (A53T) FVB/N Nussbaum Lab, NHGRI Re-derived alpha synuclein Knockout 129S6/SvEv Nussbaum Lab, NHGRI In the process of being re-derived -/-A53T/PAC Tg alpha synuclein FBV x 129/SV Nussbaum Lab, NHGRI Parkin 129S4 129S4 Mix Richard Palmiter Not breeding. Have requested more breeder pairs Information for depositors Investigators who are willing to share mice with the PD research community through this resource should send an email to PDMice@ninds.nih.gov describing the mouse. The submission will be reviewed by the PD Models Repository Oversight Committee and, if accepted, a copy of the MTA will be sent by return email. NINDS is most interested in distributing mice that have been characterized in a peer-reviewed publication, but other models will certainly be considered. The email should describe the following: The protocol for identification from tail DNA. The health report of the mice to be shipped (the report has to be less than 2 months old). Information about the strain and any special needs for care and breeding. Information about any publications involving the mice Certification that mice are not encumbered by continuing intellectual property or other rights to any research, data or discovery utilizing the animals. Information for consumers Investigators desiring to study the mice available through the repository should send a request via email to PDMice@ninds.nih.gov. Requests will be reviewed by the PD Models Repository Oversight Committee and priority will be determined on a first come, first served basis; two breeding pairs will typically be shipped to any single requestor. As detailed in the MTA, mice are not available for commercial research, including but not limited to drug screening. Neither the creator nor UCLA have a role in the governance of the Repository, and specifically, cannot impose conditions upon availability or distribution. It is anticipated that until the Repository is in a mode of steady state production, requests will be collected and mice distributed as supply allows. The email requesting mice should include: A brief description of the protocol Either a copy of the IACUC approval letter or number Retinal Degeneration Retinal Degeneration Rat Model Resource 2006-11-17T16:04:21 2006-11-17T16:04:21 KSkinner http://ucsfeye.net/mlavailRDratmodels.shtml Matthew LaVail, Ph.D mmlv@itsa.ucsf.edu 415-476-4233 Matthew LaVail, Ph.D mmlv@itsa.ucsf.edu 415-476-4233 Developed, maintain and distribute all of the known, fully penetrant rat models (inbred and congenic strains)of the retinitis pigmentosa of inherited retinal degeneration. For the investigations of retinal degeneration, many attributes of rats make them a better model than mice; the relatively large eye size for intraocular injections or surgical procedures. Mutant rhodopsin transgenic rats P23H mutant rhodopsin transgenic rats -Three lines with different rates of photoreceptor degeneration S334ter mutant rhodopsin transgenic rats -Five lines with different rates of photoreceptor degeneration RCS (Royal College of Surgeons) rats with inherited retinal dystrophy ? RCS pink-eyed inbred strain ? RCS pigmented congenic strain with slowed rate of retinal dystrophy ? RCS congenic control strains of both pigmentation types, wild-type at the retinal dystrophy (Mertk) genetic locus This project has been supported by the National Eye Institute for the past 19 years to produce and distribute breeding pairs of rat models to vision scientists. Tofacilitate rapid distribution of the transgenic rats, it has been negotiated with the commercial producer of the transgenic animals a very minimal administrative procedure for proprietary matters NIA Cell Repository AGING CELL REPOSITORY 2006-11-17T16:31:22 2006-11-17T16:31:22 dshurtle 2006-11-17T16:31:22 2006-11-17T16:31:22 dshurtle http://ccr.coriell.org/nia/ Christine M. Beiswanger, Ph.D. cbeiswan@coriell.org Coriell Cell Repositories ccr@coriell.org Sponsored by the National Institute on Aging (NIA), the AGING CELL REPOSITORY, is a resource facilitating cellular and molecular research studies on the mechanisms of aging and the degenerative processes associated with it. The cells in this resource have been collected over the past three decades using strict diagnostic criteria and banked under the highest quality standards of cell culture. Scientists use the highly-characterized, viable, and contaminant-free cell cultures from this collection for research on such diseases as Alzheimer disease, progeria, Parkinsonism, Werner syndrome, and Cockayne syndrome. Scientists can use the highly-characterized, viable, and contaminant-free cell cultures from this collection for research on such diseases as Alzheimer disease, progeria, Parkinsonism, Werner syndrome, and Cockayne syndrome The collections of the Repository include premature aging disorders, Alzheimer Disease, Gerontology Research Center samples from the Baltimore Longitudinal Study of Aging, the Longevity Collection including the Aged Sib Pair Collection, the Adolescent Study, Apparently Healthy Controls, Animal Models of Aging and both human and animal differentiated cell types need matertial transfer agreement under "license" fiield ENU Mutagenesis Mouse Mutagenesis Center for Developmental Defects 2006-11-17T16:32:01 2006-11-17T16:32:01 KSkinner http://www.mouse-genome.bcm.tmc.edu/ENU/MutagenesisProj.asp Monica Justice mjustice@bcm.tmc.edu 713-798-5440 Monica Justice mjustice@bcm.tmc.edu 713-798-5440 This project is part of the Trans-NIH Mouse Initiative The goal of project III is to determine the function of genes on mouse Chromosome 11 by saturating the chromosome with recessive mutations. The distal 40 cM of mouse Chr 11 exhibits linkage conservation with human Chromosome 17. We are using the chemical N-ethyl-N-nitrosourea (ENU) to saturate wild type chromosomes with point mutations. By determining the function of genes on a mouse chromosome, we can extrapolate to predict function on a human chromosome. We expect many of the new mutants to represent models of human diseases such as birth defects, patterning defects, growth and endocrine defects, neurological anomalies, and blood defects. Because many of the mutations we expect to isolate may be lethal or detrimental to the mice, we are using a unique approach to isolate mutations. This approach uses a balancer chromosome that is homozygous lethal and carries a dominant coat color marker to suppress recombination over a reasonable interval. WiCell National Stem Cell Bank 2006-11-17T16:39:03 2006-11-17T16:39:03 dshurtle http://www.wicell.org/ WiCell Research Institute (Andy Cohn) info@wicell.org 608-263-6297 Dr. James Thomson webmaster@wicell.org The National Stem Cell Bank (NSCB), located near the University of Wisconsin campus in Madison, Wisconsin, is a repository for the human embryonic stem cells lines listed on the National Institutes of Health (NIH) Stem Cell Registry and thus available for federally funded research in the United States. The WiCell Research Institute is dedicated to expanding the frontiers of science and medicine by unlocking the potential of stem cells. As a supporting organization of the University of Wisconsin-Madison, WiCell conducts research, supports research at UW-Madison, hosts the National Stem Cell Bank, provides training for scientists, and offers educational outreach programs for K-12 students and the community. WiCell provides scientists affordable and timely access to federally approved human embryonic stem cells and related technical support Brain Bank The Harvard Brain Tissue Resource Center 2006-11-17T16:53:42 2006-11-17T16:53:42 dshurtle 2006-11-17T16:53:42 2006-11-17T16:53:42 dshurtle http://www.brainbank.mclean.org/ Maureen Medeiros btrc@mclean.harvard.edu (617) 855-2400 FRANCINE M. BENES, M.D. PH.D., DIRECTOR BTRC@mclean.harvard.edu (617) 855-2400 NIH National Resource at McLean Hospital The Harvard Brain Tissue Resource Center has been established at McLean Hospital as a centralized resource for the collection and distribution of human brain specimens for brain research. Most recently, postmortem human brain research has played a significant role in the development of a genetic test for Huntington's disease as well as a treatment for Parkinson's disease. Similarly, neurochemical and anatomical studies focusing on the biological nature of the severe mental illnesses are now emerging and bringing forth new hope for understanding the underlying brain mechanisms responsible for psychosis and other symptoms associated with these debilitating brain disorders. In order to perform research into the neurological or psychiatric disorders, it is vital to collect normal control tissue as well. This is a national resource for the acquisition, processing, storage, distribution of high quality postmortem brain specimens for brain research. Specimens are obtained at no charge via a request form downloaded at website. Under "technique," no term for specimen preservation, such as fixed, fresh or frozen Under "method" need "downloadable request form" as option Need to be able to more clearly differentiate between material resources and information resources NNTC National NeuroAIDS Tissue Consortium 2006-11-17T17:00:30 2006-11-17T17:00:30 dshurtle https://web.emmes.com/study/hbb/ Diane K. Brandt dbrandt@emmes.com Larisa Gelya lgelya@emmes.com The National NeuroAIDS Tissue Consortium (NNTC), supported by NIMH and NINDS funding, was established in 1998 to collect, store, and distribute samples of nervous tissue, cerebrospinal fluid, blood, and other tissue from HIV-infected individuals. Nonhuman Primate Tissue Bank Aged Nonhuman Primate Tissue Bank 2006-11-17T17:12:52 2006-11-17T17:12:52 dshurtle http://www.nia.nih.gov/ResearchInformation/ScientificResources/NHPTissueBankHandbook.htm Office of Biological Resources and Resource Development (OBRRD) copet@nia.nih.gov 301-451-3857 Nancy Nadon, Ph.D. nadonn@nia.nih.gov 301-402-7744 The National Institute on Aging (NIA) supports a repository of tissue collected from nonhuman primate (NHP) species under contractual arrangement with BioReliance Corporation This tissue bank is a repository of tissue from aged non-human primates (NHP) for use in research. Some tissue from middle-aged and young NHP will also be available soon. The tissues are donated by NIA-supported NHP colonies and other NHP colonies such as the National Primate Research Centers. Orders will be accompanied by a Vital Statistics Information Sheet for each animal. The Vital Statistics Information Sheet includes the following: Accession number Species Gender Age Weight (if known) Health status Tissue from NIA's Nonhuman Primate Tissue Bank is available to investigators at academic and nonprofit research institutions who are engaged in funded research on aging. The project name and funding source must accompany all orders. It may not be possible to ship tissue to countries that have restrictions on the import of animal tissues or products. Investigators at for-profit entities are not eligible to purchase tissue from NIA's Nonhuman Primate Tissue Bank unless it is for a Small Business Innovation Research grant from NIA. Tissues are available as fresh frozen (stored at ?80 degrees Celsius), fixed blocks, slides from fixed blocks, fresh frozen in OCT medium (on a limited basis) MGC Mammalian Gene Collection 2006-11-17T17:34:37 2006-11-17T17:34:37 dshurtle http://mgc.nci.nih.gov/ Gary F. Temple gtemple@nhgri.nih.gov The goal of the Mammalian Gene Collection (MGC), a trans-NIH initiative, is to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes. In 2005, the project added the cow cDNAs generated by Genome Canada. Initially, cDNA libraries provided the source of the clones. Recently, alternative methods based on gene-specific amplification have been developed to target the recovery of human and mouse genes absent from the MGC collection. All MGC sequences are deposited in GenBank and the clones can be purchased from distributors of the IMAGE consortium. The NIH Mammalian Gene Collection (MGC) program is a multi-institutional effort to identify and sequence cDNA clones containing a full-length open reading frame (FL-ORF) for human, mouse, and rat genes. To date, the MGC has produced over 531 cDNA libraries derived from human tissue and cell lines, as well as mouse and rat tissues. The MGC has sequenced and verified the complete FL-ORFs for a non-redundant set of 14,424 human, 13,624 mouse, and 4,849 rat genes. Mitochondria research Mitochondria 2006-08-03T23:56:03 2006-08-03T23:56:03 KSkinner http://www.mitochondrial.net/ Christian Hesketh chesketh@ionchannels.org Christian Hesketh chesketh@ionchannels.org Website with multiple information including curent news and publications, clinical trials, and a mitochondria database. clinical trials related to mitochondria; publications related to mitochondria, mitochondria database Neuromantic Neuromantic 2006-09-16T12:26:54 2006-09-16T12:26:54 darrenmyatt http://www.rdg.ac.uk/neuromantic/ Darren Myatt d.r.myatt@reading.ac.uk Darren Myatt d.r.myatt@reading.ac.uk University of Reading Neuron, Morphological Reconstruction, Morphology, Freeware, Software, Dendritic Morphology Neuromantic is a freeware reconstruction tool for Windows-based machines. It is designed to allow the efficient creation of 3D neuronal reconstructions from serial stacks of images. May be used as a freeware alternative to Neurolucida or Neuron_Morpho for the 3D reconstruction of neurons from serial image stacks. VisiGene VisiGene Image Browser 2007-03-09T16:30:51 2007-03-09T16:30:51 BIRN 2007-03-09T16:30:51 2007-03-09T16:30:51 BIRN http://genome.ucsc.edu/cgi-bin/hgVisiGene UCSC Genome Bioinformatics Group cbseweb@cbse.ucsc.edu (831) 459-1544 UCSC Genome Browser VisiGene is a browser for viewing in situ images. It enables the user to examine cell-by-cell as well as tissue-by-tissue expression patterns. The browser serves as a virtual microscope, allowing users to retrieve images that meet specific search criteria, then interactively zoom and scroll across the collection. Genbank and Uniprot for genes; Theiler stages for mice Very useful interface for finding gene expression patterns across multiple sources Can't find Xenopus in list of organisms; should list to NCBI taxonomy slizer 2007-06-11T13:45:41 2007-06-11T13:45:41 nif BIRNLex BIRNLex 2007-06-25T21:21:22 2007-06-25T21:21:22 BIRN http://purl.org/birn/birnlex Maryann Martone mmartone@ucsd.edu William Bug William.Bug@drexelmed.edu Biomedical Informatics Research Network OWL BIRN?s unique lexicon (BIRNLex) is a controlled vocabulary designed for annotating BIRN data sources. These sources may include complex image databases, such as data from structural and functional magnetic resonance imaging (MRI) on human subjects involved in studies on Alzheimer?s disease or schizophrenia. The BIRNLex is a specialized vocabulary utilized by BIRN scientists in the context of their research, including common terms for neuroanatomy, molecular species, subject information, behavioral and cognitive processes, experimental practice and design, and the associated elements of primary data provenance required for large-scale data integration across disparate experimental studies. The BIRNLex offers well defined terms from several domains of importance to neuroimaging across scales. Mouse BIRN Mouse BIRN 2007-07-03T20:07:25 2007-07-03T20:07:25 nif http://nbirn.net/research/testbeds/mouse/index.shtm Arthur Toga toga@loni.ucla.edu Jyl Boline jyl.boline@loni.ucla.edu Biomedical Informatics Research Network The Mouse BIRN test bed is helping scientists study neurodegenerative diseases by marshaling multi-modal data from the mouse, as an animal model, to investigate neurological disorders. Researchers across six groups are pooling and analyzing multi-scale structural and functional data and integrating it with genomic and gene expression data acquired from the mouse brain. These correlated multi-scale analyses of data are providing a comprehensive basis upon which to interpret signals from the whole brain relative to the tissue and cellular alterations characteristic of the modeled disorder. BIRNLex Mouse BIRN makes available high resolution MRI, light and electron microscopic data from normal and genetically modified mice. It also has atlases, and the Mouse BIRN Atlasing Toolkit (MBAT) which provides a 3D visual interface to spatially registered distributed brain data acquired across scales. Pediatric MRI Data Repository The NIH MRI Study of Normal Brain Development 2007-07-04T03:14:41 2007-07-04T03:14:41 BIRN http://www.bic.mni.mcgill.ca/nihpd/info/ Alan Evans PedsMRI@mail.nih.gov MINC as well as in NIFTI-1 (ANALYZE) format This multi-site longitudinal study uses technologies (anatomical MRI, diffusion tensor imaging (DTI), and MR spectroscopy (MRS)) to map pediatric brain development and is organized around two Objectives. Data collection began in November 2001 and will continue through August 2007. Data will be released in stages. The plan is to image 500 children from infancy to young adults. The first data release includes anatomic MRI and clinical/behavioral data for the first timepoint for ages 4 1/2 to 18 years. As of this writing, there are 433 data sets available. The current data release involves raw, but not processed, imaging data. Once the data from our normal subjects is processed, the software used for processing it is to be made available to users of the database free of charge, so that they may process images from patient groups using the same procedures (should they choose to do so). Appropriate links will be added to the website at that time. This is the case for the MRI volumetric measures, but not for cortical thickness measures, under the terms of contract. The data in the database is described by a data dictionary, developed within the project, and the terminology used (instrument/variable names and descriptions) have been carefully reviewed by project members. This site looks to be a very valuable and significant site for pediatric imaging. Datasets of multiple types and viewers are available. The data in the Pediatric MRI Data Repository is being made available to biomedical and biobehavioral researchers whose institutions are covered by a federalwide assurance (FWA), are studying normal brain development, disorders, or diseases and/or developing image processing tools, and who agree to the terms of the Data Use Certification. To apply for access to data in the Pediatric MRI Data Repository, applicants must be affiliated with an institution/organization that is covered by an FWA. Diffusion Tensor Imaging NITRC Neuroimaging Informatics Tools and Resources Clearinghouse 2007-07-04T03:35:41 2007-07-04T03:35:41 BIRN http://www.nitrc.org/ David Kennedy, Ph. D. nitrcinfo@mail.nitrc.org moderator@mail.nitrc.org Once in full production, NITRC will offer comprehensive information on fMRI tools through comments and ratings from users in the research community. Peer-based ratings and comments will help users decide whether a tool or resource will be valuable. Once a tool is identified, NITRC will facilitate access to the tool and its community of users. NITRC is developing a standard vocabulary for tool descriptions in collaboration with other groups. The site is currently in beta production and in the process of cataloging tools. It looks like it will be very useful when mature. NACC National Alzheimer's Coordinating Center 2007-07-04T03:53:49 2007-07-04T03:53:49 BIRN http://www.alz.washington.edu/ naccmail@u.washington.edu Duane L. Beekly, BS beekly@u.washington.edu Duane L. Beekly, BS The National Alzheimer's Coordinating Center (NACC) was established by the National Institute on Aging (U01 AG016976) in 1999 to facilitate collaborative research among the 29 NIA-funded Alzheimer's Disease Centers (ADCs) nationwide. NACC developed and maintains a large relational database of standardized clinical and neuropathological research data collected from each ADC, and this database provides a valuable resource for both exploratory and explanatory Alzheimer's disease research. The National Alzheimer's Coordinating Center's database consists of data collected from 29 Alzheimer's Disease Centers funded by the National Institute on Aging. The database consists of several datasets, and searches may be done on the entire database or on individual datasets. Access is granted by security level. For an explanation of security levels, click here. * The Minimum Data Set (MDS) o Brief, cross-sectional clinical and demographic data abstracted for subjects enrolled in NIA Alzheimer's Disease Centers 1984 - 2005. * The Uniform Data Set (UDS) o Standardized clinical examination, testing, diagnostic evaluation and data collection protocol with annual longitudinal follow-up. Implemented September 2005 and continuing. * Neuropathology Data Set (NP) o Neuropathologic features of subjects who had post-mortem neuropathological examination, 1984 - present. These data include those subjects with MDS and/or UDS clinical data. Any researcher who is affiliated with an ADC/ADRC may obtain an account by contacting NACC via e-mail (naccmail@u.washington.edu) or telephone 206-543-8637. Researchers who are NOT affiliated with an ADC/ADRC may obtain an account by contacting their closest ADC/ADRC and requesting to be sponsored. (Select "ADC ADMINISTRATION" from the menu above, then click on "ADCs and ADRCs" to view a list of locations.) According to the website, the general public may access a limited amount of data by requesting an account. HPR Project Human Protein Atlas 2007-07-07T01:29:43 2007-07-07T01:29:43 KSkinner 2007-07-07T01:29:43 2007-07-07T01:29:43 KSkinner http://www.proteinatlas.org/index.php Dr Cristina Al-Khalili Szigyarto contact@hpr.se Prof Mathias Uhlen The HPR project is funded by the Knut & Alice Wallenberg foundation. The atlas is part of the HUPO Human Antibody Initiative (HAI).The Swedish Human Proteome Resource (HPR) Center is located at the AlbaNova University center at the Royal Institute of Technology, Stockholm and at the Rudbeck Laboratory, Uppsala University, Uppsala The human protein atlas displays expression and localization of proteins in a large variety of normal human tissues and cancer cells. The data is publically available and presented as high resolution images of immunohistochemically stained tissues and cell lines. Available proteins can be reached through searches for specific genes or by browsing individual chromosomes all images of immunohistochemically stained cell lines were annotated using an automated recognition software for image analysis. The image analysis software, TMAx, built on a object-oriented image analysis engine from Definiens, utilizes rule-based operations and multiple iterative segmentation processes together with fuzzy logic to identify cells and immunohistochemical stain deposits. BBID Biological Biochemical Image Database 2007-07-09T13:55:08 2007-07-09T13:55:08 BIRN http://bbid.grc.nia.nih.gov/ Kevin C. Becker beckerk@grc.nia.nih.gov Kevin C. Becker beckerk@grc.nia.nih.gov National Institute on Aging Blueprint for Neuroscience Images can be downloaded as jpegs The Biological Biochemical Image Database is a searchable database of images of putative biological pathways, macromolecular structures, gene families, and cellular relationships. It is of use to those who are working with large sets of genes or proteins using cDNA arrays, functional genomics, or proteomics. Site contains a list of gene names and keywords as they appear in the database. No information as to whether these were taken from a standard vocabulary. The rationale for this collection is that: 1. Except in a few cases, information on most biological pathways in higher eukaryotes is non-existent, incomplete, or conflicting. 2. Similar biological pathways differ by tissue context, developmental stages, stimulatory events, or for other complex reasons. This database allows comparisons of different variations of pathways that can be tested empirically. 3. The goal of this database is to use images created directly by biomedical scientists who are specialists in a particular biological system. It is specifically designed to NOT use average, idealized or redrawn pathways. It does NOT use pathways defined by computer algorithm or information search approaches. 4. Information on biological pathways in higher eukaryotes generally resides in the images and text of review papers. Much of this information is not easily accessible by current medical reference search engines. 5. All images are attributable to the original authors. All pathways or other biological systems described here are graphic representations of natural systems. Each pathway is to be considered a work in progress. Each carries some degree of error or incompleteness. The end user has the ultimate responsibility to determine the scientific correctness and validity in their particular biological system. This is another site with very general content that is hard to describe using the keywords above. SAO Subcellular Anatomy Ontology 2007-07-09T14:46:30 2007-07-09T14:46:30 BIRN http://ccdb.ucsd.edu/sao.html Maryann Martone mmartone@ucsd.edu 858-822-0745 Stephen Larson slarson@ncmir.ucsd.edu Cell Centered Database; National Center for Microscopy and Imaging Research and Biomedical Informatics Research Network OWL (Web Ontology Language) DL The Subcellular Anatomy Ontology (SAO) is a formal ontology developed for cellular, subcellular and supracellular entities in the nervous system. It describes the parts of neurons and glia and how these parts come together to define supracellular structures such as synapses and neuropil (Fong et al., submitted). Molecular specializations of each compartment and cell type are identified. The SAO was designed with the goal of providing a means to annotate cellular and subcellular data obtained from light and electron microscopy, including assigning macromolecules to their approporiate subcellular domains. The SAO thus provides a bridge between ontologies that describe molecular species and those concerned with more gross anatomical scales. Because it is intended to integrate into ontological efforts at these other scales, particular care was taken to construct the ontology in a way that supports such integration. The SAO provides definitions (and their sources) for each entity and imports and/or cross references existing shared ontologies, e.g., gene ontologies, when possible. The SAO utilizes the Basic Formal Ontology as its base to ensure that it can be integrated with other ontologies developed for different domains. The SAO is a comprehensive ontology specifically developed for the nervous system, built according to ontology development best practices (re-use of existing ontologies; formal definitions of terms; use of foundational ontologies). Mutant mouse aging colony NIA Mutant Mouse Aging Colony Handbook 2007-07-09T21:03:03 2007-07-09T21:03:03 BIRN http://www.nia.nih.gov/ResearchInformation/ScientificResources/NIAMutantMouseAgingColony/ Nancy L. Nadon, Ph. D. nadonn@nia.nih.gov Heidi Brogdon obrrd_order_desk@nia.nih.gov 301-496-0181 Office of Biological Resources and Resource Development, National Institute of Aging live animals The National Institute on Aging (NIA) supports a colony of aged mutant and transgenic mice for NIH-supported research directly related to the biology of aging. The mice are raised by the NIA's contractor, Taconic Farms, in Specific Pathogen-Free (SPF) barrier facilities. The strains in the mutant mouse aging colony have been donated by the investigators who developed the models, and those investigators are still the legally recognized owners of the intellectual property. The purpose of this colony is solely to supply aged mice for NIH-supported research using these models of aging and age-related diseases. Current colonies: Ames Dward Mouse; Snell Dwarf Mouse; GFP Reporter Transgenic Mouse (ubiquitin); A53T Alpha-synuclein transgenic mouse Ordering must be accompanied by a material transfer agreement Currently, only 4 types of mutant mice are available. Animals are sold by age, not weight, and ages are stated in 1 month intervals only; all animals born within a calendar month are considered to be the same age, so date of birth (DOB) is given as month/year. All mice are virgins. Tower of London The Tower of London Test 2007-09-21T17:01:36 2007-09-21T17:01:36 KSkinner http://www.catstests.com/Product03.htm Hasker P. Davis, PhD hdavis@uccs.edu 719-635-8235 This resource is part of the Colorado Assessment Tests Computer-based software test which contains the Tower of London test. This test was originally developed by Shallice to investigate problem solving in subjects with damage to the frontal lobes. A test can contain 3, 4, and 5 bead problems with varying number of moves required for the optimal solution. comes with one preprogramed test along with extensive normative data for that test. This file is approximately 0.7 MB. (Last update 10/16/02) Product is available for free. Under method for acquiring resource, no choice exists for "software download from website" Visual Span CATs Visual Span 2007-09-21T17:22:00 2007-09-21T17:22:00 KSkinner http://www.catstests.com/Product04.htm Hasker P. Davis, PhD hdavis@uccs.edu 719-635-8235 This resource is part of the Colorado Assessment Tests Computer based neuropychological test. This resource enables user to create their own unique tests or variations on previously reported versions of the visual span test. These include the Corsis Block-Tapping Test the examiner places nine blocks on a board and taps them in a designated sequence. The participant is required to repeat the sequence. Over trials the length of the sequence is increased (see Milner, 1971). The Knox Cube Imitation Test uses four blocks and essentially follows the same logic. The Wechsler Memory Scale - Revised includes a two part visual memory span test. In this test the examiner points at boxes on a eight box card in a prearranged sequence and the subject is required to repeat back the sequence. The initial trial starts with a sequence of two blocks and increases over trials. The two parts of this test are a forward visual span test and a reverse visual span test. Tests similar to these and more can be setup with the CATs Visual Span. Product is free Card Sort CATS Card Sort 2007-09-21T17:36:21 2007-09-21T17:36:21 KSkinner http://www.catstests.com/Product05.htm Hasker P. Davis, PhD hdavis@uccs.edu 719-635-8235 This resource is part of the Colorado Assessment Tests A computer based neuropsychological evaluation resource which is a general purpose card sorting program which allows the user to design sorting tasks. Raw data can be copied to the clipboard in a format acceptable for import into commonly available spreadsheets such as Excel? allowing the user to design analysis routines appropriate to their needs Software is free and can be downloaded from website. Reaction Time CATS Reaction Time 2007-09-21T17:46:50 2007-09-21T17:46:50 KSkinner http://www.catstests.com/Product06.htm Hasker P. Davis, PhD hdavis@uccs.edu 719-635-8235 This resource is one of those provided by the Colorado Assessment Tests Neuropsychological evaluation software. Reaction Time is designed to assess subjects speed of processing on three relatively simple tasks. Tasks include a simple reaction time test, a choice test, and a conditional choice test. Participants are shown a series of visual stimuli on a computer screen and asked to respond by pulling an appropriate trigger on a standard game pad. Both reaction time and the trigger pulled are recorded for subsequent analysis. Tasks to be used in the test, the average inter-stimulus interval and the number of stimuli presented for each task can be set by the investigator. The analysis includes means and standard deviations for response latencies for a single session, as well as the capability of evaluating a participants performance on a particular session against their performance on a series of sessions Resource is free and can be dowloaded from website. Test requires the use of a game pad that supports at least four buttons and provides a right and left trigger button. Provider tested several different brands of inexpensive game pads and have found them acceptable, however provider has standardized on Microsoft?s SideWinder? and have used it in collecting the normative data for this test. No choice for software download. Choices assume software is for accessing data rather than acquiring. n-Back CATS n-Back 2007-09-21T17:56:30 2007-09-21T17:56:30 KSkinner http://www.catstests.com/Product07.htm Hasker P. Davis, PhD hdavis@uccs.edu 719-635-8235 This resource is part of the Colorado Assessments Tests A neuropsychological assessment test. It has been suggested that n-Back is a working memory task measuring "updating" in executive control. The task requires the participant to monitor some dimension (e.g. content, position, numerosity) of a temporally present sequence of items, responding when the currently presented item matches on the relevant dimension an item that was just recently presented. The match can be with an item present either 1 back, 2 back, 3 back or n back. Considerable flexibility is provided to the experimenter in specifying various parameters of the experiment (e.g. presentation rate, n back, content, position, color).The n-Back task is one in which the participant is presented a series of stimuli at a constant rate. The task of the participant is to determine if the currently presented stimulus is similar (along some dimension) to one they have recently (usually one, two or three positions back) seen in the stream. Match criteria can be dimensions like material, position on the screen, color or some combination. CATs n-Back allows for substantial control over the position in which the material is presented (nine different positions), the nature of the material (any character or "dingbat" string, and any color. The experimenter can set the speed at which the sequence is presented including both the stimulus on time and the inter-stimulus interval. Participant responses can be made either using the keyboard or the mouse. Resource is free and can be downloaded from website. At this time no normative data is available for this test. Symptom Validity CATS Symptom Validity 2007-09-21T18:08:25 2007-09-21T18:08:25 KSkinner http://www.catstests.com/Product09.htm Hasker P. Davis, PhD hdavis@uccs.edu 719-635-8235 Resource is one of Colorado Assessment Tests Neuropsychological evaluation software. Software contains some of the most common tests used to detect malingering of memory impairment. Package contains a number of tests of declarative memory that assess recall of information that has a personal and temporal context. The typical example of declarative tests used for detecting malingering are the auditory verbal learning test and forced choice test. These tests are included in Symptom Validity along with other tests of declarative memory (e.g., prose recall, questionnaire tests).The nondeclarative tests included in Symptom Validity are two repetition priming tests of word stem completion and two tests of pattern categorization learning. Resource is free and can be dowloaded from website. Symptom Validity is currently available only for Windows 95 and 98) MiMi Michigan Molecular Interactions 2007-09-22T04:41:47 2007-09-22T04:41:47 KSkinner 2007-09-22T04:41:47 2007-09-22T04:41:47 KSkinner http://mimi.ncibi.org/MiMI/home.jsp Glenn Tarcea gtarcea@umich.edu H V Jagadish jag@eecs . umich . edu (734) 763-4079 This resource is part of the suite of tools of the NIH Roadmap National Center for Integrative Biomedical Informatics at the University of Michigan Michigan Molecular Interactions (MiMI) assists scientists digging through an overwhelming amount of protein interaction data. MiMI gathers data from well-known protein interaction databases and merges the information. Since these datasets often contain contradictory information, the merge is performed in such a way that all information is retained. A provenance model has been developed that tracks where each piece of data came from, and what processes have been performed upon it. A simple yet powerful user interface aids users in their queries. Thus, MiMI allows scientists to query all data, whether corroborative, or contradictory, and specify which sources to utilize. MiMI is both a web service that integrates data and the application of research and open source software to the problem of supporting that web service. MiMI currently provides three query experimental interfaces: XQuery, MQuery, and NaLIX. (See the links on the Search area at the top of most pages in the site.) The XQuery interface allows advanced user to speficify exactly what information they want using the W3C XQuery language. The MQuery interface utilizes adaptable forms and browsable schemas to assist users in generating an XQuery. The NaLIX interface (still under development) will provide a natural language interface to the intergrated data in MiMI. Each of these interfaces comes with it's own examples and/or help information. Because there is no standard identifier used in all molecular interaction sources, it is impossible to correctly identify ALL identical versions of a molecule. MiMi uses a set of identity functions to merge as many identical molecules as possible. However, if MiMi is unaware of a mapping between, say RefSeq and BioGRID identifiers, it is possible that two identical molecules will not be merged, and the user will see several versions of the same molecule. Data Sources include: BIND (Samuel Lunenfeld Research) Institute; CCSB-HI1(Center for Cancer Systems Biology,Harvard; DIP (UCLA); GO (Gene Ontology Consortium) BioGRID (Mount Sinai Hospital); HPRD (Johns Hopkins University and Institute of Bioinformatics); IntAct EMBL-EBI(InterPro EMBL-EBI) IPI EMBL-EBI; MDC PPI (Max-Delbrueck Center for Molecular Medicine)Pfam (Sanger Institute) ProtoNet (Hebrew University); SwissProt (Swiss Institute of Bioinformatics); RefSeq (NCBI); Shannon (University of Michigan) A Cytoscape plugin is available to work in conjunction with MiMi MICAD Molecular Imaging and Contrast Agent Database 2007-09-23T23:30:54 2007-09-23T23:30:54 KSkinner http://www.ncbi.nlm.nih.gov/books/bookres.fcgi/micad/home.html Chopra, Arvind (NIH/NLM/NCBI) NLM NCBI MICAD MICAD is a key component of the NIH Roadmap; it is developed by the National Center for Biotechnology Information (NCBI), at the National Institutes of Health Text The database includes but is not limited to agents developed for positron emission tomography (PET), single photon emission computed tomography (SPECT), magnetic resonance imaging (MRI), ultrasound (US), computed tomography (CT), optical imaging, planar radiogragphy, and planar gamma imaging. It contains textual information, references, numerous links to MEDLINE, and additional related resources at the National Center for Biotechnology Information (NCBI) and elsewhere. The MICAD database is structured as text-based information based on the NLM ?books? model, which was developed for the Internet by NCBI in the Entrez cross-database search system. With the use of the NCBI ?Bookshelf? structure as the backbone, the information in the MICAD database is organized to present concise, up-to-date information in a printable PDF format Chemical name 321 agents entered as of 09/23/2007 Aged Rodent Tissue Arrays Aged Rodent Tissue Bank Handbook 2007-09-25T16:35:37 2007-09-25T16:35:37 BIRN http://www.nia.nih.gov/ResearchInformation/ScientificResources/AgedRodentTissueBankHandbook/TissueArrays/ Heidi Brogdon rodents@nia.nih.gov Tracey Cope copet@nia.nih.gov National Institute on Aging 5 X 12 array of 1.5-mm tissue from brain, heart,liver and kidney ach array includes tissue cores from multiple tissues at multiple ages on one slide. Ages are chosen to span the life from young adult to very old age. The arrays are made from ethanol-fixed tissue and can be used for all techniques for which conventional tissue sections can be used. NIA aged rodent tissue arrays offer high-throughput analysis of tissue histology and protein expression for the biogerontology research community. Each array includes tissue cores from multiple tissues at multiple ages on one slide. Ages are chosen to span the life from young adult to very old age. The arrays are made from ethanol-fixed tissue and can be used for all techniques for which conventional tissue sections can be used. Tissue is available from Liver, Cardiac Muscle, and Brain. NIA aged rodent tissue arrays are available to investigators at academic and nonprofit research institutions that are engaged in projects directly related to aging and age-related disorders. BRAIN AND TISSUE BANK FOR DEVELOPMENTAL DISORDERS Brain and Tissue Bank for Developmental Disorder 2007-10-06T07:05:29 2007-10-06T07:05:29 KSkinner http://medschool.umaryland.edu/btbank/gintro.html Department of Pediatrics, Room 13-013 BRB btbumab@umaryland.edu (800)-847-1539 The National Institute of Child Health and Human Development has funded an additional bank with a common mission. Catalog in pdf format at http://medschool.umaryland.edu/btbank/NICHD_Brain_and_Tissue_Bank_Catalog_October_2007.pdf The BRAIN AND TISSUE BANK is established to advance the research of developmental disorders. The objective of this human tissue repository is to systematically collect, store, and distribute brain and other tissues for research dedicated to the improved understanding, care and treatment of individuals with developmental disorders. The National Institute of Child Health and Human Development has funded an additional bank with a common mission.Of special interest are individuals with Downs Syndrome and other chromosomal defects, mitochondrial encephalopathies, phenylketonuria and other aminoacidopathies, maternal PKU, Rett syndrome, leukodystrophies, lysosomal disorders, dyslexia, autism, and other neurodevelopmental disorders. List of tissues at http://medschool.umaryland.edu/btbank/glisoftis.html List of disorders at http://medschool.umaryland.edu/btbank/ListofDisorders.htm The recipient of tissue and the BRAIN AND TISSUE BANK are required to sign a Tissue Transfer Agreement before any tissues are transferred. The Agreement specifies that the recipient has obtained approval from the recipient's Institutional Review Board and agrees to abide by NIH-required semiannual confidential progress reports and NIH-required reimbursement for tissue processing. All requests for tissue must be in writing to the BRAIN AND TISSUE BANK. Neural Tube Defect Resource Neural Tube Defect Resource 2007-10-06T23:24:43 2007-10-06T23:24:43 BIRN http://www.jax.org/ntd/index.html Dr. Deborah Henken henkend@exchange.nih.gov Jackson Laboratories cryopreserved mouse strains This Resource maintains and distributes mouse models for neural tube defects, e.g., spina bifida, exencephaly, acrania NIH Blueprint NIH Blueprint for Neuroscience 2007-10-06T23:30:46 2007-10-06T23:30:46 BIRN http://neuroscienceblueprint.nih.gov/ blueprint@mail.nih.gov National Institutes of Health The NIH Blueprint for Neuroscience Research is a cooperative effort among the 16 NIH Institutes, Centers and Offices that support neuroscience research. By pooling resources and expertise, the Blueprint supports the development of new tools, training opportunities, and other resources to assist neuroscientists in both basic and clinical research. This site contains many external links to Neuroscience related materials and tools, organized by categories: animal models, clinical tools, imaging, neuroinformatics, core facilities, cell, tissue and DNA, gene and protein expression and training opportunities NESARC National Epidemiologic Survey on Alcohol and Related Conditions 2007-10-06T23:54:05 2007-10-06T23:54:05 BIRN http://niaaa.census.gov/ Ms. Nekisha Lakins nlakins@csrincorporated.com 703-741-7157 National Institute on Alcohol Abuse and Alcoholism ASCII file. A converter is available to convert the data from ASCII to SAS The NESARC is the primary source for information and data on the U.S. population for:alcohol and drug use; alcohol and drug abuse and dependence; and associated psychiatric and other medical comorbidities. NESARC was designed to be a longitudinal survey with its first Wave of interviews fielded in 2001-2002. The second Wave of interviews is planned for 2004-2005. The NESARC is a representative sample of the United States population and 43,093 Americans participated in the first Wave of the survey. During Wave 2, an attempt to re-interview all 43,093 of these respondents will be made. The target population of the NESARC is the non-institutionalized household population, 18 years and older, residing in the United States including the District of Columbia, Alaska, and Hawaii. Additionally the following non-institutional group quarters housing units were included as part of the NESARC sample: boarding houses, rooming houses, non-transient hotels and motels, shelters, facilities for housing workers, college quarters, and group homes. The sample provides estimates for the nation as a whole on topics related to alcohol and drug use, abuse and dependence and their associated disabilities. A Code Book and glossary of terms are provided This is a large survey conducted by the US census bureau on the alcohol, drug and tobacco habits of over 43,000 Americans over 18 years of age Need terms to describe the results of surveys like this one ETOH Alcohol and Alcohol Problems Science Database 2007-10-07T00:13:32 2007-10-07T00:13:32 BIRN http://etoh.niaaa.nih.gov/ NIAAA Webmaster niaaaweb-r@exchange.nih.gov National Institute on Alcohol Abuse and Alcoholism The National Institute on Alcohol Abuse and Alcoholism (NIAAA) has created this portal to support researchers and practitioners searching for information related to alcohol research. This page includes links to a number of databases, journals, and Web sites focused on alcohol research and related topics. Also included is a link to the archived ETOH database, the premier Alcohol and Alcohol Problems Science Database, produced by NIAAA from 1972 through December 2003. This portal provides links to databases and resources for alcohol researchers and practitioners. It includes an introduction to the National Library of Medicine's PubMed and some sample searches on alcohol to run in the PubMed database; descriptions of and links to the various databases of the National Clearinghouse for Alcohol and Drug Information (NCADI); a selection of alcohol and other drug databases with their descriptions and links; links to peer-reviewed journals most often used by alcohol researchers; and links to a selection of Web sites pertinent to the substance abuse field. The site uses the Alcohol and Other Drug (AOD) thesaurus. Documentation is provided on the site. The AOD Thesaurus provides a conceptual map of the multidisciplinary field of AOD research and practice, as well as standard terminology. This site provides links to a lot of different resources for researchers in the alcoholism field. While the resources are not centered on neuroscience per se, there is a lot of interest here for neuroscientists. The archived ETOH database is a comprehensive resource for literature published between 1972 and 2003 ARP The Antibody Resource Page 2007-10-07T06:10:38 2007-10-07T06:10:38 KSkinner http://www.antibodyresource.com/ antibody@antibodyresource.com HTML Links This page is a guide to antibody information and suppliers. In addition to supplers, contains a variet of links, including links to educational resources and tools and databases related to antibiodies. CIDR Center for Inherited Disease Research 2007-10-07T06:31:44 2007-10-07T06:31:44 KSkinner http://www.cidr.jhmi.edu/ Jerry Roberts, Ph.D. jr39m@nih.gov (301) 402-8837 CIDR was established in 1996 and is jointly supported by thirteen Institutes at the National Institutes of Health (NIH). The supporting Institutes include: * The National Human Genome Research Institute (NHGRI), serving as the lead agency * The National Cancer Institute (NCI) * The National Eye Institute (NEI) * The National Institute on Aging (NIA) * The National Institute on Alcohol Abuse and Alcoholism (NIAAA) * The National Institute of Child Health and Human Development (NICHD) * The National Institute on Deafness and Other Communication Disorders (NIDCD) * The National Institute of Dental and Craniofacial Research (NIDCR) * The National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) * The National Institute on Drug Abuse (NIDA) * The National Institute of Environmental Health Sciences (NIEHS) * The National Institute of Mental Health (NIMH) * The National Institute of Neurological Disorders and Stroke (NINDS) The Center for Inherited Disease Research (CIDR) is a centralized facility that provides genotyping and statistical genetics services for investigators seeking to identify genes that contribute to human disease. CIDR concentrates primarily on multifactorial hereditary disease although analysis of single gene disorders can also be accommodated. CIDR is available to all investigators through competitive peer review by a chartered CIDR Access Committee (CAC). CIDR offers a variety of services to meet the needs of investigators. These include SNP Genome Wide Association Studies, Whole Genome SNP Linkage Scans, Custom SNP Genotyping, Stage 2 of a Genome Wide Association Study Fine Mapping Projects, Positional or Functional Candidate Gene Studies, Cancer Panel Genotyping, Major Histocompatibility Complex (MHC) Genotyping and for Mouse:Whole Genome SNP Genotyping, Linkage Scans, Congenic/Consomic Line Construction, Custom SNP Genotyping, Fine Mapping Projects, Positional or Functional Candidate Gene Studies. List of previous projects is at http://www.cidr.jhmi.edu/projects_IC.pdf ll data generated by CIDR will be kept strictly confidential. The data belongs solely to the submitting investigator. CIDR requests only an acknowledgment upon publication of any results: "Genotyping services were provided by the Center for Inherited Disease Research (CIDR). CIDR is fully funded through a federal contract from the National Institutes of Health to The Johns Hopkins University, contract number N01-HG-65403". Inquiries should be made to Institute/Center contacts listed on web page Under Resource Type, a category for "services" is needed Xenopus Gene Collection Xenopus Gene Collection 2007-10-08T03:38:01 2007-10-08T03:38:01 KSkinner Daniela S. Gerhard (NCI) XGC Helpdesk NCIXENOPUS@mail.nih.gov Dr. Steven Klein(NICHD) 301-496-5541 KleinS@Exchange.NIH.GOV The XGC is a trans-NIH initiative Sequence and other data The generation of libraries from different stages of development and adult tissues. Sequencing of ~3,000 to 10,000 5? and 3' ESTs from each library. All sequences are deposited into GenBank. The corresponding clones are available through the IMAGE clone distribution network and are fully accessible to the community. Analysis of all available sequences into UniGene clusters. Selection of candidate complete open reading frame (ORF) clones and their sequencing. Many links to a variety of resources, both in U.S. and internationally are available. Under resource type, need provision for "clones, vectors, and tags" Under "organism" no choice for "frog" or "amphibian." Reproduction Ligand and Analysis Assay Core UVA Center for Research in Reproduction 2007-10-08T03:57:57 2007-10-08T03:57:57 KSkinner http://www.healthsystem.virginia.edu/internet/crr/ligand.cfm LigandCore@virginia.edu (434) 982-3675 This Core at the University of Virginia employs state-of-the-art methods to quantitate peptide and steroid reproductive hormones in blood and tissue. It also develops new methodology, prepares labeled reagents for immunoassays, immunocytochemistry and binding studies and assists in the transfer of technology to participating investigators Under resource type, need entry for sevices, including assay services Need category for immunoassays under techniques Need entry for "ligand" under component AGRE Autism Genetic Resource Exchange 2007-10-09T12:41:57 2007-10-09T12:41:57 BIRN http://www.agre.org/index.cfm info@agre.org Cure Autism Now Foundation DNA repository, family registry containing genotype and clinical assessments. To date, 497 families have been karyotyped, 187 analyzed for SNRPN duplications at 15q12, and 367 for telomere analyses for small-scale deletions and duplications by Dr. Christa Lese Martin?s laboratory at Emory University. These data are posted on the registered and password-protected portion of the AGRE researcher website. Single Nucleotide Polymorphism (SNP) data generated by participating researchers are currently available, including SNP data from the 10K Affymetrix arrays for 426 families. These data were generated as part of the Autism Genome Project efforts. Pedigree information is currently available for over 900 families. This is a very valuable resource for those interested in autism. Access to the data in this resource requires an application, including an approved IRB protocol. AGRE charges researchers a per sample fee for the acquisition of samples. For pricing information, please contact the Researcher Liaison. I'm not sure whether resources that are open to everyone but require approval are considered restricted/private or open with registration NIDA CTN Datashare Clincial Trials Network of the National Institute on Drug Abuse 2007-10-09T18:13:53 2007-10-09T18:13:53 KSkinner 2007-10-09T18:13:53 2007-10-09T18:13:53 KSkinner http://www.nida.nih.gov/CTN/ Prior to de-identifiying the data, all data files are converted from their native format to a modified Study Data Tabulation Model (SDTM) standard format. The SDTM is a content standard sponsored by the Clinical Data Interchange Standards Consortium (CDISC). This universal data format will be applied to each completed CTN trial's data. This will facilitate the pooling of shared data across completed studies. De-identified data are available for download in two formats: SAS (CDISC SDTM transport files) and ASCII (CSV files). Documentation regarding the data and corresponding study that generated the data are also available under each completed protocol page. This includes the annotated case report form (CRF); a define.xml file outlining the structure, variables and contents of each dataset; and SDTM mapping and de-identification rules. Protocols are listed at http://www.ctndatashare.org/studies and include both medications and behavioral approaches as well as studies on services for relates conditions such as infectious diseases in substance abusers. Data for completed protocols will be available to the public approximately 18 months after completion of the study or after publication of the primary manuscript, whichever occurs first. Data type does not work that well for behavioral therapies and combined drug/behavioral interventions. Retinal Degeneration Genes Mouse Models for Ocular Disease 2007-11-18T02:14:05 2007-11-18T02:14:05 KSkinner http://www.jax.org/mmod/retinal_degen.html Bo Chang, M.D. bchang@jax.org 207-288-6394 Supported by The National Eye Institute and the Foundation Fighting Blindness and hosted at the Jackson Laboratory. Mouse models of retinal degeneration Retinal degeneration genes 6 naturally occurring mouse mutants that manifest degeneration of photoreceptors in the retina with preservation of all other retinal cell types have been found: retinal degeneration (formerly rd , identical with rodless retina, r, now Pde6b rd1); Purkinje cell degeneration (pcd); nervous (nr); retinal degeneration slow (rds, now Prph Rd2); retinal degeneration 3 (rd3 ); motor neuron degeneration (mnd); retinal degeneration 4 (Rd4 ); retinal degeneration 5 (rd5); vitiligo (vit , now Mitf mi-vit); retinal degeneration 6 (rd6 ); retinal degeneration 7 (rd7); neuronal ceroid lipofuscinosis ( nclf ); retinal degeneration 8 (rd8 ); retinal degeneration 9 ( Rd9 ); retinal degeneration 10 (rd10); and cone photoreceptor function loss (cpfl1). Mouse Models for Cataracts Mouse Models for Ocular Disease 2007-11-18T02:27:35 2007-11-18T02:27:35 KSkinner http://www.jax.org/mmod/screening.html Bo Chang, M.D. bchang@jax.org 207-288-6394 SHosted by the Jackson Laboratory and upported by The National Eye Institute and the Foundation Fighting Blindness no choice for "eye" under neural structure and NIH has an entire institute devoted to the eye no choice available for a diseases associated with aging but which don't involve dementia (eg, cataracts and glaucoma) Eyegene National Ophthalmic Disease Genotyping Network (eyeGENETM) 2007-11-19T02:09:45 2007-11-19T02:09:45 KSkinner http://www.nei.nih.gov/resources/eyegene.asp Ajaina Nezhuvingal eyeGENEinfo@nei.nih.gov The NEI is working with the vision community to initiate a National Ophthalmic Disease Genotyping Network and Resource (eyeGENETM). The Network includes a coordinating center, a centralized repository for blood/DNA/cell lines, several CLIA laboratories and a shared genotype / phenotype database. The goal of the NEI is to augment, not diminish, existing university-based and commercial ventures, while providing a new entry portal with rapid, reliable, and easy access to medical professionals. Aniridia PAX6 Axenfeld - Rieger Syndrome PITX2, FOXC1 Best's Disease VMD2 Congenital Cranial Dysinnervation Diseases (CCDD) KIF21A, PHOX2A, SALL4, ROBO3, HOXA1 Choroideremia CHM Cone Rod Dystrophy ABCA4, RPGR Congenital Stationary Night Blindness NYX, RHO, PDE6B Corneal Anterior Stromal Dystrophies BIGH3 Meesman's Epithelial Dystrophy KRT3,KRT12 Bietti's Crystalline Corneal-Retinal Dystrophy CYP4V2 Doyne Honeycomb Dystrophy EFEMP1 Familial Exudative Vitreal Retinopathy FZD4, LRP5, NDP Glaucoma CYP1B1, OPTN, MYOC Optic Atrophy OPA1 Pattern Dystrophy RDS Pantothenate Kinase-associated Neuropathy (PKAN) PANK2 Juvenile X-linked Retinoschisis XLRS1 Retinitis Pigmentosa (RP) and Retinal Degenerations ABCA4, RHO, IMPDH1, RP1, PRPF31, RPGR, CNGA1, CRB1, C1QTNF5/ CTRP5, MERTK, PDE6A, PDE6B, RGR, RLBP1, RPE65, TULP1, CA4, RP2 Sorsby Fundus Dystrophy TIMP3 Stargardt Disease ELOVL4, ABCA4 Rembrandt Repository of molecular brain neoplasia data 2007-11-20T20:27:06 2007-11-20T20:27:06 BIRN 2007-11-20T20:27:06 2007-11-20T20:27:06 BIRN http://caintegrator-info.nci.nih.gov/rembrandt ncicb@pop.nci.nih.gov 13014514384 ncicb@pop.nci.nih.gov National Cancer Institute and National Institute of Neurological Disorders and Stroke astrocytoma, oligodendroglioma, glioblastoma multiforme Uses standard gene terminology (GeneBank accession number and LocusLink ID) and also allows query through Gene Ontology terms. This site provides an analysis portal for large number of adult and pediatric primary brain tumors and to correlate these data with extensive retrospective and prospective clinical data. Data types include gene expression profiles, real time PCR assays, CGH and SNP array information, sequencing dta, tissue array results and images, proteomic profiles and patient reponse profiles. A range of query and analysis tools are also provided. Human Brain and Spinal Fluid Resource Center Human Brain and Spinal Fluid Resource Center 2007-11-22T23:37:52 2007-11-22T23:37:52 KSkinner http://www.loni.ucla.edu/uclabrainbank/About/index.html Rashed M. Nagra, Ph.D. RMNbbank@ucla.edu (310) 268-3648 Loated at VA Greater Los Angeles Healthcare System and sponsored by NINDS/NIMH, National Multiple Sclerosis Society, and the Department of Veterans Affairs, Research & Development Service Tissue and fluid bank. Provides researchers with the higheset quality and quantity of pre- and post-mortem brains, spinal cords, cerebrospinal fluid (CSF), serum, blood cells and urine to use in their investigations of neurological and psychiatric diseases Brain Tissue: Ataxia Cancer-CNS Cancer-non-CNS Cerebrovascular Disease CNS - Signs Convulsion Disorder Dementia Demyelination-non-MS Immune System Immune System-CNS Infection-CNS Infection-non-CNS Inherited-CNS Leukodystrophy Motor Neuron Disease Movement Disorder Multiple Sclerosis Neuropathy Normal Psychiatric Post Morten Fluids: Ataxia Batten's Disease Kuf's Disease Cancer-CNS Cancer-non-CNS Cerebrovascular Disease Convulsion Disorder Dementia Dystonia HD At Risk Infection-CNS Leukodystrophy Motor Neuron Disease Movement Disorder Narcolepsy iHop Information Hyperlinked Over Proteins 2007-11-23T03:41:06 2007-11-23T03:41:06 KSkinner http://www.ihop-net.org/UniPub/iHOP/ Robert Hoffmann, Ph.. hoffmann@cbio.mskcc.org +1 646-735-8081 This work was supported in part by the ORIEL (IST-2001- 32688) and TEMBLOR (QLRT-2001-00015) EC projects A network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. iHOP provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research. Information provided on - How to link to iHOP via a gene DB-identifier (e.g. UniProt or LocusLink). - How to link to iHOP via an 'iHOP gene ID'. - How to include abstracts with iHOP functionality in a web site. - How to include an iHOP summary for each gene/protein in a web site. NIDA Drug Supply Program NIDA Drug Supply Program 2007-11-24T02:06:07 2007-11-24T02:06:07 KSkinner http://www.drugabuse.gov/about/organization/DBNBR/CPSRB.html Kevin Gormley kgormley@ngmsmtp.nida.nih.gov Hari Singh, Ph.D. hsingh@ngmsmtp.nida.nih.gov Provided through a contract supported by the National Institute on Drug Abuse The NIDA Drug Supply Program is administered by the Chemistry & Physiological Systems Research Branch. In addition to funding research in drug abuse, addiction, prevention, and treatment, NIDA facilitates such research to accomplish its mission by providing chemicals and research probes that are either unavailable, difficult to obtain, or very expensive to buy to researchers. In addition, this program also provides analytical services for the analysis of researchers experimental samples. NIMH Chemical Synthesis and Drug Supply Program NIMH Chemical Synthesis and Drug Supply Program 2007-11-24T02:20:05 2007-11-24T02:20:05 KSkinner http://nimh-repository.rti.org/ Jamie Driscoll, B.S jdrisco1@mail.nih.gov (301) 443-3636 Supplied through a contract supported by NIMH The purpose of the present the NIMH Chemical Synthesis and Drug Supply Program is to synthesize, purify, and distribute otherwise unavailable essential compounds to stimulate basic and clinical research in psychopharmacology relevant to mental health in areas such as the molecular pharmacology and signaling of CNS receptors, longitudinal studies to evaluate the molecular, biochemical, and behavioral actions of psychoactive compounds, and functional brain imaging in both primates and humans. WHAT IS AVAILABLE: Synthesis of ligands for CNS receptors, radiolabeled compounds for autoradiography and neuroimaging, biochemical markers, drug analogs and metabolites, and reference standards. GLP and GMP synthesis of promising compounds for toxicology and safety studies, especially compounds for PET neuroimaging. Compounds currently available in stock are listed in the NIMH Repository , available on-line at the web site http://nimh-repository.rti.org. WHO IS ELIGIBLE: Investigators involved in basic or clinical research relevant to mental health. To learn more about current research areas, please visit the NIMH Research Web Areas at http://www.nimh.gov/research/nimhwebs.cfm. NIMH Repository compounds are pro-vided free to qualified academic investigators Investigators interested in obtaining radiolabeled compounds but uncertain about what type of label or specific activity would work best for them may obtain help by communicating wtih the techical contacts listed on the website. Toxicological Evaluation of Novel Ligands Program Toxicological Evaluation of Novel Ligands Program 2007-11-24T02:50:21 2007-11-24T02:50:21 KSkinner http://www.sri.com/biosciences/nimh/nimh-tox.html Jaime Driscoll jdriscol@mail.nih.gov (301) 443-5288 provided through a contract supported by NIMH The purpose of the NIMH Toxicological Evaluation of Novel Ligands Program is to accelerate the discovery, development, and application of novel ligands for PET, SPECT, and MRI imaging in humans by providing toxicology and safety assessment of promising, target-selective compounds. The program will also provide limited assessment of novel psychoactive agents for clinical research and as potential therapeutics. Toxicology and safety data generated by the program will be used to support an Investigational New Drug (IND) application to the Food and Drug Administration (FDA), or for Radioactive Drug Research Committee (RDRC) evaluation of a compound for human studies. The contract will evaluate toxicity and safety of compounds submitted for testing which may include, but are not limited to, novel chemical entities, structural analogs of compounds with an IND, or analogs of FDA-approved drugs. The services available under this program fall under four general phases: (1) analytical, (2) pharmacokinetics, (3) preliminary safety, and (4) IND-directed toxicity including safety pharmacology.Specific capabilities available to investigators include: Validation of the analytical methods for quantitating drug concentrations in dosing solutions, biological fluids, and tissues, as required. Determination of plasma drug levels in animals administered the agent under study, and calculation of pharmacokinetic parameters derived from these data. Determination of bioavailability of the drug after different routes of administration, including oral, intravenous (i.v.), subcutaneous (s.c.), intramuscular (i.m.), or intraperitoneal (i.p.), as needed. Calculation of the pharmacokinetic parameters from the derived data. In vitro evaluation of hepatotoxicity in human and animal liver cells. Preclinical acute toxicity evaluations on lead compounds, evaluating clinical observations, body weights, clinical pathology, histopathology, and plasma drug levels in rodents and non-rodent species. Other toxicology endpoints may be selected if needed. Subacute and subchronic toxicity evaluations in rodents and large animal species, evaluating clinical observations, body weights, clinical pathology, and histopathology. Genotoxicity assessments using a battery of appropriate assays. Who is eligible: Academic investigators involved in basic or clinical research relevant to mental health.Priority for assignment of NIMH resources will be based on which agents have the most complete data packages; i.e., investigators who can provide information in all of the requested areas will be given highest priority. Vision Network Vision Public Information Network 2007-11-26T02:27:55 2007-11-26T02:27:55 BIRN http://www.visionnetwork.nei.nih.gov/ National Eye Institute, National Institutes of Health, US Department of Health and Human Services The National Eye Institute (NEI) created the VISION Public Information Network for the purpose of communicating vision research results to the public through its grantee institutions. Public Information Officers from NEI grantee institutions work with the NEI to develop ongoing programs to educate the public about the benefits of vision research. The Network's primary mission is to work with the NEI in disseminating research results to the national and local media. The Network meets annually, shares information, pools resources, and collaborates on community outreach programs. The Network also works to inform the public of the mission of the National Institutes of Health (NIH) to improve the health of America through medical research. The NEI is part of the NIH, U.S. Department of Health and Human Services (DHHS). General information portal for eye and vision related resources for the public Clinical Studies Database National Eye Institute Clinical Studies Database 2007-11-26T02:41:23 2007-11-26T02:41:23 BIRN http://www.nei.nih.gov/neitrials/index.aspx NEI Information Office 2020@nei.nih.gov (301) 496-5249 National Eye Institute web pages This database contains information on clinical studies, both ongoing and completed, that have been conducted and supported by the National Eye Institute (NEI) since 1970. Areas covered: corneal diseases, glaucoma, epidemiology, lens and cataract, retinal diseases, strabismus, amblyopia and visual processing Large database of clinical trials, providing information on sight-saving results that may be available to health care professionals. May also be of use to the general public This is very hard to classify using the terms specified. NeuronBank NeuronBank 2007-11-27T01:44:11 2007-11-27T01:44:11 KSkinner http://neuronbank.org/ Paul S. Katz pkatz (at) gsu.edu 404-413-5398 Resource description framework (RDF) Nervous systems from different species will be represented in different branches. Users can search within one branch or search across branches for features of neurons and neural circuits. Resource in very early stages of development. Has some information on Tritonia. Autism Chromosome Database The Autism-related chromosome rearrangement databasehttp://projects.tcag.ca/autism/ 2007-11-27T02:38:40 2007-11-27T02:38:40 BIRN 2007-11-27T02:38:40 2007-11-27T02:38:40 BIRN http://projects.tcag.ca/autism/ Center for Applied Genomics, The Hospital for Sick Children, Toronto HTML table with links The Autism Chromosome Rearrangement Database is a collection of hand curated breakpoints and other genomic features, including phenotypes, organized by chromosome, related to autism, taken from publicly available literature: databases and unpublished data. The database is continuously updated with information from in-house experimental data as well as data from published research studies. Keywords: mental retardation, Asperger syndrome, karyotype, phenotype, chromosome CGC Caenorhabditis Genetics Center 2007-11-28T00:56:17 2007-11-28T00:56:17 BIRN 2007-11-28T00:56:17 2007-11-28T00:56:17 BIRN http://biosci.umn.edu/CGC/ Theresa Stiernagle cgc@umn.edu 612-625-2265 University of Minnesota The CGC collects, maintains, and distributes stocks of C. elegans. Keywords: mutant strain Utilizes nomenclature conventions for genes and strains established by Wormbase Small fee required to order strains BDSC Bloomington Drosophila Stock Center at Indiana University 2007-11-28T01:07:43 2007-11-28T01:07:43 BIRN http://flystocks.bio.indiana.edu/bloomhome.htm flystocksat signbio.indiana.edu Luke Jacobus lmjacobuat signindiana.edu 812-855-5783 Indiana University The BDSC collects, maintains and distributes Drosophila melanogaster strains for research. Keywords: genetically modified strain, Uses nomenclature standards for genes and strains adopted by Flybase ZIRC Zebrafish International Resource Center 2007-11-28T01:29:02 2007-11-28T01:29:02 BIRN http://zebrafish.org zirc@zebrafish.org 541-346-6028 University of Oregon Provides access to fish, EST's/cDNAs, antibodies and health services for zebrafish. ZIRC Health Services provides diagnostic pathology testing for zebrafish and other small laboratory fish species. Specific recommendations for control or treatment of a disease problem are made based upon a review of test results and clinical history. Utilizes terminology from Zfin IGTC International Gene Trap Consortium 2007-11-28T13:29:22 2007-11-28T13:29:22 KSkinner http://www.genetrap.org/ Thomas Ferrin, Ph.D. igtc-help@genetrap.org Funding by NIH grants 2-U01-HL66621 and 5-P41-RR01081; consortium members incude:BayGenomics (USA), Centre for Modelling Human Disease (Toronto, Canada),Embryonic Stem Cell Database (University of Manitoba, Canada), Exchangeable Gene Trap Clones (Kumamoto University, Japan, German Gene Trap Consortium (Germany),Sanger Institute Gene Trap Resource, Soriano Lab Gene Trap Database (Fred Hutchinson Cancer Research Center, Seattle, USA, TIGEM-IRBM Gene Trap (Naples, Italy) The International Trap Consortium (IGTC) consists of laboratories around the world working together to generate a public library of mutated murine ES cell lines. Such cell lines can be obtained on a non-collaborative basis by scientists interested in generating reporter-tagged, loss-of-function mutations in mice. In addition to loss of function, newer gene trap vectors offer a variety of post-insertional modification strategies to allow for the generation of other experimental alleles. Cell line requests are handled by the IGTC members, and users should contact the IGTC member directly with all correspondences regarding cell line distribution GenMAPP Gene Map Annotator and Pathway Profiler 2007-11-28T13:49:52 2007-11-28T13:49:52 KSkinner http://www.genmapp.org/ Bruce R. Conklin, M.D. bconklin@gladstone.ucsf.edu 415-734-2712 Coolaborators include: Cytoscape.org, NetPath,BiGCaT University of Maastricht, UCSF Library CKM, Agilent Funded by the National Institute for General Medical Sciences, Agilent Foundation and NHLBI-BayGenomics GenMAPP is a free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes. Integrated with GenMAPP are programs to perform a global analysis of gene expression or genomic data in the context of hundreds of pathway MAPPs and thousands of Gene Ontology Terms. The GenMAPP application is a free downloadable program intended to be used soley for research purposes. IGTC Pathways International Gene Trap Consortium Pathways 2007-11-28T14:11:16 2007-11-28T14:11:16 KSkinner http://www.genetrap.org/dataaccess/pathways.html International Gene Trap Consortium Uses GenMAPP to provide maps of public gene trap data from members of the International Gene Trap Consortium (IGTC) to map sets of biological pathways and gene groupings. Users can browse the pathway diagrams and view which genes within the pathway have been trapped. Genes with gene trap insertions are colored on the pathway diagram depending upon the number of traps to the gene. Clicking on a gene of interest will bring up a backpage of annotation data and detailed information about the gene trap cell lines. Stem Cell Registry Adult mesenchymal stem cell registry 2007-11-28T17:24:01 2007-11-28T17:24:01 BIRN http://www.som.tulane.edu/gene_therapy/distribute.shtml MSC Distribution msc@tulane.edu (504) 988-7711 Tulane Center for Gene Therapy Provides access to human adult stem cells, rat stem cells, and mouse stem cells to academic researchers worldwide upon request. The adult stem cells are the plastic adherent cells from bone marrow referred to as mesenchymal stem cells or marrow stromal cells (MSCs). The cells are isolated, expanded and extensively characterized in our own laboratories. We provide a detailed protocol for expansion of the cells. We also provide a Product Specification Sheet on each lot of cells that indicates many of the characteristics of the cells, including the proliferation rate we have observed in expanding the frozen vials of cells, data on colony forming units, and differentiation into mineralizing cells, adipocytes and chondrocytes. No information was found as to what strains were available Cells may be used for academic purposes only. Use of cells is covered by US patents and may only be used in ways that does not infringe on these patents. More information can be found at the web site. Neuroanatomy and Neurovascular Atlas Salamon's Neuroanatomy and Neurovasculature Web-Atlas Resource 2007-11-29T02:50:11 2007-11-29T02:50:11 BIRN http://www.radnet.ucla.edu/sections/DINR/index.htm University of California, Los Angeles Annotated images of human brain derived from CT, MRI, angiography and post-mortem sections and drawings. Brain vasculature: arteries, arterioles, veins. Pathological specimens. Quizes and general information on brain structures and clinical syndromes. Fairly standard labels for brain regions. Some a little out of date, e.g., CA4 Extensive collection of images, many from pathological conditions. Physiobank Physiobank 2007-11-29T05:36:32 2007-11-29T05:36:32 KSkinner http://physionet.org/physiobank/ Ary LGoldberger, Ph.D. AGOLDBER@BIDMC.HARVARD.EDU (617) 667-4267 Component of Physionet, supported by NIGMS and NIBIB PhysioBank currently includes databases of multi-parameter cardiopulmonary, neural, and other biomedical signals from healthy subjects and patients with a variety of conditions with major public health implications, including sudden cardiac death, congestive heart failure, epilepsy, gait disorders, sleep apnea, and aging.PhysioBank currently contains well over 7000 recordings of annotated, digitized physiologic signals and time series, organized in over 40 databases (collections of recordings) Brainbow mice B6;CBA-Tg(Thy1-Brainbow1.0)LLich/J 2007-11-29T06:28:16 2007-11-29T06:28:16 KSkinner 2007-11-29T06:28:16 2007-11-29T06:28:16 KSkinner 2007-11-29T06:28:16 2007-11-29T06:28:16 KSkinner http://jaxmice.jax.org/strain/007910.html Orders & Technical Support orderquest@jax.org 00.422.MICE (6423) or 207.288.5845 Jackson Laboratories. This strain is included in the Induced Mutant Resource Colony collection The mice possess multiple fluorescent protein sequences uniquely flanked with pairs of incompatible Lox sites alternated to create mutually exclusive recombination events; allowing stochastic expression of multiple fluorescent proteins from a single transgene. Prior to Cre-mediated recombination, the fluorescent protein immediately adjacent to the promoter, dTomato (RFP), is expressed in peripheral and central neurons. When bred to Cre recombinase expressing mice, the resulting offspring can have one of three recombination outcomes for each transgene in each cell of the cre expressing tissue(s): dTomato (RFP), mCerulean (CFP), or mYFP expression. Integration of tandem transgene copies yields combinatorial fluorescent protein expression in each cell, and thus many possible cell colors, providing a way to distinguish adjacent neurons and visualize other cellular interactions. Of note, the single FRT site inserted in the transgene allows tandem transgene copy number reduction through Flp-mediated recombination if desired. These Brainbow 1.0 (founder line L) mice were found to have multiple transgene copies that allow labeling of individual neurons and glia (specifically hippocampal neuron cell bodies) with approximately 166 distinguishable color variations in cre recombined cells, and may also be useful in conjunction with other Brainbow strains (Stock No. 007901, Stock No. 007911, Stock No. 007921) for neurobiological studies.This mouse can be used to support research in many areas including: Neurobiology Research Cre-lox System (loxP-flanked Sequences) Fluorescent protein expression in neural tissue Research Tools Cre-lox-System (loxP-flanked Sequences: Test/Reporter) Developmental Biology Research (Cre-lox system) Developmental Biology Research (transplantation marker for embryonic and adult tissue) FLP-FRT System (FRT-flanked Sequences) Fluorescent Proteins Genetics Research (Mutagenesis and Transgenesis: Cre-lox system) Genetics Research (Tissue/Cell Markers: Cre-lox system) Genetics Research (Tissue/Cell Markers: astrocyte-specific marker) Genetics Research (Tissue/Cell Markers: astrocytes) Genetics Research (Tissue/Cell Markers: astrocytes, neurons) Genetics Research (Tissue/Cell Markers: glial cells) Genetics Research (Tissue/Cell Markers: multiple) Genetics Research (Tissue/Cell Markers: neurons) Genetics Research (Tissue/Cell Markers: transplantation marker for embryonic and adult tissue) Neurobiology Research (astrocyte-specific marker) Neurobiology Research (cell marker) Physionet Physionet 2007-11-29T06:44:02 2007-11-29T06:44:02 KSkinner http://www.physionet.org/ PhysioNet offers free access via the web to large collections of recorded physiologic signals and related open-source softwareThe PhysioNet Resource has three interdependent components: PhysioBank is a large and growing archive of well-characterized digital recordings of physiologic signals. PhysioToolkit is a library of open-source software for physiologic signal processing and analysis, as well as the detection of physiologically significant events. PhysioNet is not only the name of the Resource, but also of its web site, physionet.org. In addition to providing free web access to PhysioBank and PhysioToolkit, physionet.org offers tutorials to assist users, reference materials, related publications, an annual series of open challenges, on-line discussions, and much more. BCI2000 BCI2000 2007-11-29T17:54:34 2007-11-29T17:54:34 KSkinner 2007-11-29T17:54:34 2007-11-29T17:54:34 KSkinner 2007-11-29T17:54:34 2007-11-29T17:54:34 KSkinner www.bci2000.org info@bci2000.org Gerwin Schalk, Ph.D. gschalk@usa.net BCI2000 native GDF ASCII Matlab BCI2000 is a general-purpose system for brain-computer interface (BCI) research. It can also be used for data acquisition, stimulus presentation, and brain monitoring applications. Success stories are provided on the URL: http://www.bci2000.org/BCI2000/Success_Stories.html. Users seem very happy with the resource and support provided by the developers. Supported by NIH grants: (NINDS/NIBIB) BRP grant to Jonathan Wolpaw (EB000856) R01 grant to Gerwin Schalk (EB006356) 1) data format should be separated into one field for input and one for output; 2) in the questions with controlled vocabulary pull-down menus, it's not clear if one should select the parent category in addition to the child category (or if the child will imply the parent); 3) when the answer is "all of the above", should one select all the options? none? or perhaps an all-of-the-above option shoudl be added for questions for which that makes sense. 4) It takes more time than I had expected to register a resource. I think that would be a disincentive to anyone other than the resource owner. I'm not sure what could be done about that. 5) Perhaps an option could be provided to save a less-than complete entry. It would then be flagged (or perhaps an email generated to the administrator) to request further information. [This is Zohara Cohen, registering a resource under Karen Skinner's account.] International Stroke Database International Stroke Database 2007-11-30T00:05:04 2007-11-30T00:05:04 KSkinner http://www.strokedatabase.org/pages/data_download.html A. Gregory Sorensen sorensen@nmr.mgh.harvard.edu 617-726-3914 Deidentified data from stroke patients Imaging (e.g. CT, MRI, PET) Clinical demographic Genetic Simulation perfusion data for verifying deconvolution algorithms used in bolus-tracking perfusion-weighted imaging (PWI) Programs for performing deconvolution of bolus-tracking PWI Programs for performing DTI tractography An automated program for etiologic classification of ischemic stroke -- Causative Classification System for Ischemic Stroke (CCS) International Stroke Database/Software International Stroke Database/Software 2007-11-30T00:17:11 2007-11-30T00:17:11 KSkinner http://www.strokedatabase.org/pages/software.html Diffusion tensor imaging (DTI) tractography DTI Task Card for Siemens systems DTI Visualization platform independent tool kit PWI analysis tools for bolus-tracking data An automated system for etiologic classification of ischemic stroke -- Causative Classification System for Ischemic Stroke 2007-11-30T00:18:37 2007-11-30T00:18:37 KSkinner NCC NIH Clinical Collection 2008-02-04T11:45:10 2008-02-04T11:45:10 KSkinner 2008-02-04T11:45:10 2008-02-04T11:45:10 KSkinner http://www.nihclinicalcollection.com Lauren Zamler lauren.zamler@glpg.com BioFocus DPI NCC@glpg.com (650) 228-1400 NIH Molecular Libraries Roadmap Initiative six 96-well plates A plated array of approximately 450 small molecules that have a history of use in human clinical trials. The collection was assembled by the National Institutes of Health (NIH) through the Molecular Libraries Roadmap Initiative as part of its mission to enable the use of compound screens in biomedical research.50 ?l of each compound is supplied, as an approximately 10 mM solution in 100% DMSO. Compounds were plated at varying concentrations due to solubility levels. Contains drugs that have been used in prior clinical trials, so already have been studied and documented to some extent. May be useful in other applications. Only one NCC kit will be distributed per individual academic lab or for-profit organization. Must sign Material Transfer Agreement. 1. Vocabulary seems to be geared for electronic data resources. I feel like all I can say about this is that it includes "chemicals". 2. How about a box to check if it costs money? test 2008-07-02T16:53:35 2008-07-02T16:53:35 lni crcns Collaborative Research in Computational Neuroscience - Data sharing 2008-09-18T18:06:32 2008-09-18T18:06:32 jeffteeters http://crcns.org Fritz Sommer fsommer@berkeley.edu 510-642-7251 Jeff Teeters jteeters@berkeley.edu 510-642-7252 Primarily Matlab format and some custom formats. Varies with the data set. Electrophysiological data from different brain regions and species and eye movement data from human. Each data contributor documents their data using the terminology they think most appropriate. Hosts high-quality electrophysiology data sets useful for computational neuroscience. 3D Slicer 3D Slicer 2006-10-01T23:06:40 2006-10-01T23:06:40 iatr IATR 74 http://slicer.org slicer@ai.mit.edu slicer@ai.mit.edu MIT AI Lab and Surgical Planning Lab, Brigham and Women's Hospital, Harvard Medical School unknown MIT AI Lab; Surgical Planning Lab, Brigham and Women's Hospital The 3D Slicer is freely available, open-source software for visualization, registration, segmentation, and quantification of medical image data. Slicer provides a graphical user interface to a powerful set of tools so they can be used by end-user clinicians and researchers alike. Slicer is based on VTK (http://public.kitware.com/vtk) and has a modular architecture for easy addition of new functionality. Slicer uses an XML-based file format called MRML - Medical Reality Markup Language which can be used as an interchange format among medicical imaging applications. Slicer is primarily written in C++ and Tcl. 3DViewnix 3DViewnix 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 82 http://mipgsun.mipg.upenn.edu/~Vnews/ unknown vhelp@mipg.upenn.edu Jayaram K. Udupa unknown The University of Pennsylvania 3DViewnix is a data-, machine-, and application- independent software system for the visualization and analysis of multidimensional images. DPTools DPTools 3 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 104 http://www.fmritools.org/Activ2000/activ2000.htm Denis Ducreux denis.ducreux@bct.ap-hop-paris.fr Denis Ducreux unknown Neuroradiology Dpt, C.H.U. de Bic??tre fMRI Analysis software for windows. fMRI spatial and temporal pre-processing (gaussian filtering) with motion correction, time slicing and template co-registration ; fMRI multithreaded bloc processing with one or more conditions (up to 999), lateralization index, paradigm design (box-car style with HRF convolution), anatomic coregistration, multiplanar reconstructions, opengl 3D surfacic rendering. All the features already included in DPTools are available for the fMRI processings (statistics, motion correction, time slicing, aso). DICOM, Genesis, Analyze and SPM compatible (and more...). AFNI Analysis of Functional NeuroImages 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 69 http://afni.nimh.nih.gov/afni/ rwcox@nih.gov rwcox@nih.gov Robert W Cox, PhD unknown AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data. It is freely distributed (in source code format, and some precompiled binaries) for research purposes. Since AFNI is free, all users are "beta testers for life". The code is updated frequently in response to bug reports and feature creep. There is no support guarantee, but in practice you can usually get a quick response by posting problems/questions on the AFNI Message Board. AIR Automated Image Registration 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 13 http://bishopw.loni.ucla.edu/AIR5 Roger P. Woods, M.D.(rwoods@ucla.edu) rwoods@ucla.edu Roger P. Woods, M.D., UCLA unknown AIR allows automated registration of 3D (and 2D) images within and across subjects and within and sometimes across imaging modalities. AMIDE Amide's a Medical Image Data Examiner 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 159 http://amide.sourceforge.net Andy Loening loening@alum.mit.edu Andy Loening amide-users@lists.sourceforge.net Amide's a Medical Image Data Examiner DICOM 3.0, ECAT 6.4/7.2, Acr/Nema 2.0, Analyze (SPM) InterFile 3.3, Concorde. AMIDE is a free and open source tool for viewing and analyzing both single and multimodality volumetric data sets. The program incorporates automatic non-orthogonal data reslicing, allowing multiple data sets to be fused without imposed constraints on the dimensions, anisotrophy, or voxel sizes of the data. Additional features include 3D ROI's (ellipses, cylinders, boxes, and isocontours), multi-slice viewing, volume rendering, and data importing through the (X)MedCon library (http://xmedcon.sourceforge.net). Amira Advanced 3D Visualization and Volume Modeling 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 84 http://www.amiravis.com unknown info@amiravis.com Indeed - Visual Concepts GmbH unknown Visual Concepts GmbH Wherever 3D data sets have to be processed, e.g. in medicine, biology, physics or engineering, Amira offers fascinating new opportunities. State-of-the-art visualization techniques allow you to gain detailed insight into your data. Graphics hardware support is utilized to display even very large data sets at interactive speed. Powerful automatic and interactive segmentation tools support processing of 3D image data. Novel, fast, and robust reconstruction algorithms make it easy to create polygonal models from segmented objects. In addition, true volumetric tetrahedral meshes can be generated, suitable for advanced finite-element simulations. Simulation results as well as other data defined on a variety of different grids can be investigated using a large set of powerful visualization methods. (From the Amira web site.) Analyze Analyze Software System 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 73 http://www.mayo.edu/bir/Software/Analyze/Analyze.html unknown Richard Robb unknown Mayo Clinic Integrated suite of complementary tools for fully interactive display, manipulation, and measurement of multidimensional biomedical images have been used in applications involving many different imaging modalities, including CT, MRI, SPECT, PET, ultrasound and digital microscopy. BrainVISA BrainVISA / Anatomist 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 129 http://anatomist.info Jean-Francois Mangin mangin@shfj.cea.fr http://brainvisa.info/forum unknown BrainVISA Anatomist is the visualization software used by BrainVISA to show its pipeline results. For this purpose, BrainVISA remote controls Anatomist main menus. However Anatomist can be used separately, as visualization software dealing with structural data in the form of sets of objects linked to one another into a graph structure. These objects may be cortical folds inferred from T1 weighted MR data, fiber bundles inferred from MR diffusion weighted data, activated clusters inferred from Statistical Parametric Maps, etc... This module includes a nomenclature control panel, which can drive several brains simultaneously. Anatomist also provides some tools to easily map Statistical Parametric Maps on 3D renderings of the brain, inflated meshes of the cortical surface, etc... Finally, a toolbox is dedicated to the manual drawing of Volumes Of Interest made up of set of voxels. Parts of BrainVISA / Anatomist are distributed open source, others are closed-source. Atrophy Simulation Package Atrophy Simulation Package 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 399 https://www.rad.upenn.edu/sbia/ Xue Zhong Zhong.Xue@uphs.upenn.edu Zhong Xue, Dinggang Shen, Bilge Karacali, Joshua Stern, David Rottenberg, and Christos Davatzikos unknown SBIA Radiology, University of Pennsylvania This software package is used to simulate brain images with local growth/atrophy within a prescribed spherical region. Specifically, given an input image and its segmented image, the location of the center of the spherical region, and the radius of that sphere, it simulates new images that have tissue growth or shrinkage within that pre-specified brain region according to given rates (atrophy for rates less than one and growth for rates greater than one). The algorithm uses an iterative procedure that tries to achieve the given level of volumetric change for brain tissues within the region, by seeking a smooth deformation field, whose Jacobian determinants match the prescribed volume change rate within the region. Note that in the current software, the simulation of growth or atrophy for brain tissue requires that the input spherical region has to cover some CSF or background regions. Autoaligner Autoaligner 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 174 http://www.bitplane.com/products/autoaligner/autoaligner_product.shtml unknown ussales@bitplane.com Bitplane Inc. unknown Bitplane Inc. Microtomy is a standard technique used for 2D microscopy, but it can also provide the foundation for 3D analysis using AutoAligner. AutoAligner reads a stack of serial sections and automatically aligns the single images, building up a 3D space that can be explored using Imaris. Each image is aligned in translation and rotation relative to its precursor image in the sequence. In addition to a fully automated mode, AutoAligner also provides manual control for neighboring images that are too different from each other for automatic alignment. The visual alignment tool uses fast display techniques for aligning images in real time. Commercial software. CamBA Cambridge Brain Analysis 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 133 http://www-bmu.psychiatry.cam.ac.uk/software/ Cinly Ooi co224@cam.ac.uk John Suckling js369@cam.ac.uk University of Cambridge, King's College London and the Wellcome Trust A complete fMRI analysis package created with batch processing in mind. The software comprises the following general functions at the first level of individual image analysis: movement correction (interpolation and regression), time series modeling, data resampling in the wavelet domain, hypothesis testing at voxel and cluster levels. Additionally, there is code for second level analysis - group and factorial or ANOVA mapping - after co-registration of voxel statistic maps from individual images in a standard space. The main point of difference from other fMRI analysis packages is the emphasis throughout on the use of data resampling (permutation or randomization) as a basis for inference on individual, group and factorial test statistics at voxel and cluster levels of resolution. The software is mostly written in C. Development of this software is supported as Human Brain Project/Neuroinformatics research (http://www.nimh.nih.gov/neuroinformatics/index.cfm) funded by the National Institute of Biomedical Imaging and Bioengineering (http://www.nibib.nih.gov/), and the National Institute of Mental Health (http://www.nimh.nih.gov). Bioelectromagnetism Matlab Toolbox Bioelectromagnetism Matlab Toolbox 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 316 http://eeg.sf.net darren.weber _at_ radiology.ucsf.edu unknown Darren L. Weber unknown matlab tools for eeg/meg/mri Matlab tools for EEG/MEG/MRI. BIRN HID BIRN Human Imaging Database 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 387 http://www.nbirn.net/Resources/Downloads/HIDapplication/index.htm David Keator dbkeator@uci.edu jeffrey Grethe jgrethe@ncmir.ucsd.edu Biomedical Informatics Research Network (BIRN) The Human Imaging Database (HID) has been developed to address the problems associated with managing the increasingly large and diverse datasets collected throughout clinical and imaging communities. The HID is an extensible database management system that is comprised of three core components: * Human Imaging Database Schema - The HID Schema has been designed so that it can be customized and extended to contain relevant information from any particular sites needs without requiring modification to the schema itself. This information can consist of data concerning the research subjects used in an experiment, subject assessments and demographics, the experimental data collected, the experimental protocols used and any annotations or statistics (metadata) normally included with an experiment or study. * Clinical Assessment Layout Manager - This application works in conjunction with the HID and facilitates the preparation and incorporation of on online clinical assessment entry forms. * Human Imaging Database Graphical User Interface - The HID user interface allows for the management of research subjects and experiments. Blox Blox 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 68 http://sourceforge.net/projects/blox patr@jhmi.edu patr@jhmi.edu Patrick Barta, M.D., Ph. D. unknown Kennedy Krieger Institute & Johns Hopkins Hospital Blox is a quantitative medical imaging and visualization program for use on brain MR, DTI, and MRS data. Brain Atlas for Functional Imaging Brain Atlas for Functional Imaging 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 61 http://www.cerefy.com/ Wieslaw Nowinski wieslaw@cerefy.com Wieslaw L. Nowinski, A. Thirunavuukarasuu, and David N. Kennedy; Kent Ridge Digital Labs, Singapore, and Massachusetts General Hospital unknown Theime Medical Publishers This is a CD ROM Product distributed by Theime Medical Publishers. It supports a complete electronic version of the Talairach Atlas, as well as gyral-level description of the human brain. In addition, this tool permits the incorporation of user image data, both structural and functional, into the viewer for direct co-visualization with the atlas. This CD-ROM provides numerous tools for the analysis of functional images: It contains the fully color-coded and labeled Talairach-Tournoux brain atlas in the axial, coronal and sagittal orientations, along with Brodmann's areas and gyri in the axial orientation. -Allows anatomical and functional images to be loaded and registered. -Enables interactive placement of the Talairach landmarks in 3D Space. -Provides automatic data-to-atlas warping based on the Talairaich proportional grid system transformation. In addition, real-time interactive warping for fine tuning is available. -Allows the user to place marks on the activation loci in the warped functional images, display these marks with the atlas, and edit them simultaneously on the axial, cornal and sagittal orientations. Mark placement is assisted by a grey-value thresholding feature. -Provides simultaneous display of the atlas, anatomical image and functional image withing one interactively blended image. Atlas-data blending and anatomical-functional image blending are controlled independently. -Labels the data by means of the atlas. The atlas can be flipped left/right so that Brodmann's areas areas and gyri can be labeled on both hemispheres. -Provides additional functions such as friendly navigation, simultaneous display of axial, coronal and sagittal atlas plates, cross-referenced display, image and atlas sequencing, readout of the Talairach coordinates and intensities, save, print, help. Commercial atlas distributed on CDROM. BrainImage BrainImage Software 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 14 http://spnl.stanford.edu/tools/brainimage.htm Keith Bettinger Keith.Bettinger@stanford.EDU Dr. Allan L. Reiss and Staff of the Stanford Psychiatry Neuroimaging Lab unknown Stanford Psychiatry Neuroimaging Laboratory BrainImage is an advanced 2D and 3D image processing and analysis program for the Apple Macintosh PowerPC based on the public domain application, NIH Image. It includes interactive procedures for 3D MRI quantification including semi-automated procedures for removing non-brain tissues from images, fuzzy segmentation of tissue compartments, global or local parcellation (based on the Talairach atlas), region-growing, etc. BRAINS Brain Research: Analysis of Images, Networks, and Systems 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 126 http://www.psychiatry.uiowa.edu/wiki/index.php?title=BRAINS_USERS_NOTES Nancy C. Andreasen Hans J. Johnson (hans-johnson@uiowa.edu) Hans J. Johnson hans-johnson@uiowa.edu Iowa Mental Helath Clinical Research Center BRAINS (Brain Research: Analysis of Images, Networks, and Systems) contains manual and automated tools for structural identification and methods for tissue classification and cortical surface generation. BRAINS2 is most commonly used to analyze magnetic resonance (MR) scans, but the package can also be used to analyze images acquired with positron emission tomography (PET), single photon emission computed tomography (SPECT), and functional magnetic resonance (fMR). It is implemented in an object-oriented, cross-platform compatible manner and includes a toolbar and command line interface, a graphical interface, and a computational kernel. BrainVISA BrainVISA 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 130 http://brainvisa.info Jean-Francois Mangin mangin@shfj.cea.fr http://brainvisa.info/forum unknown IFR 49 Paris/SHFJ CEA BrainVISA is a software, which embodies an image processing factory. A simple control panel allows the user to trigger some sequences of processing on series of images. These treatments are performed by calls to command lines provided by different laboratories. These command lines, hence, are the building blocks on which are buit the assembly lines of the factory. BrainVISA is distributed with a toolbox of building blocks dedicated to the segmentation of T1-weighted MR images. The product of the main assembly line made up from this toolbox is the following: grey/white classification for Voxel Based Morphometry, Meshes of each hemisphere surface for visualization purpose, Spherical meshes of each hemisphere white matter surface, a graph of the cortical folds, a labeling of the cortical folds according to a nomenclature of the main sulci. A new pipeline has been recently released to perform fiber tracking from MR diffusion weighted images. BrainVoyager BrainVoyager QX 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 71 http://www.BrainVoyager.com/ Brain Innovation B.V. info@brainvoyager.com Brain Innovation B.V. unknown Brain Innovation B.V. BrainVoyager QX / 2000 is a highly optimized and user friendly software package for the analysis and visualization of functional and structural magnetic resonance imaging data sets. Highlights - Extremely fast and highly optimized 2D and 3D analysis and visualization routines - Standard and advanced volume-based statistical analysis methods including conjunction and random effects analysis - Integration of volume and surface rendering with powerful tools for creation of high-quality figures and movies - Advanced methods for automatic brain segmentation, surface reconstruction, cortex inflation and flattening - Cortex-based statistical data analysis and inter-subject alignment based on gyral / sulcal pattern - Creation ("seeding") and visualization of EEG / MEG multiple dipole models (in combination with BESA 2000) - Multi-processor support, open architecture including scripting and automation support - Programmable with all major computer languages (i.e. C/C++, VB, Java) and Matlab through COM-based interfaces - Comprehensive solution embodied in a single program - The only complete solution available for Windows XP / 2000 / NT 4.0 / ME / 98 / 95, Linux/Unix and Mac OS X Commercial product. Brede Toolbox Brede Toolbox 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 260 http://hendrix.imm.dtu.dk/software/brede/ Fin Arup Nielsen fn@imm.dtu.dk Finn ?Örup Nielsen unknown IMM, Techical University of Denmark "Brede" is a neuroinformatics toolbox primarily written in the Matlab language running under Matlab 6.0 or later. Its primary purposes are handling, analyzing and visualizing data from functional neuroimaging experiments, - not the original data but rather the summary images (e.g., statistical parametric images) and location data in stereotactic space. It includes Corner Cube visualization, VRML97 generation, text and link analysis, and probabilistic modeling of activation foci (a la Peter T. Fox's "functional volumes modeling"). Btrack Btrack 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 87 http://ncmir.ucsd.edu/Software/btrack.htm Steve Lamont spl@ncmir.ucsd.edu Steve Lamont unknown National Center for Microscopy and Imaging Research Bio-Rad BTrack analyzes and graphs time-lapse imaging data as acquired by a Bio-Rad confocal microscope, for experiments using nonratiometric fluorescent indicator dyes. Btrack can accommodate changes in the positions of imaged cells/tissue regions and can be used for analyzing an unlimited number of areas (cells/tissue regions) in an imaged field. BYU2Vox BYU2Vox 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 363 http://www.ia.unc.edu/dev/download/byu2vox/index.htm unknown gouttard@email.unc.edu Matthieu JOMIER unknown University of North Carolina at Chapel Hill, Psychiatry and computer sciences departments Byu2Vox is a program that converts a BYU surface to a voxel volume. The specifiation of bounding boxes can be done. A batch mode allows to process many images. Cardviews CARDinal Plane VIEWing System 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 1 (none) David Kennedy, Co-Director, Center for Morphometric Analysis dave@cma.mgh.harvard.edu Jim Meyer and staff at the Center for Morphometric Analysis at the Massachusetts General Hospital. unknown Center for Morphometric Analysis, Massachusetts General Hospital Cardviews is a CARDinal plane VIEWing System developed at the Center for Morphometric Analysis at the Massachusetts General Hospital. It is a tool for brain morphometry (including volumetric analysis using xvol) and this program emerged as a product of our methodological development. While some of its functionality is specifically tailored for our general segmentation and neocortical parcellation routines, the imaging interface, segmentation tools, and localization capacity have utility extending beyond the specific aims motivating its initial conception. CARET Computerized Anatomical Reconstruction and Editing Toolkit 2006-10-01T23:06:41 2006-10-01T23:06:41 iatr IATR 3 http://brainvis.wustl.edu/caret/ John Harwell caret@v1.wustl.edu http://brainmap.wustl.edu/mailman/listinfo/caret-users caret-users@brainvis.wustl.edu Washington University in St. Louis School of Medicine Caret (Computerized Anatomical Reconstruction and Editing Toolkit) is designed for interactively generating (segmenting), viewing, manipulating, registering, and analyzing surface reconstructions of the cerebral cortex. The Caret User's Guide contains detailed tutorials for segmentation generation, surface reconstruction, surface visualization, flattening, and registration using downloadable exemplar data sets. CellProfiler Cell Image Analysis Software 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 408 http://cellprofiler.org Anne E. Carpenter carpenter@wi.mit.edu Anne E. Carpenter and Thouis Ray Jones unknown Whitehead Institute & MIT CellProfiler cell image analysis software is free and open-source software designed for biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. It counts cells and also measures the size, shape, intensity and texture of every cell (and every labeled subcellular compartment) in every image. It was designed for high-throughput screening but can perform automated image analysis for images from time-lapse movies and low-throughput experiments. It currently does not have neurite-identifying algorithms, but these could easily be added to CellProfiler's modular architecture. COMKAT Compartment Model Kinetic Analysis Tool 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 21 http://comkat.uhrad.com/ Raymond F. Muzic, Jr. muzic@uhrad.com Raymond F. Muzic, Jr. and Shawn Cornelius, University Hospitals of Cleveland muzic@uhrad.com University Hospitals of Cleveland Matlab GUI and command line interface for defining, solving, and fitting related to compartment models. User can design his/her own models without deriving equations. Free for research use. Runs on Windows, Linux, Unix, Mac. Includes source code. Corner Cube Environment Corner Cube Environment 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 11 http://neurovia.umn.edu/distrib/cce.html K. Rehm k.rehm@neurovia.umn.edu K. Rehm; University of Minnesota unknown University of Minnesota A symbolic visualization environment known as the Corner Cube Environment has been developed to facilitate rapid examination and comparison of activated foci defined by analyses of functional neuroimaging datasets. DCMTK DCMTK: DICOM Toolkit 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 131 http://dicom.offis.de/dcmtk.php.en dicom (at) offis.de dicom@offis.de OFFIS e.V., Oldenburg, Germany unknown OFFIS e.V., Oldenburg, Germany (http://offis.de) DCMTK is a collection of libraries and applications implementing large parts of the DICOM standard for medical image communication. It includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstration image storage and worklist servers. DCMTK includes complete source code and is written in a mixture of ANSI C and C++. DCSearch DCSearch 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 409 http://www.fmridc.org/fmridc/dcsearch/DCSearch.html unknown support@fmridc.org fMRI Data Center, Dartmouth College unknown fMRI Data Center, Dartmouth College A java tool to search published activation data. All data from papers submitted to the fMRI Data center are included, and may be referenced online or via flat file. Users may create their own data files, by saving subsets of original data or creating their own comma seperated value files (with simple formatting information included on the top row). Searches may be made based on coordinate space (MNI or T-space), anatomical area, author, and a number of other fields. Searched points may be displayed on a 3-d brain representation, as well. DCViewer DCViewer 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 327 http://www.fmridc.org/view/jnlp.php unknown support@fmridc.org fMRI Data Center, Dartmouth College unknown fMRI Data Center, Dartmouth College DCViewer opens img/hdr file pairs, allows browsing along X,Y Z and Time dimensions (if present) with configurable color and intensity settings. The files can be opened remotely from URLs if desired. Entire directories of files can be automatically combined into a single image. Multiple images can be layered for comparison. Dend Dend 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 90 http://ncmir.ucsd.edu/Software/dend.htm Steve Lamont spl@ncmir.ucsd.edu & mona@ncmir.ucsd.edu Steve Lamont & Mona Wong spl@ncmir.ucsd.edu National Center for Microscopy and Imaging Research An interactive program for resectioning and deriving measurements from contoured structures. It creates structural measurements obtaining lengths, surfaces, and volumes from volume data. Investigation of 3D structures and communication to others are greatly facilitated by this computer-based visualization. DICOMscope DICOMscope 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 156 http://dicom.offis.de/dscope/ OFFIS dicom@offis.de OFFIS (Oldenburg, Germany), Institute for Microtherapy (Bochum, Germany), OTech, Inc. (Aubrey, TX, USA) unknown OFFIS (Oldenburg, Germany), Institute for Microtherapy (Bochum, Germany), OTech, Inc. (Aubrey, TX, USA) DICOMscope is a free DICOM viewer which can display uncompressed, monochrome DICOM images from all modalities and which supports monitor calibration according to DICOM part 14 as well as presentation states. DICOMscope offers a print client (DICOM Basic Grayscale Print Management) which also implements the optional Presentation LUT SOP Class. The development of this prototype was commissioned by the "Committee for the Advancement of DICOM" and demonstrated at the European Congress of Radiology ECR 1999. An enhanced version was developed for the "DICOM Display Consistency Demonstration" at RSNA InfoRAD 1999. Release 3.5.1 was demonstrated at ECR 2001 and contained numerous extensions, including a print server, support for encrypted DICOM communication, digital signatures and structured reporting. DICOMscope is not meant as a competition for commercial DICOM viewers. The application is rather a feasibility study for DICOM presentation states. Any use of the program in a clinical environment is not recommended. DicomWorks DicomWorks 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 150 http://www.dicomworks.com Philippe PUECH puech@inviweb.com Philippe PUECH and Lo??c BOUSSEL unknown Universities of Lille and Lyon, France DicomWorks is a DICOM viewer and converter dedicated to radiologists or people working with DICOM files. It includes : - a smart DICOM viewer with 4 panel display, annotations, arrows, multimodality synchronization, etc... - an export wizard to the most common picture or movie file formats - an export wizard to Microsoft PowerPoint - the most simple and compatible DICOM CD-ROM reader - the most simple and smart DICOM CD-ROM WRITER - an archiving solution with lossless compression of the data - a DICOM creation module to "dicomize" images from any image source (even video capture) - e-mail or FTP import end export functions (teleradiology) ...and much, much more Our software includes some functions that are usually lacking in most DICOM viewers, such as AVI export of a series, the transfer of "windowable" and annotated images by e-mail for teleradiology purpose. With DicomWorks and a simple PC, you can easily and efficiently view, share, and present your DICOM files and have very powerful export tools at your disposal. So where it the trap ? None; it's FREE. Enjoy and tell us about your experience. dTV diffusion TENSOR Visualizer 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 249 http://www.ut-radiology.umin.jp/people/masutani/dTV.htm Yoshitaka MASUTANI masutani-utrad@umin.ac.jp Yoshitaka MASUTANI unknown Image Computing & Analysis Lab., Radiology, The Univ. of Tokyo Hospital The "diffusion TENSOR Visualizer" (dTV) is an analysis tool for diffusion MRI including diffusion tensor images. Several basic functions are available in dTV: - fiber tracking and 3D display - diffusion profile visualization as ellipsoid, etc. - compute grey/color-coded FA map, ADC map, etc. - analysis DT-related values within ROI - customizing MPG data Current version is dTV.II SR (Second Release). The dTV works as an extension software, i.e. plugin, for a volume data viewer software "VOLUME-ONE", which is also in this database. DPTools DPTools 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 103 http://193.55.58.11/DPTools/DPTools.htm Denis Ducreux denis.ducreux@bct.ap-hop-paris.fr Denis Ducreux unknown Neuroradiology Dpt, C.H.U. de Bic??tre MR Diffusion and CT/MR Perfusion analysis software for DTI and Fiber Tracking, Quantitative perfusion (FFT and SVD), Time series realignment, Normalization, Statistics. DtiStudio DtiStudio 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 389 http://lbam.med.jhmi.edu Susumu Mori susumu@mri.jhu.edu Hangyi Jiang unknown Laboratory of Brain Anatomical MRI, Johns Hopkins Radiology raw, DICOM This software allows us to process and analyze DTI data including fiber tracking. It can read raw and DICOM formats of major clinical scanners. It has a flexibility to read any combination of gradient encoding orientations and b-values. Data analyses include ROI-based and tractography-based quantification. MedINRIA MedINRIA 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 319 http://www-sop.inria.fr/asclepios/software/MedINRIA/ Pierre Fillard medinria@lists-sop.inria.fr Pierre Fillard unknown INRIA Sophia Antipolis, France MedINRIA is a free software library aiming at providing state-of-the-art algorithms dedicated to medical image processing and visualization for clinicians. Each application is called a module, and can be loaded dynamically from a single main window. MedINRIA is available for Microsoft Windows XP and Linux Fedora Core 3. - The DTI Track module provides all necessary tools for in-deep DT-MRI analysis and fiber tracking. From diffusion tensor field estimation, to FA/ADC computation, tensor smoothing, and fiber extraction, this module will help you to extract a fiber bundle of interest. - The Tensor Viewer is complementary to DTI Track. It allows you to visualize tensor fields obtained with the DTI module. Edgewarp3D The Edgewarp3D Browser 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 81 http://vhp.med.umich.edu/edgewarpss.html Fred Bookstein flb@stat.washington.edul Bill Green wdkg@brainmap.med.umich.edu The University of Michigan/Visible Human Project Utilizes NLM Visible Human Data sets Edgewarp3D is a sophisticated workstation package for manipulation of 2D and 3D biomedical images and related data structures by a combination of landmark location, thin-plate spline, and image unwarping and averaging. Utilizes NLM Visible Human data sets EM3D EM3D 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 304 http://em3d.stanford.edu The McMahan Lab contact@em3d.stanford.edu David Ress, Mark Harlow, David Yip, Robert Marshall, Cornelia Koch-Stoschek, Mira Raman and Uel J. McMahan unknown Uel J. McMahan Laboratory, Stanford University, Dept. of Neurobiology, Dept. of Structural Biology EM3D is a software application designed to facilitate the analysis and visualization of electron microscope (EM) tomography data by cellular and molecular biologists. Such data are collected as a tilt series, a sequence of 2D electron micrographs taken at many tilt angles with respect to the electron beam. EM3D features an integrated graphical user interface that automates most of the initial alignment and reconstruction of the tilt-series data to form a 3D volume. These functions seamlessly connect with segmentation and model-generation tools that permit the user to easily and reliably extract specific structural components from the reconstructed volume. The 3D models can then be visualized and manipulated using an extensive package of surface- and volume-rendering techniques. EM3D also provides a set of analysis tools to quantify structural information from the models, including their moments, proximity relationships, and spatial reliability. Altogether, EM3D facilitates the analysis of 3D cell structure at the full resolution of a reconstructed volume (2-3 nm). EMS Expectation-Maximization Segmentation 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 93 http://bilbo.esat.kuleuven.ac.be/web-pages/downloads/ems/ems.html Koen Van Leemput koen.vanleemput@hut.fi Medical Image Computing, Leuven, Belgium EMS is a freely available suite of Matlab functions and subroutines (with some externally compiled C routines) for fully-automated multi-spectral classification of brain tissues in Magnetic Resonance (MR) images. It uses a model based approach (including an explicit model for MR bias fields) in which all the model parameters are automatically estimated for each individual scan. This enables it to process large amounts of data from normal subjects and subjects suffering from Multiple Sclerosis without need for user intervention or preceeding manual training phase. ezDICOM ezDICOM 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 102 http://www.sph.sc.edu/comd/rorden/ezdicom.html Chris Rorden chris@mricro.com Chris Rorden unknown University of Nottingham Analyze, DICOM, NEMA, GE, Interfile, ECAT, Picker, Siemens, Elscint, VFF, VoxBo A simple drag and drop medical image viewer for Windows. This software can view Analyze, DICOM, NEMA, GE, Interfile, ECAT, Picker, Siemens, Elscint, VFF, VoxBo, and raw format images. This open source project is a good starting point for new projects. FACT Functional MRI Analysis and Clustering Tools 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 132 http://mr.ee.ntu.edu.tw/~khchuang/fact.html Kai-Hsiang Chuang khchuang@ntu.edu.tw Kai-Hsiang Chuang khchuang@ntu.edu.tw Interdisciplinary MRI/MRS Lab, National Taiwan University FACT (Functional MRI Analysis and Clustering Tools) is free software for analyzing time series data like fMRI and perfusion MRI. It provides correlation analysis, t-test and temporal clustering analysis -- Kohonen Clustering Network and Fuzzy Clustering. A set of analysis tools applicable to fMRI time-series data. FIASCO Functional Image Analysis Software Computational Olio 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 101 http://www.stat.cmu.edu/~fiasco/ Jennifer Bakal bakalj@stat.cmu.edu Joel Welling fiasco@stat.cmu.edu CMU Statistics Department FIASCO is a collection of software designed to analyze fMRI data using a series of processing steps. The input is the raw data, and the outputs are statistical brain maps showing regions of neural activation. Corrections for different systematic variations in the k-space (raw) data obtained from an fMRI session (head motion, ghosting, etc) are performed first. The image is then reconstructed (using the Fast Fourier Transform) and statistical analyses run. The user has a great deal of flexibility in choosing which corrections and statistics are executed. FIASCO emphasizes correct statistical models, for example for group comparisons. A software toolkit for preprocessing and analyzing fMRI data. Requires usse of the Pittsburgh MRI data format. Fiber Tracking Fiber Tracking / DTI Checker 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 359 http://www.ia.unc.edu/dev/download/fibertracking/index.htm Pierre Fillard pierre.fillard@wanadoo.fr Pierre Fillard, Matthieu Jomier. unknown University of North Carolina at Chapel Hill, Psychiatry and computer sciences departments The Fiber Tracking tool is a cross-platform system that is intended to help doctors, medical technicians or medical researchers to explore diffusion tensor images and to reconstruct fiber tracts between two regions of interest. The Fiber-Tracking tool allows the user to load data from MRIs or similar images (like a basic 3D image viewer), load DTI datasets (7 diffusion- weighted images), calculate the fractional anisotropy (FA) and the mean diffusivity (MD) images, and also load ROIs to reconstruct fibers. Fiber Viewer Fiber Viewer 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 361 http://www.ia.unc.edu/dev/download/fiberviewer/index.htm Sylvain Gouttard gouttard@email.unc.edu Matthieu JOMIER, Sylvain GOUTTARD unknown UNC at Chapel Hill, Psychiatry and Computer Sciences departments The Fiber Viewer allows us to display the fibers tracked by the Fiber Tracking tool, to sort them, remove the outliers, and compute some properties. This software uses several gathering algorithms to create bundles within the fiber dataset. There are also easy to use tools to cut the fibers, compute mean properties. (Tutorial at http://www.ia.unc.edu/dev/tutorials/FiberViewer/index.htm .) Windows and Linux only. XFido XFido 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 88 http://ncmir.ucsd.edu/doc/xfido/ Steve Lamont spl@ncmir.ucsd.edu Steve Lamont (XFido) & Tomas Molina (JFido) unknown National Center for Microscopy and Imaging Research An interactive, graphic, fiducial marking software for placing, editing and tracking fiducial marks on images in a tomography tilt series. You can also use this tool to view the tilt series as well as crop it. FilamentTracer FilamentTracer 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 169 http://www.bitplane.com/products/filamenttracer/filamenttracer_product.shtml unknown ussales@bitplane.com Bitplane Inc. unknown Bitplane Inc. FilamentTracer is the leading software product for the automatic detection of filaments in 3D microscopic images. It automatically converts a volume image into a graph that retains the topological information of the filament and calculates essential information including the length and diameter of the segments, and the number of branch points. FisWidgets FisWidgets 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 17 http://neurocog.lrdc.pitt.edu/fiswidgets/ Kate Fissell fissell+@pitt.edu University of Pittsburgh A set of Java libraries for rapidly creating GUIs for software modules (C, C++, Fortan, PERL scripts, etc.), and graphically controlling process flow among them. This allows a GUI to be created for existing image processing and analysis routines, which provides: 1) graphic elements for setting parameters, arguments, etc. (i.e., text dialogs, file browsers, etc.); 2) links to web based documentation; 3) simple point-and-click interface for setting up a path for data flow from one module to another. The purpose of FisWidgets is to provide an integrated and user-friendly environment for using the disparate and growing array of image processing and analysis tools created by different laboratories. fMRIstat fMRIstat 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 162 http://www.math.mcgill.ca/keith/fmristat Keith Worsley keith.worsley@mcgill.ca Montreal Neurological Institute FMRIstat implements a method for the statistical analysis for fMRI data that seeks a compromise between efficiency, generality, validity, simplicity and execution speed. The main differences between this analysis and previous ones are: a simple bias reduction and regularization for voxel-wise autoregressive model parameters; the combination of effects and their estimated standard deviations across different scans/sessions/subjects via a hierarchical random effects analysis using the EM algorithm; overcoming the problem of a small number of scans/session/subjects using a regularized variance ratio to increase the degrees of freedom. FMRIstat also implements a fast, efficient, general, simple, valid and robust method of estimating and making inference about the delay of the fMRI response modeled as a temporal shift of the hemodynamic response function (HRF). We estimate the shift unbiasedly using two optimally chosen basis functions for a spectrum of time shifted HRFs. This is done at every voxel, to create an image of estimated delays and their standard deviations. This can be used to compare delays for the same stimulus at different voxels, or for different stimuli at the same voxel. A set of Matlab tools for analysis of fMRI data FreeSurfer FreeSurfer 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 31 http://surfer.nmr.mgh.harvard.edu Bruce Fischl fischl@nmr.mgh.harvard.edu Anders Dale, Bruce Fischl, Marty Sereno, Doug Greve NMR Center, Massachusetts General Hospital FreeSurfer is a set of semi-automated tools for reconstruction of the brain's cortical surface and overlay of functional data onto the reconstructed surface. A powerful and widely used set of analysis and visualization tools for surface-based representations of cerebral cortex An open source release is planned. FSL FMRIB Software Library 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 66 http://www.fmrib.ox.ac.uk/fsl Oxford FMRIB Image Analysis Group fsl@jiscmail.ac.uk Oxford University ANALYZE, NIFTI The FMRIB Software Library (FSL) is a collection of functional and structural brain image analysis tools. FSL is completely self-contained. Most of the tools can be run both from the command line and through graphical interfaces. Tools include: STRUCTURAL TOOLS BET - Brain Extraction Tool - segments brain from non-brain in structural and functional data. SUSAN - Nonlinear noise reduction. FAST - FMRIB's Automated Segmentation Tool - brain segmentation (into different tissue types) and bias field correction. FLIRT - FMRIB's Linear Image Registration Tool - linear inter- and intra-modal registration. FUGUE - Unwarps distortion in EPI images using B0 field maps. SIENA - Structural brain change analysis, for estimating brain atrophy. (BET, FLIRT and FUGUE are also used in FMRI analysis) FUNCTIONAL TOOLS FEAT - Advanced FMRI analysis with easy-to-use yet powerful GUI. Includes all necessary preprocesing, model-based and semi-model-free statistical analysis, automatic registration to structural and/or standard space, and fixed- and random-effects group statistics. MCFLIRT - FMRI motion correction. MELODIC - ICA-based model-free analysis of FMRI (and other 4D) data. An excellent set of tools for many types of anaysis of neuroimaging structural and functional data geWorkbench genomics Workbench 2006-10-01T23:06:42 2006-10-01T23:06:42 iatr IATR 388 http://www.geworkbench.org Center for Computational Biology and Bioinformatics, Columbia University geworkbench-users@gforge.nci.nih.gov Center for Computational Biology and Bioinformatics, Columbia University geWorkbench (genomics Workbench) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 30 available plug-ins (http://www.geworkbench.org/workbench/index.php/Plugins) supporting the visualization and analysis of gene expression and sequence data. Example use cases include: - loading data from local or remote data sources; - visualizing gene expression and sequence data in a variety of ways; - providing access to client- and server-side computational analysis tools such as t-test analysis, hierarchical clustering, self organizing maps, regulatory neworks reconstruction, BLAST searches, pattern/motif discovery, etc.; - validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis. geWorkbench is the Bioinformatics platform of MAGNet (http://magnet.c2b2.columbia.edu), the National Center for the Multi-scale Analysis of Genomic and Cellular Networks (one of the 7 National Centers for Biomedial Computing (http://www.bisti.nih.gov/ncbc/index.cfm) funded through the NIH Roadmap Initiative (http://nihroadmap.nih.gov)). GpetView Gtk-based Analyze Image Viewer 2006-10-01T23:06:43 2006-10-01T23:06:43 iatr IATR 155 http://homepage2.nifty.com/peco/gpetview/gpetview.html Hiroshi Watabe watabe@ri.ncvc.go.jp Gtk-base Analyze image viewer ANALYZE GpetView is light-weight image viewer based on Gtk+ library. The supported image format is ANALYZE (TM) format (Mayo Foundation ). GpetView can run on Unix-systems, such as Linux, Solaris, IRIX, MacOSX etc as well as Win32 system. GpetView has the following features: * very light-weight * view images as transverse, coronal, or sagittal * change color-map (support Analyze lkup file) * zoom images * ROI (Region-Of-Interest) with shapes of circle, ellipse, rectangle, polygon and automatic edge detection * Image histogram and profile Gradient Non-linearity Distortion Correction Gradient Non-linearity Distortion Correction 2006-10-01T23:06:43 2006-10-01T23:06:43 iatr IATR 397 http://www.nbirn.net/Resources/Downloads/GradientNonLinearity/index.htm Silvester Czanner czanner@nmr.mgh.harvard.edu Martinos Center, MGH, Boston The software distributed provides a 3D distortion correction based on knowledge of the spherical harmonic coefficients from the imaging gradients. addresses a specific issue relating to spatial distortions that differ across scanner types. GIFT Group ICA of fMRI Toolbox (GIFT) 2006-10-01T23:06:43 2006-10-01T23:06:43 iatr IATR 330 http://icatb.sourceforge.net Vince Calhoun vince.calhoun@yale.edu Olin Neuropsychiatry Research Center GIFT is a Matlab toolbox which implements multiple algorithms for independent component analysis (ICA) and blind source separation of group (and single subject) functional magnetic resonance imaging (fMRI) data.