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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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UBERON Resource Report Resource Website 50+ mentions |
UBERON (RRID:SCR_010668) | UBERON | controlled vocabulary, data or information resource, ontology | An integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. Uberon consists of over 10000 classes (March 2014) representing structures that are shared across a variety of metazoans. The majority of these classes are chordate specific, and there is large bias towards model organisms and human. | anatomy, comparative, evolution, organ system, anatomical structure, body part, organ, tissue, body, vertebrate, function, phenotype, expression, model organism, obo |
is used by: Neuroscience Information Framework is listed by: BioPortal is related to: Gene Ontology has parent organization: OBO |
ARRA ; NSF ; NHGRI 5R01HG004838; NHGRI P41HG002273; DOE DE-AC02-05CH11231; NCRR 1U24RR029825-01; NHGRI P41HG002273-09S1 |
PMID:22293552 | nlx_74404 | SCR_010668 | Uber anatomy ontology, Uber-anatomy ontology | 2026-08-29 11:23:44 | 62 | ||||||
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Montage RTS2000 Resource Report Resource Website |
Montage RTS2000 (RRID:SCR_013439) | data processing software, image processing software, software application, software resource | Software program for creating montages from multiphoton microscopy. | microscopy, mosaic, montage, image |
is listed by: 3DVC has parent organization: National Center for Microscopy and Imaging Research |
NCRR P41 RR04050 | GNU General Public License | nif-0000-10515 | SCR_013439 | 2026-08-29 11:24:39 | 0 | ||||||||
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CTSpedia Resource Report Resource Website |
CTSpedia (RRID:SCR_008733) | CTSpedia | data or information resource, knowledge environment, knowledgebase, narrative resource, software resource, training material, wiki | CTSpedia is a national effort to collect wisdom, tools, educational materials, and other items useful for clinical and translational researchers and to provide timely and useful advice to clinical and translational researchers with specific problems. The CTSpedia is a collaborative vehicle for the CTSA''s Biostatistics/Epidemiology/Research/Design (BERD) Online Resources and Education taskforce to identify and share resources across the national consortium and community researchers world-wide. With the support of the national BERD consortia, the project obtained funding and support from the National Center for Research Resources (NCRR) to expand the original scope and content of CTSpedia and foster collaboration amongst CTSAs. The main goal of CTSpedia.org is to create a definable academic home on the internet for the discipline of clinical and translational sciences across the country and the world. * While the CTSA consortium serves the onsite physical level of the institutions involved, CTSpedia.org seeks to fill the gaps where the network is lacking, and to augment that network as the central hub for the peer to peer sharing of knowledge and resources. * While the CTSA national scope comes to fruition, the international scope of the consortia is more readily facilitated with an online resource like CTSpedia. * Utilizing the collaborative nature of the wiki-style website, CTSpedia.org allows for researchers anywhere in the world to ask questions and receive answers and related information in a timely and efficient manner, overcoming the logistical issues of distance and scheduling. * The streamlined availability of an online resource and knowledge repository will aid in addressing common issues that arise in clinical research, which will filter out consultation requests for minor questions, allowing for CTSA consultants to address more prevalent consultations. | clinical research, translational research, statistical tool, statistical graphic, presentation, graphic, discussion forum, dataset, ctsa, biostatistics |
has parent organization: University of California at San Francisco; California; USA has parent organization: University of Rochester; New York; USA has parent organization: University of California at Davis; California; USA has parent organization: Vanderbilt University; Tennessee; USA |
NCRR RR024146 | nlx_143799 | SCR_008733 | CTSpedia: A Knowledge Base for Clinical and Translational Research, CTSpedia.org | 2026-08-29 11:23:11 | 0 | |||||||
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GOMO - Gene Ontology for Motifs Resource Report Resource Website 1+ mentions |
GOMO - Gene Ontology for Motifs (RRID:SCR_008864) | GOMO | analysis service resource, data analysis service, data processing software, production service resource, service resource, software application, software resource | Gene Ontology for Motifs (GOMO) is an alignment- and threshold-free comparative genomics approach for assigning functional roles to DNA regulatory motifs from DNA sequence. The algorithm detects associations between a user-specified DNA regulatory motif (expressed as a position weight matrix; PWM) and Gene Ontology terms. The original method for predicting the roles of transcription factors (TFs starts with a PWM motif describing the DNA-binding affinity of the TF. GOMO uses the PWM to score the promoter region of each gene in the genome for its likelihood to be bound by the TF. The resulting ''''affinity'''' scores are then used to test each term in the Gene Ontology for association with high-scoring genes. The algorithm was subsequently extended to leverage conserved signals using multiple, related species in a comparative approach, which greatly improves the resulting annotations. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, motif, genomics, gene ontology, function, compare, ontology or annotation editor, statistical analysis, dna binding motif, dna binding, dna, transcription factor, sequence |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Queensland; Brisbane; Australia has parent organization: MEME Suite - Motif-based sequence analysis tools |
Australian Research Council ; University of Queensland; Brisbane; Australia ; International Research Tuition Award ; NCRR R01 RR021692 |
PMID:20147307 PMID:18544606 |
Free for academic use | nlx_149250 | SCR_008864 | Gene Ontology for Motifs | 2026-08-29 11:23:14 | 3 | |||||
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iTools Resource Report Resource Website 50+ mentions |
iTools (RRID:SCR_009626) | iTools | data access protocol, data or information resource, data repository, database, service resource, software repository, software resource, storage service resource, web service | An infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org). | computational neuroscience, data, experiment control, hardware, imaging genomics, information specification, java, loni pipeline, model, ontology, os independent, metadata |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: National Centers for Biomedical Computing has parent organization: Laboratory of Neuro Imaging |
NIH Roadmap for Medical Research ; NCRR U54-RR021813; NIDA U54-DA021519; NCI U54-CA121852; NHGRI U54-HG004028; NIGMS U54-GM072970; NIBIB U54-EB005149; NLM U54-LM008748 |
PMID:18509477 | GNU Lesser General Public License | nlx_155852 | http://www.nitrc.org/projects/itools, http://www.loni.usc.edu/research/software | http://itools.loni.ucla.edu/ | SCR_009626 | ITools Resourceome, NCBC iTools | 2026-08-29 11:23:36 | 53 | |||
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Induced Mutant Resource Resource Report Resource Website 1+ mentions |
Induced Mutant Resource (RRID:SCR_008366) | IMR | biomaterial supply resource, material resource, organism supplier | THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 08, 2012. The function of the IMR is to select, import, cryopreserve, maintain, and distribute these important strains of mice to the research community. To improve their value for research, the IMR also undertakes genetic development of stocks, such as transferring mutant genes or transgenes to defined genetic backgrounds and combining transgenes and/or targeted mutations to create new mouse models for research. The function of the IMR is to: * select biomedically important stocks of transgenic, chemically induced, and targeted mutant mice * import these stocks into the Jackson Laboratory by rederivation procedures that rid them of any pathogens they might carry * cryopreserve embryos from these stocks to protect them against accidental loss and genetic contamination * backcross the mutation onto an inbred strain, if necessary * distribute them to the scientific community More than 1000 mutant stocks have been accepted by the IMR from 1992 through December 2006. Current holdings include models for research on cancer; breast cancer; immunological and inflammatory diseases; neurological diseases; behavioral, cardiovascular and heart diseases; developmental, metabolic and other diseases; reporter (e.g., GFP) and recombinase (e.g., cre/loxP) strains. About eight strains a month are being added to the IMR holdings. Research is being conducted on improved methods for assisted reproduction and speed congenic production. Most of the targeted mutants arrive on a mixed 129xC57BL/6 genetic background, and as many of these as possible are backcrossed onto an inbred strain (usually C57BL/6J). In addition, new mouse models are being created by intercrossing carriers of specific transgenes and/or targeted mutations. Simple sequence length polymorphism DNA markers are being used to characterize and evaluate differences between inbred strains, substrains, and embryonic stem cell lines. | embryo, genetic, behavioral, biomedical, breast cancer, cancer, cardiovascular, chemical, cre, cryopreserved, developmental, disease, distribution, dna, gfp, heart, immunological, inflammatory, loxp, marker, metabolic, model, mouse, mutation, neurological, pathogen, polymorphism, recombinase, research, stock, targeting, transgene | has parent organization: Jackson Laboratory | March of Dimes Birth Defects Foundation ; American Cancer Society ; American Heart Association ; Cystic Fibrosis Foundation ; National Multiple Sclerosis Society ; Amyotrophic Lateral Sclerosis Association ; NIAID ; NIAMS ; Howard Hughes Medical Institute ; Department of the Army Breast Cancer Research Initiative. ; NCRR P40 RR009781 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25566 | SCR_008366 | 2026-08-29 11:23:29 | 3 | |||||||
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jViewbox Resource Report Resource Website |
jViewbox (RRID:SCR_008274) | data processing software, image processing software, software application, software resource | A portable software framework for medical imaging research. jViewbox consists of a set of Java classes organized under a simple but extensive API that provides the core functionality of 2D image presentation needed by most imaging applications. It follows Java's Swing model closely to make it easy for application developers to build GUIs where end users can use various tools in a tool bar to manipulate the image displays. No optional add-ons or native code is used, which makes jViewBox compatible with any standard Java 2 Runtime Environment (version 1.3 or later). | imaging, magnetic resonance imaging, image processing software |
is related to: Laboratory of Neuro Imaging has parent organization: University of Southern California; Los Angeles; USA |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15 |
Available for educational and research purposes only | nif-0000-23317 | SCR_008274 | 2026-08-29 11:23:02 | 0 | ||||||||
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Northwestern University Schizophrenia Data and Software Tool (NUSDAST) Resource Report Resource Website |
Northwestern University Schizophrenia Data and Software Tool (NUSDAST) (RRID:SCR_014153) | NUSDAT | data or information resource, database, image collection | A repository of schizophrenia neuroimaging data collected from over 450 individuals with schizophrenia, healthy controls and their respective siblings, most with 2-year longitudinal follow-up. The data include neuroimaging data, cognitive data, clinical data, and genetic data. | database, neuroimaging, clinical, cognitive, genetic, schizophrenia, longitudinal |
uses: CAWorks is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Northwestern University; Illinois; USA |
Schizophrenia | NIMH 1R01 MH084803; NIMH 1U01 MH097435; NIMH P50 MH071616; NIMH R01 MH056584; NCRR P41 RR15241; NIGMS U24 GM104203; NIH Bio-Informatics Research Network Coordinating Center |
Available to the research community | SCR_014153 | Northwestern University Schizophrenia Data and Software Tool | 2026-08-29 11:24:42 | 0 | ||||||
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oligo Resource Report Resource Website 1000+ mentions |
oligo (RRID:SCR_015729) | data analysis software, data processing software, software application, software resource, source code | Software package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files). | oligonucleotide, microarray gene expression, r, oligonucleotide array, snp, gene expression, probe-level, affymetrix array, cel file, and nimblegen array, xys file, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
CAPES (Coordenação de Aprimoramento Pessoal de Nível Superior) ; NCRR R01RR021967; NHGRI P41HG004059 |
PMID:20688976 | Free, Available for download, Runs on Mac OS, Runs on Windows | biotools:oligo | https://bio.tools/oligo | SCR_015729 | oligo package | 2026-08-29 11:25:00 | 1808 | |||||
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CD-HIT Resource Report Resource Website 1000+ mentions |
CD-HIT (RRID:SCR_007105) | CD-HIT | data processing software, software application, software resource, source code | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for clustering biological sequences with many applications in various fields such as making non-redundant databases, finding duplicates, identifying protein families, filtering sequence errors and improving sequence assembly etc. It is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset. The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT, CD-HIT-OTU and over a dozen scripts. * CD-HIT (CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a user-defined similarity threshold. * CD-HIT-2D (CD-HIT-EST-2D) compares 2 datasets and identifies the sequences in db2 that are similar to db1 above a threshold. * CD-HIT-454 identifies natural and artificial duplicates from pyrosequencing reads. * CD-HIT-OTU cluster rRNA tags into OTUs The usage of other programs and scripts can be found in CD-HIT user''s guide. CD-HIT was originally developed by Dr. Weizhong Li at Dr. Adam Godzik''s Lab at the Burnham Institute (now Sanford-Burnham Medical Research Institute)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | cluster, protein, sequence, classification, domain, analysis, nucleotide sequence, dna, protein sequence, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: University of California at San Diego; California; USA has parent organization: Google Code is parent organization of: CD-HIT-OTU |
NCRR 1R01RR025030 | PMID:20053844 PMID:16731699 DOI:10.1093/bioinformatics/btl158 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05157, biotools:cd-hit, nif-0000-30240 | http://cd-hit.org, https://code.google.com/p/cdhit/, https://bio.tools/cd-hit, https://sources.debian.org/src/cd-hit/ | http://bioinformatics.ljcrf.edu/cd-hi/ |
SCR_007105 | CD-HIT Program | 2026-08-29 11:22:51 | 3223 | |||
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Combine RTS2000 Resource Report Resource Website 1+ mentions |
Combine RTS2000 (RRID:SCR_007104) | data processing software, image processing software, software application, software resource | Software program that performs the auto-alignment and the composition of images to create the mosaic. | program, auto, alignment, composition, image, create, mosaic | has parent organization: National Center for Microscopy and Imaging Research | NCRR P41 RR04050 | Free, no longer available | nif-0000-10511 | SCR_007104 | 2026-08-29 11:22:47 | 1 | ||||||||
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Biological General Repository for Interaction Datasets (BioGRID) Resource Report Resource Website 1000+ mentions |
Biological General Repository for Interaction Datasets (BioGRID) (RRID:SCR_007393) | BioGRID | data or information resource, database | Curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts. | budding yeast, fission yeast, protein, gene, protein interaction, genetic interaction, model organism, interaction, dataset, gene annotation, phenotype, orthologous interaction, yeast, cellular interaction network, physical interaction, protein-peptide, protein-rna, protein-protein interaction, genetics, publication, raw protein, genetic interaction, web service, pathway, network, biology, gene mapping, statistics, bio.tools, FASEB list |
is used by: NIF Data Federation is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: OMICtools is listed by: DataCite is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions is related to: Pathway Commons is related to: Cytoscape is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: FlyMine is related to: IMEx - The International Molecular Exchange Consortium is related to: Integrated Molecular Interaction Database is related to: PSICQUIC Registry is related to: PSI-MI is related to: NIH Data Sharing Repositories is related to: Agile Protein Interactomes DataServer is related to: Integrated Manually Extracted Annotation has parent organization: Princeton University; New Jersey; USA has parent organization: University of Edinburgh; Scotland; United Kingdom has parent organization: University of Montreal; Quebec; Canada works with: IMEx - The International Molecular Exchange Consortium |
BBSRC ; Canadian Institutes of Health Research ; NCRR R01 RR024031; NHGRI HG02223; NIH Office of the Director R24 OD011194 |
PMID:23203989 PMID:21071413 PMID:16381927 PMID:12620108 |
Free, Freely available | nif-0000-00432, r3d100010350, OMICS_01901, biotools:the_grid | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources, https://bio.tools/the_grid, https://doi.org/10.17616/R34C7G | SCR_007393 | , BioGRID, Biological General Repository for Interaction Datasets | 2026-08-29 11:23:10 | 2824 | ||||
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Primate Info Net Resource Report Resource Website 1+ mentions |
Primate Info Net (RRID:SCR_007380) | PIN | data or information resource, database, portal, topical portal | Portal covering the broad field of primatology, providing original content and links to resources about nonhuman primates in research, education and conservation. Through email lists and other resources, PIN also supports an informal primate information network comprised of thousands of individuals around the world working with nonhuman primates in a variety of roles. Services Provided: - Primate Info Net (PIN): A comprehensive Web site with links to research, conservation, and education resources related to nonhuman primates. - PrimateLit Database (1940 to date): PrimateLite is a free, bibliographic database of more than 200,000 citations to the nonhuman primate literature. Indexing for PrimateLit is provided by the Primate Information Center, Washington NPRC, Seattle. - International Directory of Primatology: The International Directory of Primatology is a searchable directory of the field of primatology with detailed information about organizations, field studies, population management groups, and contact information for more than 3,000 primatologists. - Primate-Science: Primate-Science is a professionally oriented, e-mail-based electronic discussion forum for people engaged in research with nonhuman primates. - Primate-News: Primate-News is an e-mailed-based news clipping service open to anyone interested in nonhuman primates. - Primate Enrichment Forum: Primate Enrichment Forum is a professionally oriented, e-mail-based electronic discussion forum for individuals interested in environmental enrichment for nonhuman primates. - AskPrimate: AskPrimate is a cooperative e-mail reference service available to the research community and the general public. - Primate-Jobs: Primate-Jobs is a job listing service that includes paid and volunteer positions, wanted and available. - Careers in Primatology: Careers in Primatology is a resource for people considering careers in primate research, education, conservation, or veterinary medicine. - Audiovisual Resources: Audiovisual Resources is a collection of primate-related videotapes, slides, and audiotapes available for research and educational uses. - The Callicam: The Callicam is a Webcam feature of the Wisconsin NPRC''s common marmoset site that allows students in the classroom to observe marmoset behavior and learn about their natural history, care, and management. | primatology, conservation, network, database, literature, information, organization, field study, population | has parent organization: Wisconsin National Primate Research Center | NCRR RR000167; NCRR RR015311 |
nif-0000-00371 | SCR_007380 | 2026-08-29 11:23:10 | 3 | ||||||||
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3D Slicer Resource Report Resource Website 1000+ mentions |
3D Slicer (RRID:SCR_005619) | Slicer | data processing software, data visualization software, image analysis software, software application, software resource | A free, open source software package for visualization and image analysis including 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. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X. Slicer is based on VTK (http://public.kitware.com/vtk) and has a modular architecture for easy addition of new functionality. It uses an XML-based file format called MRML - Medical Reality Markup Language which can be used as an interchange format among medical imaging applications. Slicer is primarily written in C++ and Tcl. | birn, diffusion, functional, na-mic (ncbc), nifti-1 support, registration, segmentation, visualization, volume, warping |
uses: 3DSlicerLupusLesionModule uses: ShapePopulationViewer uses: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI uses: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: Slicer3 Example Modules is related to: Stereoscopic Atlas of Intrinsic Brain Networks is related to: VMTK in 3D Slicer is related to: Diffusion Tractography with Kalman Filter is related to: Fast Nonlocal Means for MRI denoising is related to: SpineSegmentation module for 3DSlicer is related to: BioImage Suite is related to: NA-MIC Kit is related to: Hammer And WML Modules for 3D Slicer is related to: ABC (Atlas Based Classification) is related to: ARCTIC is related to: Finsler tractography module for Slicer is related to: GAMBIT is related to: GPU based affine registration is related to: GTRACT is related to: LEAD-DBS has parent organization: Harvard University; Cambridge; United States is parent organization of: Level-set Segmentation for Slicer3 is parent organization of: Slicer3 Module Rician noise filter has plug in: MultiXplore works with: UManitoba - JHU Functionally Defined Human White Matter Atlas works with: SlicerMorph |
NIH ; NCRR ; NIBIB ; NCI ; US Army ; Telemedicine and Advanced Technology Research Center |
3D Slicer License | nif-0000-00256 | http://www.nitrc.org/projects/slicer | SCR_005619 | Slicer, 3D Slicer: A multi-platform free and open source software package for visualization and medical image computing, 3D Slicer, 3DSlicer | 2026-08-29 11:22:23 | 3187 | |||||
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GOEx - Gene Ontology Explorer Resource Report Resource Website 10+ mentions |
GOEx - Gene Ontology Explorer (RRID:SCR_005779) | GOEx | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented July 5, 2018. Gene Ontology Explorer (GOEx) combines data from protein fold changes with GO over-representation statistics to help draw conclusions in proteomic experiments. It is tightly integrated within the PatternLab for Proteomics project and, thus, lies within a complete computational environment that provides parsers and pattern recognition tools designed for spectral counting. GOEx offers three independent methods to query data: an interactive directed acyclic graph, a specialist mode where key words can be searched, and an automatic search. A recent hack included in GOEx is to load the sparse matrix index file directly into GOEx, instead of going through the report generation using the AC/T-fold methods. This makes it easy for GOEx to analyze any list of proteins as long as the list follows the index file format (described in manuscript) . Please note that if using this alternative strategy, there will be no protein fold information. Platform: Windows compatible | proteomics, visualization, statistical analysis, gene ontology, parse, pattern recognition, spectral counting, analysis, protein fold |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Scripps Research Institute |
CNPq ; CAPES ; FAPERJ BBP grant ; PAPES ; PDTIS ; Ary Frauzino Foundation ; NIAID ; NIH ; genesis molecular biology laboratory ; Fiocruz-INCA collaboration ; NIAID UCSD/MCB0237059; NCRR P41RR011823; NIMH 5R01 MH067880 |
PMID:19239707 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149249 | http://pcarvalho.com/patternlab/goex.shtml | SCR_005779 | Gene Ontology Explorer, GO Explorer | 2026-08-29 11:22:29 | 32 | ||||
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Proteome Commons Resource Report Resource Website 10+ mentions |
Proteome Commons (RRID:SCR_006234) | Proteome Commons | community building portal, data or information resource, data repository, database, portal, service resource, software resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A public resource for sharing general proteomics information including data (Tranche repository), tools, and news. Joining or creating a group/project provides tools and standards for collaboration, project management, data annotation, permissions, permanent storage, and publication. | proteomics, protein, peptide, data sharing, data, tool, news, annotation, proteome, genome |
is listed by: re3data.org has parent organization: University of Michigan; Ann Arbor; USA is parent organization of: Proteome Commons Tranche repository |
NCI ; Clinical Proteomics Technologies for Cancer ; NCRR P41-RR018627 |
PMID:20356086 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151800 | SCR_006234 | ProteomeCommons.org, ProteomeCommons | 2026-08-29 11:22:32 | 12 | |||||
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BrainInfo Resource Report Resource Website 10+ mentions |
BrainInfo (RRID:SCR_003142) | atlas, data or information resource, database, narrative resource, portal, standard specification, topical portal | Portal to neuroanatomical information on the Web that helps you identify structures in the brain and provides a variety of information about each structure by porting you to the best of 1500 web pages at 100 other neuroscience sites. BrainInfo consists of three basic components: NeuroNames, a developing database of definitions of neuroanatomic structures in four species, their most common acronyms and their names in eight languages; NeuroMaps, a digital atlas system based on 3-D canonical stereotaxic atlases of rhesus macaque and mouse brains and programs that enable one to map data to standard surface and cross-sectional views of the brains for presentation and publication; and the NeuroMaps precursor: Template Atlas of the Primate Brain, a 2-D stereotaxic atlas of the longtailed (fascicularis) macaque brain that shows the locations of some 250 architectonic areas of macaque cortex. The NeuroMaps atlases will soon include a number of overlays showing the locations of cortical areas and other neuroscientific data in the standard frameworks of the macaque and mouse atlases. Viewers are encouraged to use NeuroNames as a stable source of unique standard terms and acronyms for brain structures in publications, illustrations and indexing systems; to use templates extracted from the NeuroMaps macaque and mouse brain atlases for presenting neuroscientific information in image format; and to use the Template Atlas for warping to MRIs or PET scans of the macaque brain to estimate the stereotaxic locations of structures. | brain, neuroanatomy |
is used by: NIF Data Federation is listed by: Biositemaps is related to: INIA19 Primate Brain Atlas has parent organization: University of Washington; Seattle; USA has parent organization: University of California at San Diego; California; USA |
The Human Brain Project ; NIBIB ; NLM LM/OD-06243; NIH Office of the Director LM/OD-06243; NIMH MHO69259; NCRR RR-00166 |
PMID:21789500 PMID:21163300 PMID:18368361 PMID:15055392 |
Free, Freely available | nif-0000-00019 | SCR_003142 | Brain Info | 2026-08-29 11:21:23 | 16 | ||||||
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Statistics Online Computational Resource Resource Report Resource Website 10+ mentions |
Statistics Online Computational Resource (RRID:SCR_003378) | SOCR | data or information resource, narrative resource, software application, software resource, software toolkit, training material | A hierarchy of portable online interactive aids for motivating, modernizing probability and statistics applications. The tools and resources include a repository of interactive applets, computational and graphing tools, instructional and course materials. The core SOCR educational and computational components include the following suite of web-based Java applets: * Distributions (interactive graphs and calculators) * Experiments (virtual computer-generated games and processes) * Analyses (collection of common web-accessible tools for statistical data analysis) * Games (interfaces and simulations to real-life processes) * Modeler (tools for distribution, polynomial and spectral model-fitting and simulation) * Graphs, Plots and Charts (comprehensive web-based tools for exploratory data analysis), * Additional Tools (other statistical tools and resources) * SOCR Java-based Statistical Computing Libraries * SOCR Wiki (collaborative Wiki resource) * Educational Materials and Hands-on Activities (varieties of SOCR educational materials), * SOCR Statistical Consulting In addition, SOCR provides a suite of tools for volume-based statistical mapping (http://wiki.stat.ucla.edu/socr/index.php/SOCR_EduMaterials_AnalysesCommandLine) via command-line execution and via the LONI Pipeline workflows (http://www.nitrc.org/projects/pipeline). Course instructors and teachers will find the SOCR class notes and interactive tools useful for student motivation, concept demonstrations and for enhancing their technology based pedagogical approaches to any study of variation and uncertainty. Students and trainees may find the SOCR class notes, analyses, computational and graphing tools extremely useful in their learning/practicing pursuits. Model developers, software programmers and other engineering, biomedical and applied researchers may find the light-weight plug-in oriented SOCR computational libraries and infrastructure useful in their algorithm designs and research efforts. The three types of SOCR resources are: * Interactive Java applets: these include a number of different applets, simulations, demonstrations, virtual experiments, tools for data visualization and analysis, etc. All applets require a Java-enabled browser (if you see a blank screen, see the SOCR Feedback to find out how to configure your browser). * Instructional Resources: these include data, electronic textbooks, tutorials, etc. * Learning Activities: these include various interactive hands-on activities. * SOCR Video Tutorials (including general and tool-specific screencasts). | probability, statistics, instruction, statistical computing, applet, computational tool, graphing tool, course material, computation, java, statistical mapping, graphing, computational neuroscience, java, loni pipeline, educator, student, tool developer |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of California at Los Angeles; California; USA |
NIH Roadmap for Medical Research ; NSF 0442992; NSF DUE 0716055; NSF 1023115; NCRR U54 RR021813 |
PMID:21451741 PMID:21297884 |
Free, Freely available | nif-0000-32655 | http://www.nitrc.org/projects/socr | SCR_003378 | 2026-08-29 11:21:31 | 13 | |||||
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Mouse Biomedical Informatics Research Network Resource Report Resource Website |
Mouse Biomedical Informatics Research Network (RRID:SCR_003392) | MouseBIRN, mBIRN | atlas, data or information resource, data set, reference atlas | Animal model data primarily focused on mice including 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. The goal of the Mouse BIRN is to help scientists utilize model organism databases for analyzing experimental data. Mouse BIRN has ended. The next phase of this project is the Mouse Connectome Project (https://www.nitrc.org/projects/mcp/). The Mouse BIRN testbeds initially focused on mouse models of neurodegenerative diseases. Mouse BIRN testbed partners provide multi-modal, multi-scale reference image data of the mouse brain as well as genetic and genomic information linking genotype and brain phenotype. 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. BIRN's infrastructure is providing the collaborative tools to enable researchers with unique expertise and knowledge of the mouse an opportunity to work together on research relevant to pre-clinical mouse models of neurological disease. The Mouse BIRN also maintains a collaborative Web Wiki, which contains announcements, an FAQ, and much more. | electron microscopy, expression, functional, gene, 3-dimentional, brain, cellular, disorder, genomic, genotype, mouse, neurodegenerative disease, phenotype, molecular neuroanatomy resource, mri, light microscopy, model organism, gene expression, atlas data, imaging genomics, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Mouse BIRN Atlasing Toolkit is related to: Mouse Connectome Project has parent organization: Biomedical Informatics Research Network |
Normal, Neurodegenerative disease, Multiple Sclerosis, Alzheimer's disease, Parkinson's disease | NIH ; Collaborative Tools Support Network Award ; NCRR 1U24-RR025736; NCRR U24-RR021992; NCRR U24-RR021760; NCRR 1U24-RR026057-01 |
Free, Available for download, Freely available | nif-0000-00200 | https://loni.usc.edu/research/software?name=MBATWA | http://www.loni.ucla.edu/BIRN/Projects/Mouse/index.shtml | SCR_003392 | Mouse BIRN | 2026-08-29 11:21:31 | 0 | |||
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MiMI Plugin for Cytoscape Resource Report Resource Website 1+ mentions |
MiMI Plugin for Cytoscape (RRID:SCR_003424) | MiMI Plugin | data processing software, data visualization software, software application, software resource | The Cytoscape MiMI Plugin is an open source interactive visualization tool that you can use for analyzing protein interactions and their biological effects. The Cytoscape MiMI Plugin couples Cytoscape, a widely used software tool for analyzing bimolecular networks, with the MiMI database, a database that uses an intelligent deep-merging approach to integrate data from multiple well-known protein interaction databases. The MiMI database has data on 119,880 molecules, 330,153 interactions, and 579 complexes. By querying the MiMI database through Cytoscape you can access the integrated molecular data assembled in MiMI and retrieve interactive graphics that display protein interactions and details on related attributes and biological concepts. You can interact with the visualization by expanding networks to the next nearest neighbors and zooming and panning to relationships of interest. You also can perceptually encode nodes and links to show additional attributes through color, size and the visual cues. You can edit networks, link out to other resources and tools, and access information associated with interactions that has been mined and summarized from the research literature information through a biology natural language processing database (BioNLP) and a multi-document summarization system, MEAD. Additionally, you can choose sub-networks of interest and use SAGA, a graph matching tool, to match these sub-networks to biological pathways. | protein interaction, network visualization, xquery, interactive database, information refining, molecular interaction, bioinformatics tool, java, protein-protein interaction, interaction network, biological effect, bimolecular, interaction, molecular, network, pathway, protein, visualization, plugin |
is listed by: Biositemaps is related to: Cytoscape is related to: Michigan Molecular Interactions has parent organization: University of Michigan; Ann Arbor; USA has parent organization: National Center for Integrative Biomedical Informatics |
NIH ; NIDA U54 DA021519; NLM R01 LM008106; NCRR P41 RR018627 |
PMID:18812364 | nif-0000-33090 | http://mimiplugin.ncibi.org/index.html | SCR_003424 | Cytoscape Plugin for MiMI, MiMI Plugin - Cytoscape Plugin for MiMI | 2026-08-29 11:21:56 | 1 |
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