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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Protein Data Bank Markup Language Resource Report Resource Website 1+ mentions |
Protein Data Bank Markup Language (RRID:SCR_005085) | PDBML | data or information resource, interchange format, markup language, narrative resource, standard specification | Markup Language that provides a representation of PDB data in XML format. The description of this format is provided in XML schema of the PDB Exchange Data Dictionary. This schema is produced by direct translation of the mmCIF format PDB Exchange Data Dictionary Other data dictionaries used by the PDB have been electronically translated into XML/XSD schemas and these are also presented in the list below. * PDBML data files are provided in three forms: ** fully marked-up files, ** files without atom records ** files with a more space efficient encoding of atom records * Data files in PDBML format can be downloaded from the RCSB PDB website or by ftp. * Software tools for manipulating PDB data in XML format are available. | xml |
is related to: RCSB PDB Software Tools has parent organization: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
NSF ; NIGMS ; DOE ; NLM ; NCI ; NCRR ; NIBIB ; NINDS |
PMID:15509603 | nlx_144096 | SCR_005085 | PDBML: Protein Data Bank Markup Language | 2026-09-12 12:56:20 | 2 | ||||||
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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 | 2026-09-12 12:56:29 | 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 | 2026-09-12 12:56:31 | 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 | 2026-09-12 12:56:37 | 12 | |||||
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Chimpanzee Biomedical Research Resource Resource Report Resource Website 1+ mentions |
Chimpanzee Biomedical Research Resource (RRID:SCR_006289) | CBRR | data or information resource, organism-related portal, portal, topical portal | One of only four NCRR-supported centers with the capability to conduct biomedical research in the chimpanzee, it offers chimpanzee-derived cell lines, antibodies and other biological materials, along with a registry of biologic reagents that are known to work in the chimpanzee. The Resource and Management Core is responsible for providing animal resources, tissues/biological fluids, cell lines, expert advice and research support to NIH extramural and intramural programs, other federal agencies and private sponsors. The Resource-Related Research Core conducts research to improve the health of the animals maintained, with special emphasis on studies that will enhance the usefulness of the chimpanzee as a model for studies of human disease. Resource-related research will focus on characterization of the immune system of the chimpanzee, expansion of our understanding of chimpanzee cardiomyopathy as a potential human disease model and comparisons of the physiologic and immunological consequences of research manipulations on chimpanzees trained to voluntarily cooperate with research procedures. By expanding the resources available, conducting resource-related research and containing costs, the CBRR will continue to provide a critically important, highly specialized research resource to address important human health issues. | cardiomyopathy, immune system, animal model, human disease, biological material, cell line, antibody |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of Texas MD Anderson Cancer Center |
NCRR | Free, Freely available | nlx_151945 | http://www.kccmr.org/ | SCR_006289 | , KCCMR Chimpanzee Biomedical Research Resource, Keeling Center for Comparative Medicine and Research Chimpanzee Care Center | 2026-09-12 12:56:37 | 1 | |||||
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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 | 2026-09-12 12:56:50 | 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 | 2026-09-12 12:56:50 | 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 | 2026-09-12 12:56:54 | 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 | 2026-09-12 12:56:54 | 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 | 2026-09-12 12:57:14 | 53 | |||
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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 | 2026-09-12 12:57:21 | 62 | ||||||
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FURTHeR Resource Report Resource Website 50+ mentions |
FURTHeR (RRID:SCR_006383) | FURTHeR | community building portal, data or information resource, data repository, database, portal, service resource, storage service resource | Data and knowledge management infrastructure for the new Center for Clinical and Translational Science (CCTS) at the University of Utah. This clinical cohort search tool is used to search across the University of Utah clinical data warehouse and the Utah Population Database for people who satisfy various criteria of the researchers. It uses the i2b2 front end but has a set of terminology servers, metadata servers and federated query tool as the back end systems. FURTHeR does on-the-fly translation of search terms and data models across the source systems and returns a count of results by unique individuals. They are extending the set of databases that can be queried. | biomedical, clinical, informatics, platform, federated, translation, institutional review board, data management software, clinical data, federation, FASEB list |
is related to: Clinical and Translational Science Awards Consortium has parent organization: University of Utah School of Medicine; Utah; USA |
National Center for Advancing Translational Sciences ; NCRR UL1 RR025764; U.S. Department of Health and Human Services ; University of Utah Research Foundation |
PMID:20351825 PMID:18999122 |
Restricted | nlx_152164 | http://www.further.utah.edu/ | SCR_006383 | Federated Utah Research and Translational Health Electronic Repository, FURTHeR - Federated Utah Research and Translational Health Electronic Repository | 2026-09-12 12:56:39 | 79 | ||||
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Ligand Expo Resource Report Resource Website |
Ligand Expo (RRID:SCR_006636) | data or information resource, database, resource | An integrated data resource for finding chemical and structural information about small molecules bound to proteins and nucleic acids within the structure entries of the Protein Data Bank. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry. A sketch tool is also provided for building new chemical definitions from reported PDB chemical components. | element, fingerprint, formula, amino acid, aromatic ring, atom, bound, carbon, chemical, component, depot, ligand, molecular, molecule, nitrogen, nucleic acid, nucleotide, pharmaceutical, protein, small molecule, structure, macromolecule, model |
uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) uses: Worldwide Protein Data Bank (wwPDB) has parent organization: Rutgers University; New Jersey; USA has parent organization: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
NSF ; NIGMS ; DOE ; NLM ; NCI ; NCRR ; NIBIB ; NINDS ; NIDDK |
PMID:15059838 | nif-0000-21237, OMICS_02751 | http://ligand-depot.rutgers.edu/ | SCR_006636 | Ligand Depot | 2026-09-12 12:56:43 | 0 | ||||||
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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 | 2026-09-12 12:57:03 | 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 | 2026-09-12 12:57:02 | 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 | 2026-09-12 12:57:08 | 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 | 2026-09-12 12:57:10 | 3 | |||||
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ADAPT Resource Report Resource Website 500+ mentions |
ADAPT (RRID:SCR_006769) | ADAPT | data analysis software, data processing software, software application, software resource | Software tool as plug-in developed for ImageJ/FIJI platform to automatically detect and analyse cell migration and morphodynamics. Provides whole cell analysis of multiple cells, while also returning data on individual membrane protrusion events. | Cell migration analysis, morphodynamics analysis, whole cell analysis |
has parent organization: Biomedical Simulations Resource is a plug in for: ImageJ |
NIBIB P41-EB001978; NCRR P41-RR01861 |
DOI:10.1083/jcb.201501081 | Acknowledgement requested, Registration required | nlx_152570 | https://github.com/djpbarry/Adapt | SCR_006769 | Automated Detection and Analysis of ProTrusions | 2026-09-12 12:56:45 | 603 | ||||
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GeneNetwork Resource Report Resource Website 100+ mentions |
GeneNetwork (RRID:SCR_002388) | GeneNetwork, WebQTL | data or information resource, data repository, database, service resource, storage service resource | Web platform that provides access to data and tools to study complex networks of genes, molecules, and higher order gene function and phenotypes. Sequence data (SNPs) and transcriptome data sets (expression genetic or eQTL data sets). Quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. Used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Users are welcome to enter their own private data. | Variation, trait, vertebrate trait ontology, phenotype, systems genetics, quantitative trait, gene mapping, experimental precision medicinenetwork analysis, causal modeling, genomic location, genotype, inbred strain, sex, heterogeneous stock, phenome, phenotype, QTL, expression QTL, genetic reference population, single nucleotide polymorphism, RNA expression, protein expression, metabolite expression, metagenomics, epigenomics, gene-by-environmental interaction, epistasis, FAIR data standards, open source software, FASEB list |
is used by: NIF Data Federation is used by: Hypothesis Center is related to: NIH Data Sharing Repositories has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
NCI U01 CA105417; NCRR U24 RR021760; NIAAA U01 AA014425; NIAAA U01 AA016662; NIAAA U01 AA13499; NIAAA U24 AA13513; NIA R01 AG043930; NIDA P20 DA21131; NIGMS R01 GM123489 |
PMID:8043953 PMID:11737945 PMID:15043217 PMID:15114364 PMID:15043220 PMID:15043219 PMID:15711545 PMID:18368372 PMID:27933521 |
Restricted | nif-0000-00380 | SCR_002388 | GeneNetwork and WebQTL, GeneNetwork / WebQTL, www.genenetwork.org, GeneNetwork WebQTL, The GeneNetwork / WebQTL | 2026-09-12 12:55:40 | 499 | |||||
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Macaque.org Resource Report Resource Website 1+ mentions |
Macaque.org (RRID:SCR_002767) | Macaque.org | data or information resource, disease-related portal, laboratory portal, organization portal, portal, research forum portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on June 8, 2020.Macaque genomic and proteomic resources and how they are providing important new dimensions to research using macaque models of infectious disease. The research encompasses a number of viruses that pose global threats to human health, including influenza, HIV, and SARS-associated coronavirus. By combining macaque infection models with gene expression and protein abundance profiling, they are uncovering exciting new insights into the multitude of molecular and cellular events that occur in response to virus infection. A better understanding of these events may provide the basis for innovative antiviral therapies and improvements to vaccine development strategies. | genomic, hiv, infection, proteomic, virus, simian immunodeficiency virus, influenza virus, animal model | has parent organization: University of Washington; Seattle; USA | Viral infection, Infectious disease | NCRR ; NIAID ; NHLBI ; NIDA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-24370 | SCR_002767 | Macaque.org | 2026-09-12 12:55:46 | 3 |
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