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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Clinical Data Interchange Standards Consortium Resource Report Resource Website 10+ mentions |
Clinical Data Interchange Standards Consortium (RRID:SCR_000219) | CDISC | data or information resource, narrative resource, nonprofit organization, standard specification | A global, open, multidisciplinary, non-profit organization that has established standards to support the acquisition, exchange, submission and archive of clinical research data and metadata. Its mission is to develop and support global, platform-independent data standards that enable information system interoperability to improve medical research and related areas of healthcare. CDISC standards are vendor-neutral, platform-independent and freely available via the CDISC website. | clinical, data sharing, interoperability, medical, healthcare, clinical research data and metadata, |
is used by: TRANSFoRm Clinical Research Information Model is related to: Critical Path to TB Drug Regimens is related to: eTRIKS |
Free | nlx_157914 | SCR_000219 | 2026-09-12 12:55:05 | 11 | ||||||||
|
GENIE3 Resource Report Resource Website 10+ mentions |
GENIE3 (RRID:SCR_000217) | GENIE3 | software resource | An algorithm for the inference of gene regulatory networks from expression data. | javascript, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20927193 | Free, Available for download, Freely available | biotools:genie3, OMICS_01683 | https://bio.tools/genie3 | http://www.montefiore.ulg.ac.be/~huynh-thu/software.html | SCR_000217 | 2026-09-12 12:55:05 | 10 | |||||
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Inferelator Resource Report Resource Website 1+ mentions |
Inferelator (RRID:SCR_000218) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Algorithm for learning parsimonious regulatory networks from systems biology data sets de novo. Software that utilizes inference algorithm to model genetic regulatory networks.Inferelator 2.0 is scalable framework for reconstruction of dynamic regulatory network models., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | modeling, inference algorithm, halobacterium, genetic regulatory network, learning regulatory network, model gene regulatory network | is listed by: OMICtools | PMID:23525069 PMID:16686963 PMID:19964678 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01684 | SCR_000218 | 2026-09-12 12:55:05 | 3 | ||||||||
|
High-Throughput GoMiner Resource Report Resource Website 1+ mentions |
High-Throughput GoMiner (RRID:SCR_000173) | software resource, web application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A web program that organizes lists of genes of interest (for example, under- and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology and automates the analysis of multiple microarrays then integrates the results across all of them in exportable output files and visualizations. High-Throughput GoMiner is an enhancement of GoMiner and is implemented with both a command line interface and a web interface. The program can also: efficiently perform automated batch processing of an arbitrary number of microarrays; produce a human- or computer-readable report that rank-orders the multiple microarray results according to the number of significant GO categories; integrate the multiple microarray results by providing organized, global clustered image map visualizations of the relationships of significant GO categories; provide a fast form of false discovery rate multiple comparisons calculation; and provide annotations and visualizations for relating transcription factor binding sites to genes and GO categories. | term enrichment, gene ontology, gene, microarray, common variable immune deficiency, high-throughput, visualization, database |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: GoMiner has parent organization: National Cancer Institute has parent organization: National Cancer Institute |
NCI 1Z01BC010842-01 | PMID:15998470 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149300 | SCR_000173 | 2026-09-12 12:55:04 | 2 | |||||||
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c3net Resource Report Resource Website 1+ mentions |
c3net (RRID:SCR_000212) | software resource | Software package that allows inferring gene regulatory networks with direct physical interactions from microarray expression data using C3NET. | gene regulation, microarray expression, c3net | is listed by: OMICtools | PMID:20920161 | Free, Available for download, Freely available | OMICS_01681 | SCR_000212 | 2026-09-12 12:55:05 | 4 | ||||||||
|
Washington University School of Medicine Knight Alzheimers Disease Research Center Resource Report Resource Website 1+ mentions |
Washington University School of Medicine Knight Alzheimers Disease Research Center (RRID:SCR_000210) | ADRC, Knight ADRC | biomaterial supply resource, brain bank, data or information resource, material resource, organization portal, portal, tissue bank | The Charles F. and Joanne Knight Alzheimer Disease Research Center (Knight ADRC) supports researchers and our surrounding community in their pursuit of answers that will lead to improved diagnosis and care for persons with Alzheimer disease (AD). The Center is committed to the long-term goal of finding a way to effectively treat and prevent AD. The Knight ADRC facilitates advanced research on the clinical, genetic, neuropathological, neuroanatomical, biomedical, psychosocial, and neuropsychological aspects of Alzheimer disease, as well as other related brain disorders. | genetic, alzheimers disease, biomedical, brain, clinical, cure, dementia, development, disease, neuroanatomical, neurodegenerative disease, neuropathological, neuropsychological, research, senile, treatment, aging |
has parent organization: Washington University in St. Louis; Missouri; USA is parent organization of: Washington University School of Medicine Knight ADRC Request Center Resources Core Facility |
Alzheimer's disease, Dementia, Aging | NIA P50 AG05681 | Available to affiliated researchers, Public | SCR_008779, nif-0000-11285, nlx_144153 | SCR_000210 | Knight Alzheimers Disease Research Center, Washington University School of Medicine in St. Louis Knight ADRC, ADRC, WU Knight ADRC, WUADRC, Knight ADRC, Knight Alzheimer's Disease Research Center, Charles F. and Joanne Knight Alzheimer's Disease Research Center | 2026-09-12 12:55:05 | 2 | |||||
|
Fiduswriter Resource Report Resource Website |
Fiduswriter (RRID:SCR_000204) | Fiduswriter | authoring tool, software application, software resource | An online collaborative editor for academics that use citations and/or formulas. The editor focuses on the content rather than the layout, so that with the same text, it can be published in multiple ways: On a website, as a printed book, or as an ebook. | authoring, collaboration, academic, citation | is listed by: FORCE11 | Free, Available for download, Freely available | nlx_156046 | http://www.force11.org/node/4729 | SCR_000204 | Fidus Writer | 2026-09-12 12:55:04 | 0 | ||||||
|
GraBCas Resource Report Resource Website |
GraBCas (RRID:SCR_000205) | GraBCas | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software tool for predicting granzyme B and caspase cleavage sites. | matlab, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:15980455 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01674, biotools:grabcas | https://bio.tools/grabcas | SCR_000205 | 2026-09-12 12:55:05 | 0 | ||||||
|
GPS-Calpain Cleavage Detector Resource Report Resource Website 1+ mentions |
GPS-Calpain Cleavage Detector (RRID:SCR_000202) | GPS-CCD | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software package for the prediction of calpain cleavage sites. | calpain, cleavage detector, prediction | is listed by: OMICtools | PMID:21533053 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01673 | SCR_000202 | Calpain Cleavage Detector | 2026-09-12 12:55:04 | 4 | ||||||
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Queensland Cyber Infrastructure Foundation Ltd Resource Report Resource Website |
Queensland Cyber Infrastructure Foundation Ltd (RRID:SCR_000208) | QCIF | nonprofit organization | Provides digital infrastructure capabilities for research and innovation across Queensland and Australia. Provides services, infrastructure and support for computation and data driven collaborative research and its application in industry. Members are six Queensland universities – The University of Queensland, Queensland University of Technology, Griffith University, James Cook University, CQUniversity, and the University of Southern Queensland. The University of the Sunshine Coast is an associate member. Member employees provide support and development services. | bioinformatics, contract, software, infrastructure, proteomics, metabolomics, clinical, dataset, analysis |
is listed by: ScienceExchange has parent organization: University of Queensland; Brisbane; Australia is parent organization of: QFAB Bioinformatics |
Commonwealth Government of Australia ; funded through its members ; Queensland Government Department of Employment Economic Development and Innovation |
Available to the research community in Australia | SciEx_4541 | http://www.scienceexchange.com/facilities/4541 | SCR_000208 | Queensland Parallel Supercomputing Foundation, qcif, the Queensland Cyber Infrastructure Foundation | 2026-09-12 12:55:05 | 0 | |||||
|
Multiple Myeloma Research Foundation Resource Report Resource Website 1+ mentions |
Multiple Myeloma Research Foundation (RRID:SCR_000207) | MMRF | institution | Research foundation that funds research to develop new treatments for multiple myeloma, an incurable blood cancer. | drug, treatment, cancer | is parent organization of: MMRF CoMMpass Study | Multiple myeloma | ISNI: 0000 0000 9350 5788, Crossref funder ID: 100001253, nlx_157895, Wikidata: Q6934894, grid.429426.f | https://ror.org/03ww1bx13 | SCR_000207 | 2026-09-12 12:55:05 | 9 | |||||||
|
Ohio Northern University; Ohio; USA Resource Report Resource Website |
Ohio Northern University; Ohio; USA (RRID:SCR_000362) | ONU | university | A public university in Ohio with land, sea and space grants that offers degree programs and research at the undergraduate and graduate level. | land, sea, space, grant, ohio, public | is parent organization of: Ohio Northern University College of Pharmacy | Wikidata:Q1683585, grid.261323.7, nlx_143792, ISNI:0000 0001 2187 1348 | https://ror.org/052963a64 | SCR_000362 | 2026-09-12 12:55:08 | 0 | ||||||||
|
riboPicker Resource Report Resource Website 1+ mentions |
riboPicker (RRID:SCR_000360) | software resource | Software to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. | standalone software, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22155869 | Free, Available for download, Freely available | OMICS_02618, biotools:ribopicker | https://bio.tools/ribopicker | SCR_000360 | 2026-09-12 12:55:07 | 2 | |||||||
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ARACHNE Resource Report Resource Website 1+ mentions |
ARACHNE (RRID:SCR_000351) | ARACHNE | software resource | A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads. | genome, sequencing, analysis, sanger, chemistry, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
PMID:11779843 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01812, biotools:arachne | https://bio.tools/arachne | SCR_000351 | ARACHNE: a whole-genome shotgun assembler, ARACHNE (Unsupported) | 2026-09-12 12:55:07 | 3 | |||||
|
ParseCNV Resource Report Resource Website 1+ mentions |
ParseCNV (RRID:SCR_000355) | software resource | Software that takes CNV calls as input and creates SNP based statistics for CNV occurrence in cases and controls then calls CNVRs based on neighboring SNPs of similar significance. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23293001 | Free, Available for download, Freely available | OMICS_02566 | SCR_000355 | 2026-09-12 12:55:07 | 1 | ||||||||
|
Kinannote Resource Report Resource Website 1+ mentions |
Kinannote (RRID:SCR_000352) | software resource | Software that identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine / threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com. | standalone software, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23904509 | Free, Available for download, Freely available | OMICS_05965 | SCR_000352 | 2026-09-12 12:55:07 | 2 | ||||||||
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HudsonAlpha Genomics Services Lab Resource Report Resource Website |
HudsonAlpha Genomics Services Lab (RRID:SCR_000353) | HudsonAlpha Genomics Services Lab | service resource | A lab that offers genetic research tools such as RNA sequencing and a variety of arrays. | genome, sequencing, assembly, rna, microarray, exome | is listed by: ScienceExchange | THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_221 | SCR_000353 | HudsonAlpha Institute for Biotechnology Genomics Services Lab, Genomics Services Lab | 2026-09-12 12:55:07 | 0 | |||||||
|
Jnomics Resource Report Resource Website |
Jnomics (RRID:SCR_000348) | software resource | A collection of cloud-scale DNA sequence analysis tools. | mapreduce |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_04074 | SCR_000348 | 2026-09-12 12:55:07 | 0 | |||||||||
|
ABrowse Resource Report Resource Website 1+ mentions |
ABrowse (RRID:SCR_000345) | software resource | A genome browser framework which gives an open browsing experience, open data access, collaborative work support, and a framework to import annotations. Multiple data access approaches are supported for external platforms to retrieve data from ABrowse. This resource also contains an online user-space in which users can create, store and share comments, annotations and landmarks. | genome browser, collaborative work, open data access, collaborative work support, framework, import annotation |
is listed by: OMICtools is related to: Galaxy |
PMID:22222089 | Free, Available for download, Freely available | OMICS_00899 | SCR_000345 | 2026-09-12 12:55:07 | 4 | ||||||||
|
GPViz Resource Report Resource Website |
GPViz (RRID:SCR_000346) | GPViz | software resource | A versatile Java-based software used for dynamic gene-centered visualization of genomic regions and/or variants. | gene, visualization, genomic, variant, bioinformatics, java | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_00915 | SCR_000346 | 2026-09-12 12:55:07 | 0 |
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