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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Glide Resource Report Resource Website 10+ mentions |
Glide (RRID:SCR_000187) | Glide | simulation software, software application, software resource | Software package which approximates a complete search of the conformational, orientational, and positional space of the ligand in a given receptor. Used in drug development for predicting protein ligand binding modes and ranking ligands via high throughput virtual screening. | ligand, receptor, docking, computation, virtual, screening, drug, discovery |
is listed by: OMICtools is listed by: SoftCite has parent organization: Schrodinger works with: Ligprep |
PMID:18428795 | Restricted | OMICS_01601 | SCR_000187 | SciCrunch Registry | 2026-11-07 11:53:56 | 17 | |||||||
|
MODENT - A Tool For Reconstructing Gene Regulatory Networks Resource Report Resource Website 1+ mentions |
MODENT - A Tool For Reconstructing Gene Regulatory Networks (RRID:SCR_000220) | ModEnt | software resource | A computational tool that reconstructs gene regulatory networks from high throughput experimental data. | gene regulatory network, experimental data, computation, computational tool, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Tel Aviv University; Ramat Aviv; Israel |
PMID:22216865 | Free, Available for download, Freely available | biotools:modent, OMICS_01685 | https://bio.tools/modent | SCR_000220 | SciCrunch Registry | 2026-11-07 11:53:58 | 1 | ||||||
|
GOLD Resource Report Resource Website 10+ mentions |
GOLD (RRID:SCR_000188) | GOLD | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software for virtual screening and identifying the binding mode of active molecules. It is comprehensively validated, widely used, and allows for high database enrichments. The software utilizes a novel methodology which avoids computationally expensive sequential docking of ligands into multiple protein structures. | virtual screening, binding, active molecules, ligand-protein bonding, computation, protein structures, lead optimization |
is listed by: OMICtools is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01602 | SCR_000188 | SciCrunch Registry | 2026-11-07 11:53:54 | 18 | ||||||||
|
Context Likelihood of Relatedness Resource Report Resource Website 1+ mentions |
Context Likelihood of Relatedness (RRID:SCR_000216) | CLR | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software that infers regulatory interactions between transcription factors and their targets using a compendium of gene expression profiles. | transcription factors, gene expression profile, regulatory interactions, likelihood, relatedness | is listed by: OMICtools | PMID:17214507 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01682 | http://gardnerlab.bu.edu/software&tools.html, | SCR_000216 | SciCrunch Registry | 2026-11-07 11:53:57 | 1 | ||||||
|
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 | SciCrunch Registry | 2026-11-07 11:53:55 | 10 | |||||
|
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 | SciCrunch Registry | 2026-11-07 11:53:54 | 3 | ||||||||
|
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 | SciCrunch Registry | 2026-11-07 11:53:55 | 4 | ||||||||
|
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 | SciCrunch Registry | 2026-11-07 11:53:55 | 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 | SciCrunch Registry | Calpain Cleavage Detector | 2026-11-07 11:53:56 | 4 | ||||||
|
GEB Resource Report Resource Website 1+ mentions |
GEB (RRID:SCR_007395) | GEB | software resource | A Java application developed to visualise distribution of genomic features in high resolution. | is listed by: OMICtools | OMICS_00911 | SCR_007395 | SciCrunch Registry | Genome Environment Browser | 2026-11-07 11:56:13 | 2 | |||||||||
|
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; OD 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 | SciCrunch Registry | , BioGRID, Biological General Repository for Interaction Datasets | 2026-11-07 11:56:23 | 2824 | ||||
|
Taipan Resource Report Resource Website 1+ mentions |
Taipan (RRID:SCR_007330) | Taipan | software resource | A fast hybrid short-read assembly tool. | c, unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19535537 | GNU General Public License, v2 | OMICS_00035, biotools:taipan | https://bio.tools/taipan | SCR_007330 | SciCrunch Registry | 2026-11-07 11:56:22 | 2 | ||||||
|
YM500 Resource Report Resource Website |
YM500 (RRID:SCR_007429) | YM500 | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | An Integrative small RNA Sequencing database for miRNA research and provides an integrative web interface for miRNA quantification, isomiR identification, arm switching discovery, and, most of all, novel miRNA predictions. |
is listed by: OMICtools has parent organization: National Yang-Ming University; Taipei; Taiwan |
OMICS_00386 | SCR_007429 | SciCrunch Registry | YM500 miR-Seq Database | 2026-11-07 11:56:23 | 0 | |||||||||
|
INVERTER Resource Report Resource Website 1+ mentions |
INVERTER (RRID:SCR_007956) | INVERTER | software resource | Software for a de novo exact match tandem repeat finder which main advantage is without the need to specify either the pattern or a particular pattern size, integrated with a data visualization tool and has a built-in user-friendly Graphical User Interface. | is listed by: OMICtools | OMICS_00108 | SCR_007956 | SciCrunch Registry | 2026-11-07 11:56:27 | 3 | ||||||||||
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BigWig and BigBed Resource Report Resource Website 10+ mentions |
BigWig and BigBed (RRID:SCR_007708) | BigWig and BigBed | software resource | Allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser. |
is listed by: OMICtools is related to: UCSC Genome Browser is related to: bedGraphToBigWig has parent organization: University of California at Santa Cruz; California; USA |
OMICS_00626 | SCR_007708 | SciCrunch Registry | 2026-11-07 11:56:26 | 43 | ||||||||||
|
HighSSR Resource Report Resource Website 1+ mentions |
HighSSR (RRID:SCR_007949) | HighSSR | software resource | Software that predicts microsatellites with Tandem Repeats Finder (TRF). |
is listed by: OMICtools has parent organization: Google Code |
PMID:22954626 | OMICS_00107 | SCR_007949 | SciCrunch Registry | highssr - Microsatellites prediction and analysis with next generation sequencing data | 2026-11-07 11:56:27 | 1 | ||||||||
|
GenoTan Resource Report Resource Website 1+ mentions |
GenoTan (RRID:SCR_007935) | GenoTan | software resource | A free software tool to identify length variation of microsatellites from short sequence reads. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24135263 | GNU General Public License, v3 | biotools:genotan | https://bio.tools/genotan | SCR_007935 | SciCrunch Registry | GenoTan - Genotyping of microsatellite loci | 2026-11-07 11:56:27 | 1 | |||||
|
VISTA Enhancer Browser Resource Report Resource Website 100+ mentions |
VISTA Enhancer Browser (RRID:SCR_007973) | VISTA Enhancer Browser | data or information resource, data repository, database, service resource, storage service resource | Resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. Central public database of experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to particular tissue, or download entire collections of enhancers with defined tissue specificity or conservation depth. | human, noncoding fragment, mutant mouse strain, molecular neuroanatomy resource, image, telencephalon, development, genome, enhancer, dna fragment, embryo, embryonic mouse, brain, neural tube, eye, ear, heart, tail, limb, nose, cranial nerve, trigeminal, dorsal root ganglia, face, branchial arch, gene expression, annotation, vector, transgenic embryo, lacz reporter vector, lacz, biomaterial supply resource, in vivo, image collection, transcriptional enhancer, chip-seq, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: NIF Data Federation is related to: One Mind Biospecimen Bank Listing is related to: OMICtools has parent organization: Lawrence Berkeley National Laboratory |
American Heart Association ; DOE contract DE-AC02-05CH11231; DOE DE020060; NHGRI HG003988; NHLBI HL066681; NIDCR ; NINDS NS062859 |
PMID:17130149 | Free, Freely available | nif-0000-03637, OMICS_01568, biotools:vista_enhancer_browser | https://bio.tools/vista_enhancer_browser | SCR_007973 | SciCrunch Registry | 2026-11-07 11:56:22 | 249 | |||||
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RSEG Resource Report Resource Website 10+ mentions |
RSEG (RRID:SCR_007695) | RSEG | software resource | Software package aimed to analyze ChIP-Seq data, especially for identifying genomic regions and their boundaries marked by diffusive histone modification markers, such as H3K36me3 and H3K27me3. |
is listed by: OMICtools has parent organization: University of Southern California; Los Angeles; USA |
PMID:21325299 | Free | OMICS_00459 | SCR_007695 | SciCrunch Registry | 2026-11-07 11:56:18 | 14 | ||||||||
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Annotation-Modules Resource Report Resource Website |
Annotation-Modules (RRID:SCR_008025) | Annotation-Modules | software resource | A tool for finding significant combinations of multisource annotations in gene lists. | is listed by: OMICtools | OMICS_00630 | SCR_008025 | SciCrunch Registry | 2026-11-07 11:56:23 | 0 |
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