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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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3DMeshMetric Resource Report Resource Website 1+ mentions |
3DMeshMetric (RRID:SCR_000043) | 3DMeshMetric | data processing software, data visualization software, software resource, software application | Software visualization tool based on the VTK library. Its main feature is to measure and display surface-to-surface distance between two triangle meshes using user-specified uniform sampling. Offers all the basic tools to visualize meshes such as color, opacity, smoothing, down sampling or type of representation. | visualize meshes, color, opacity, smoothing, down sampling, type of representation, | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155578 | SCR_000043 | 2026-08-12 10:48:09 | 2 | ||||||||
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OntoMorph Tab Resource Report Resource Website |
OntoMorph Tab (RRID:SCR_000443) | data processing software, data analysis software, software resource, software application | OntoMorph is a tab plugin for Protege-OWL 3 that allows a user to mark-up portions of a Neurolucida neuron morphology with OWL instances. A user loads a Neurolucida morphology file, either from their hard drive or from an arbitrary URL, into an interface that allows them to zoom, rotate, and translate the morphology. The interface allows them to select points on the morphology to indicate points, segments, or subtrees of the morphology they wish to assign to an OWL instance. After this selection has been made, OntoMorph saves the selection to the currently active OWL instance in the ontology that is currently loaded into Protege. No modifications are made to the Neurolucida file itself. As a result, an association is created between that portion of the morphology and the OWL instance, such that selecting the OWL instance allows retrieval of the portion. Upon retrieval, the morphology portion can be highlighted, so the user can keep track of what pieces each instance refer to. | annotation, java, morphology, neurolucida, neuron, neuroscience, plugin, protege, software, ontology, owl | has parent organization: University of California at San Diego; California; USA | Free, Available for download, Freely available | nif-0000-24916 | SCR_000443 | OntoMorph | 2026-08-12 10:48:13 | 0 | ||||||||
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GMATo Resource Report Resource Website 1+ mentions |
GMATo (RRID:SCR_000165) | sequence analysis software, software application, data processing software, software resource, data analysis software | A software tool used for simple sequence repeats (SSR) or microsatellite characterization. It also facilitates SSR marker design on a genomic scale, microsatellite mining at any length, and comprehensive statistical analysis for DNA sequences in any genome at any size. Analysis parameters are customizable. | simple sequence repeat, ssr, microsatellite, genomic, marker design, sequence analysis software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23861572 | Free, Available for download, Freely available | OMICS_00106 | SCR_000165 | Genome-wide Microsatellite Analyzing Tool, Genome Microsatellite Analyzing Tool, Genome-wide Microsatellite Analyzing Tool (GMATo) | 2026-08-12 10:48:10 | 1 | |||||||
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TADS - Treatment for Adolescents with Depression Study Resource Report Resource Website 1+ mentions |
TADS - Treatment for Adolescents with Depression Study (RRID:SCR_000037) | TADS | portal, data or information resource, clinical trial, disease-related portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Multi-site clinical research study examining the short- and long-term effectiveness of an antidepressant medication and psychotherapy alone and in combination for treating depression in adolescents ages 12 to 17. For teens treated in TADS, the trial is designed to provide best-practice practical care for depression. | clinical trial, adolescent, major depressive disorder, depressive disorder, cognitive behavioral therapy, psychotherapy, drug, fluoxetine, nct00006286, young human |
is used by: Limited Access Datasets From NIMH Clinical Trials has parent organization: Duke University School of Medicine; North Carolina; USA has parent organization: ClinicalTrials.gov |
Major Depressive Disorder, Depressive Disorder | NIMH 1U01MH064107-01A1 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_146236 | SCR_000037 | Treatment for Adolescents with Depression Study (TADS), Treatment for Adolescents with Depression Study | 2026-08-12 10:48:09 | 2 | |||||
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INCF Dataspace Resource Report Resource Website 1+ mentions |
INCF Dataspace (RRID:SCR_000158) | DataSpace | service resource, data repository, storage service resource |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 21, 2017. Repository for sharing of neuroscience data, text, images, sounds, movies, models and simulations. |
neuroscience, text, image, sound, video, model, simulation, data sharing, preservation | has parent organization: International Neuroinformatics Coordinating Facility | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157665 | SCR_000158 | 2026-08-12 10:48:10 | 2 | ||||||||
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University of Tennessee Genome Science and Technology Graduate Program Resource Report Resource Website |
University of Tennessee Genome Science and Technology Graduate Program (RRID:SCR_000038) | UTK GST, UT Knoxville GST | data or information resource, portal, graduate program resource, organization portal | Graduate School of Genome Science and Technology (GST) is a Life Science graduate program founded on two premises. First, whole-genome sequences and related large-scale datasets have transformed how we perform biological research, a trend that is gathering momentum and is anticipated to frame the way the biology research is accomplished for many years to come. Second, advances in technology, whether at the level of instrumentation, computation, or wet lab reagents, have long been a powerful driving force in biology. The GST program is home to faculty mentors from many walks of life. The virulence factors of pathogenic fungi and the engineering of photosynthetic reaction complexes for bioenergy harvesting are just two examples from the cornucopia of research projects being pursued in GST. | genome, molecular genetics, biochemistry, bioinformatics | has parent organization: University of Tennessee Knoxville; Tennessee; USA | nlx_149162 | SCR_000038 | UTK Genome Science & Technology, UT Genome Science & Technology, UT-ORNL Graduate School of Genome Science and Technology, Graduate School of Genome Science and Technology, University of Tennessee Genome Science & Technology, University of Tennessee Genome Science Technology | 2026-08-12 10:48:09 | 0 | ||||||||
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BlackOPs Resource Report Resource Website |
BlackOPs (RRID:SCR_000032) | sequence analysis software, software application, data processing software, software resource, data analysis software | Open source software tool that simulates experimental RNA-seq and DNA whole exome sequences derived from reference genome, aligns these sequences by custom parameters, detects variants and outputs blacklist of positions and alleles caused by mismapping. Used to characterize mappability of RNA-Seq reads and create blacklist of genomic positions of mismapped reads. This blacklist is used to filter potential false positives from variant or RNA editing calls. | rna seq, false positive, genome editing, rna editing, mismapped reads | has parent organization: SourceForge | PMID:23935067 | Free, Available for download, Freely available | OMICS_01229 | SCR_000032 | BlackOPs: RNA-Seq Variant Blacklist Tool | 2026-08-12 10:48:09 | 0 | |||||||
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WILEY Interdisciplinary Reviews Resource Report Resource Website |
WILEY Interdisciplinary Reviews (RRID:SCR_000392) | WIREs | data or information resource, topical portal, portal | Wiley Interdisciplinary Reviews series combines features of encyclopedic reference works and review journals in innovative online format. They are designed to promote cross-disciplinary research ethos while maintaining the highest scientific and presentational standards, but should be viewed first and foremost as evolving online databases of cutting-edge reviews. | encyclopedic reference works, review journals, databases of reviews, | nif-0000-10668 | http://www.wiley.com/WileyCDA/Section/id-370078.html | SCR_000392 | Wiley Interdisciplinary Reviews series | 2026-08-12 10:48:13 | 0 | ||||||||
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RCSB PDB Software Tools Resource Report Resource Website 1+ mentions |
RCSB PDB Software Tools (RRID:SCR_000035) | data or information resource, topical portal, portal, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Information Portal to Biological Macromolecular Structures provides variety of software tools made available through the RCSB. These tools include: data extraction and deposition preparation tools, data format conversion and validation tools, data parsing tools, dictionary and data management tools, visualization tools that support PDBx/mmCIF, and other PDBx/mmCIF software library tools. | Information Portal, Biological Macromolecular Structure, RCSB, RCSB software tools, data extraction, format conversion, data parsing, data management, visualization, pdbx/mmcif, pdbx, mmcif |
is listed by: LabWorm is related to: Protein Data Bank Markup Language has parent organization: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31399 | SCR_000035 | RCSB Software Tools | 2026-08-12 10:48:09 | 2 | ||||||||
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DESeq Resource Report Resource Website 500+ mentions |
DESeq (RRID:SCR_000154) | DESeq | data processing software, data analysis software, software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Software for differential gene expression analysis based on the negative binomial distribution. It estimates variance-mean dependence in count data from high-throughput sequencing assays and tests for differential expression. | gene expression, binomial, differential, negative binomial distribution, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is hosted by: Bioconductor |
PMID:20979621 DOI:10.1186/s13059-014-0550-8 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01306, biotools:deseq | https://bio.tools/deseq, https://sources.debian.org/src/r-bioc-deseq2/ | SCR_000154 | 2026-08-12 10:48:10 | 529 | ||||||
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POPBAM Resource Report Resource Website |
POPBAM (RRID:SCR_000464) | POPBAM | data processing software, data analysis software, software resource, software application | A tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome. | next-generation sequencing, evolution, population, bam, genome, evolutionary genetics, c++, short read, sequence alignment, sliding window, command-line, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: University of Rochester; New York; USA |
PMID:24027417 | Free, Available for download, Freely available | biotools:popbam, OMICS_01559 | https://bio.tools/popbam | http://popbam.sourceforge.net/ | SCR_000464 | 2026-08-12 10:48:13 | 0 | |||||
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Glide Resource Report Resource Website 10+ mentions |
Glide (RRID:SCR_000187) | Glide | simulation software, software resource, software application | 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 | 2026-08-12 10:48:11 | 17 | |||||||
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UNAVCO Geodetic Web Services Resource Report Resource Website |
UNAVCO Geodetic Web Services (RRID:SCR_000181) | software resource, data access protocol, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Web services to access UNAVCO data collection. Adding /gps, /met, /pore, /tilt, and /strain gives the sensor JSON description. | geodesy, geophysics, gps, pore, tilt, strain, json, met, data |
is listed by: CINERGI has parent organization: UNAVCO |
THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000177 | SCR_000181 | 2026-08-12 10:48:11 | 0 | |||||||||
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GASV Resource Report Resource Website 1+ mentions |
GASV (RRID:SCR_000061) | GASV | data processing software, data analysis software, software resource, software application | Software tool for identifying structural variants (SVs) from paired-end sequencing data.GASV distribution includes three components that are typically run in succession: the BAM file of unique paired-read mappings is processed; structural variants are identified by clustering discordant fragments; and a probabilistic algorithm improves the specificity of GASV predictions. | paired-end sequencing data, structural variant, probabilistic algorithm, discordant fragment, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GASVPro has parent organization: Brown University; Rhode Island; USA |
Burroughs Wellcome Fund ; Department of Defense Breast Cancer Research ; ADVANCE Program at Brown University ; NSF 0548311 |
PMID:19477992 | Free, Available for download, Freely available | biotools:gasv, OMICS_01352 | http://compbio.cs.brown.edu/projects/gasv/, https://bio.tools/gasv | SCR_000061 | Geometric Analysis of Structural Variants | 2026-08-12 10:48:10 | 4 | ||||
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rtd Resource Report Resource Website |
rtd (RRID:SCR_000337) | data processing software, data analysis software, software resource, software application | Reference-free ddRADseq analysis software tools. The pipeline script generates reference-sorted, indexed BAM from uniqued reads from radtag sequencing lanes. | standalone software | is listed by: OMICtools | PMID:22675423 | Free, Available for download, Freely available | OMICS_03723 | SCR_000337 | 2026-08-12 10:48:12 | 0 | ||||||||
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Clinical Data Interchange Standards Consortium Resource Report Resource Website 10+ mentions |
Clinical Data Interchange Standards Consortium (RRID:SCR_000219) | CDISC | standard specification, nonprofit organization, narrative resource, data or information resource | 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 | 2026-08-12 10:48:11 | 11 | ||||||||
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ChIPmeta Resource Report Resource Website |
ChIPmeta (RRID:SCR_000054) | data processing software, data analysis software, software resource, software application | Software using a Hierarchical hidden Markov model for jointly analyzing ChIP-chip and ChIP-seq datasets. | chip-chip, chip-seq, ChIP-chip and ChIP-seq datasets analysis, | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_02172 | SCR_000054 | ChIPmeta with HHM | 2026-08-12 10:48:09 | 0 | ||||||||
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oneClickCGH Resource Report Resource Website |
oneClickCGH (RRID:SCR_000294) | oneClickCGH | data processing software, data analysis software, software resource, software application | Platform-independent array copy number analysis software that provides straightforward yet comprehensive detection and reporting of copy number changes. | array, comparative genomic hybridization, cytogenetics, copy number variant, copy number analysis, | is listed by: OMICtools | Restricted | OMICS_02050 | SCR_000294 | 2026-08-12 10:48:12 | 0 | ||||||||
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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 | portal, data or information resource, brain bank, material resource, biomaterial supply resource, organization 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 | 2026-08-12 10:48:11 | 2 | |||||
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Fiduswriter Resource Report Resource Website |
Fiduswriter (RRID:SCR_000204) | Fiduswriter | authoring tool, software resource, software application | 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 | 2026-08-12 10:48:11 | 0 |
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