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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 | software resource, software application, data visualization software, data processing software | 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 | 2026-08-08 11:57:11 | 2 | ||||||||
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GUARDD Resource Report Resource Website |
GUARDD (RRID:SCR_000040) | software resource | MATLAB software designed to organize, automate, and enhance the analytical procedures which operate on CPMG RD NMR data. | standalone software, matlab, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:22160811 | Free, Available for download, Freely available | biotools:guardd, OMICS_04020 | https://bio.tools/guardd | SCR_000040 | Graphical User-friendly Analysis of Relaxation Dispersion Data | 2026-08-08 11:57:11 | 0 | ||||||
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flowCL Resource Report Resource Website |
flowCL (RRID:SCR_000046) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for semantic labelling of flow cytometric cell populations. | software package, mac os x, unix/linux, windows, r, flow cytometry |
has parent organization: Bioconductor has parent organization: BC Cancer Agency |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05594 | SCR_000046 | flowCL - Semantic labelling of flow cytometric cell populations | 2026-08-08 11:57:11 | 0 | ||||||||
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CG-Pipeline Resource Report Resource Website |
CG-Pipeline (RRID:SCR_000047) | software resource | A software tool for assembling genome sequence data and running feature prediction and annotation tools on the assembly. | perl | has parent organization: SourceForge | PMID:20519285 | Free, Available for download, Freely available | OMICS_04062 | http://sourceforge.net/projects/cg-pipeline/ | SCR_000047 | 2026-08-08 11:57:11 | 0 | |||||||
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Cbrowse Resource Report Resource Website |
Cbrowse (RRID:SCR_000044) | software resource | Software providing an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs. | unix/linux, mac os x, windows |
has parent organization: Google Code has parent organization: Miami University; Ohio; USA |
PMID:22789590 | Free, Available for download, Freely available | OMICS_04048 | SCR_000044 | 2026-08-08 11:57:11 | 0 | ||||||||
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Institute for Magnetic Resonance Safety, Education and Research Resource Report Resource Website 1+ mentions |
Institute for Magnetic Resonance Safety, Education and Research (RRID:SCR_000039) | institution | The Institute for Magnetic Resonance Safety, Education, and Research (IMRSER) was formed in response to the growing need for information and research on matters pertaining to magnetic resonance (MR) safety. The IMRSER is the first independent, multidisciplinary, professional organization devoted to promoting awareness, understanding, and communication of MR safety issues through education and research. Mission Statement To promote awareness and understanding of MR safety, To disseminate information regarding current and emerging MR safety issues, To develop and provide materials and resources to facilitate MR safety-related education and training, To respond to critical MR safety issues with a sense of urgency, and To advance the field of MR safety through support of scientific research. Functions and activities of the IMRSER include development of up-to-date MR safety materials and dissemination of this information to the MR community. This is accomplished predominantly through the efforts of the Advisory Boards. Members of the Advisory Boards of the Institute for Magnetic Resonance Safety, Education, and Research (IMRSER) are charged with creating recommendations, guidelines, position papers, and educational materials pertaining to existing or emerging MR safety issues. This is achieved by utilizing the pertinent peer-reviewed literature and by relying on each members extensive clinical, research, or other appropriate experience. Notably, documents developed by the IMRSER incorporate MR safety guidelines and recommendations created by the International Society for Magnetic Resonance in Medicine (ISMRM), the American College of Radiology (ACR), the Food and Drug Administration (FDA), the National Electrical Manufacturers Association (NEMA), the Medical Devices Agency (MDA), the International Electrotechnical Commission (IEC), and other similar organizations. The IMRSERs rigorous development and review process for MR safety documents ensures that authoritative and relevant information is produced in a timely manner for rapid dissemination to the MR community. The MR safety information is provided to MR healthcare professionals and others as hard copy and electronic publications. Additionally, this information is posted on the IMRSER web site as well as on www.MRIsafety.com (currently with over 92,000 registered users). The Institute for Magnetic Resonance Safety, Education, and Research permits all members of the MR community to use the MRI Safety Guidelines posted on this web site. Please be sure to read and understand our disclaimer. | guidelines, human, magnetic resonance, mri, safety | nif-0000-10678 | SCR_000039 | IMRSER | 2026-08-08 11:57:11 | 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 | data or information resource, topical portal, clinical trial, portal, disease-related 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 | 2026-08-08 11:57:11 | 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 | 2026-08-08 11:57:11 | 0 | ||||||||
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BlackOPs Resource Report Resource Website |
BlackOPs (RRID:SCR_000032) | sequence analysis software, software resource, software application, data analysis software, data processing 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 | 2026-08-08 11:57:11 | 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, portal, software resource, topical portal | 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 | 2026-08-08 11:57:10 | 2 | ||||||||
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RmiR.Hs.miRNA Resource Report Resource Website |
RmiR.Hs.miRNA (RRID:SCR_000101) | software resource | Software package for various databases of microRNA Targets. | software package, unix/linux, mac os x, windows, r, annotation data, custom db schema, mirna |
is listed by: OMICtools is related to: CRAN has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05797 | SCR_000101 | RmiR.Hs.miRNA: Various databases of microRNA Targets | 2026-08-08 11:57:13 | 0 | ||||||||
|
GeneTex Resource Report Resource Website 500+ mentions |
GeneTex (RRID:SCR_000069) | commercial organization | An antibody supplier for the purposes of life science and biomedical research. This company has a wide variety of immunological reagents that focus on areas of research such as cancer, cell biology, epigenetics, immunology and infectious diseases. | antibody, antibodies, supplier, immunology, research, cell biology, cancer, epigenetics, infectious diseases, reagents | nlx_152372 | SCR_000069 | 2026-08-08 11:57:12 | 691 | |||||||||||
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nFuse Resource Report Resource Website 1+ mentions |
nFuse (RRID:SCR_000066) | nFuse | software resource | Software that predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole Genome Shotgun Sequencing (WGSS). | cancer, genomics |
is listed by: OMICtools is listed by: Google Code has parent organization: Simon Fraser University; British Columbia; Canada |
Cancer | PMID:22745232 | Free, Available for download, Freely available, | OMICS_01353 | SCR_000066 | nFuse: Discovery of Complex Genomic Rearrangements in Cancer | 2026-08-08 11:57:12 | 2 | |||||
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GASV Resource Report Resource Website 1+ mentions |
GASV (RRID:SCR_000061) | GASV | software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 11:57:12 | 4 | ||||
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ChIPmeta Resource Report Resource Website |
ChIPmeta (RRID:SCR_000054) | software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 11:57:12 | 0 | ||||||||
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FACS Resource Report Resource Website 1+ mentions |
FACS (RRID:SCR_000055) | FACS | software resource | Software for classification of Sequences using Bloom filters that can accurately and rapidly align sequences to a reference sequence. | unix/linux, sequence, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SciLifeLab |
PMID:20472541 | Free, Available for download, Freely available | OMICS_02147, biotools:facs | https://bio.tools/facs | SCR_000055 | Fast and Accurate Classification of Sequences | 2026-08-08 11:57:11 | 6 | |||||
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Batman-Seq Resource Report Resource Website |
Batman-Seq (RRID:SCR_000048) | Batman-Seq | software resource | A fast BWT-based short reads mapping tools which uses additional statistical method to model error profile of the sequencing experiment. | c++ | is hosted by: SourceForge | Free, Available for download, Freely available | OMICS_00651 | SCR_000048 | Basic Alignment Tool for MAny Nucleotides | 2026-08-08 11:57:11 | 0 | |||||||
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HUPO Antibody Initiative Resource Report Resource Website 1+ mentions |
HUPO Antibody Initiative (RRID:SCR_004568) | HAI | data or information resource, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022.The mission of the Human Antibody Initiative (HAI) aims to promote and facilitate the use of antibodies for proteomics research. The initiative consists of two separate activities; (1) the generation of a catalogue of validated antibodies from many different sources and (2) a protein atlas for the expression and localization of human proteins in normal and disease tissue. The two separate activities have as their primary deliverables to generate databases with free public accessibility. The Antibody Resource database (www.antibodypedia.org) is aimed to produce a comprehensive catalogue of validated antibodies towards human proteins. This initiative depends on input from a large number of academic groups and commercial companies. The Protein Atlas initiative (www.proteinatlas.org) is aimed to provide comprehensive and annotated database of high-resolution images showing tissue profiles in normal and cancer tissues. Both databases will be open to the public without restriction (no passwords). | antibody, human |
has parent organization: HUPO - Human Proteome Organisation is parent organization of: The Human Protein Atlas |
Knut and Alice Wallenberg Foundation | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_56399 | http://www.hupo.org/research/hai/ | SCR_004568 | HUPO Human Antibody Initiative, HUPO HAI, Human Antibody Initiative | 2026-08-08 11:58:24 | 1 | |||||
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Brighter Ideas Inc. Resource Report Resource Website |
Brighter Ideas Inc. (RRID:SCR_004689) | commercial organization, antibody supplier, reagent supplier, material resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 17,2021. An Antibody supplier | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152322 | SCR_004689 | Bii, Brighter Ideas Inc., Brighter Ideas Inc | 2026-08-08 11:58:25 | 0 | ||||||||||
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Oscar3 Resource Report Resource Website 1+ mentions |
Oscar3 (RRID:SCR_004561) | Oscar | software resource | OSCAR is software for the semantic annotation of chemistry papers. The modules OPSIN (a name to structure converter) and ChemTok (a tokeniser for chemical text) are also available as standalone libraries. This tool for shallow, chemistry-specific parsing of chemical documents identifies (or attempts to identify): * Chemical names: singular nouns, plurals, verbs etc., also formulae and acronyms, some enzymes and reaction names. * Ontology terms: if you can do it by string-matching, you can get OSCAR to do it. * Chemical data: Spectra, melting/boiling point, yield etc. in experimental sections. In addition, where possible the chemical names that are detected are annotated with structures, either via lookup or name-to-structure parsing (OPSIN), and with identifiers from the chemical ontology ChEBI Current work on OSCAR3 by Peter Corbett focuses on its use in SciBorg, a framework for the deep parsing of chemical text. OSCAR3 also includes the Oscar Server, a Jetty-powered set of servlets. These provide the following services: * Parsing of text/HTML by OSCAR. * Text/InChI/SMILES/SMILES substructues/SMILES similarity search of papers, coupled with keyword and ontology-based search, using Lucene and the CDK. * List of all names found / all names that co-occur with a search term or terms. * Online management of a chemical/stopword lexicon. * Manual editing of SciXML fragments containing named entities, for creating of gold standards and training data. Oscar3 can be found on SourceForge: http://sourceforge.net/projects/oscar3-chem/ | annotation, chemistry |
is related to: U-Compare has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:21999457 | nlx_55584 | SCR_004561 | OSCAR, Open Source Chemistry Analysis Routines | 2026-08-08 11:58:23 | 3 |
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