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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
QC-Chain
 
Resource Report
Resource Website
1+ mentions
QC-Chain (RRID:SCR_005438) QC-Chain software resource A software package of quality control tools for next generation sequencing (NGS) data, consisting of both raw reads quality evaluation and de novo contamination screening, which could identify all possible contamination sequences. This QC pipeline supplies a fast, easy-to-use, and parallel processing approach to accomplish the comprehensive QC steps, which could be applied widely to almost all kinds of NGS reads, including genomic, transcriptomic and metagenomic data. next generation sequencing is listed by: OMICtools
has parent organization: Chinese Academy of Sciences; Beijing; China
OMICS_01070 SCR_005438 2026-09-12 12:56:26 4
Bisque database
 
Resource Report
Resource Website
1+ mentions
Bisque database (RRID:SCR_005559) Bisque analysis service resource, data analysis service, data or information resource, data repository, database, image collection, image repository, production service resource, service resource, storage service resource Open source database for exchange and exploration of biological images. Used to store, visualize, organize and analyze images in cloud. Centered around database of images and metadata. microscopy, cell, mouse, confocal, medical, biology, hippocampus, macular degeneration, maize, microtubule, plant, retina has parent organization: Center for Bio-Image Informatics
has parent organization: University of California at Santa Barbara; California; USA
iPlant Collaborative ;
NSF Information Technology Research ;
NSF infrastructure awards ;
NSF IIS-0808772;
NSF ITR-0331697
PMID:20031971 Restricted SCR_008430, nlx_144652, nif-0000-30205 http://bisque.ece.ucsb.edu/client_service/ SCR_005559 Bisque Image Repository, Bio-Image Semantic Query User Environment, Bio-Image Semantic Query User Environment database, Bio-Image Semantic Query User Environment Database 2026-09-12 12:56:28 5
CBRAIN
 
Resource Report
Resource Website
10+ mentions
CBRAIN (RRID:SCR_005513) CBRAIN analysis service resource, data analysis service, production service resource, service resource, software resource, storage service resource A flexible software platform for distributed processing, analysis, exchange and visualization of brain imaging data. The expected result is a middleware platform that will render the processing environment (hardware, operating systems, storage servers, etc...) transparent to a remote user. Interaction with a standard web browser allows application of complex algorithm pipelines to large datasets stored at remote locations using a mixture of network available resources such as small clusters, neuroimaging tools and databases as well as Compute Canada's High Performance Computing Centers (HPC). Though the focus of CBRAIN is providing tools for use by brain imaging researchers, the platform is generalizable to other imaging domains, such as radiology, surgical planning and heart imaging, with profound consequences for Canadian medical research. CBRAIN expanded its concept to include international partners in the US, Germany and Korea. As of December 2010, GBRAIN has made significant progress with the original three partners and has developed new partners in Singapore, China, India, and Latin America. CBRAIN is currently deployed on 6 Compute Canada HPC clusters, one German HPC cluster and 3 clusters local to McGill University Campus, totaling more than 80,000 potential CPU cores. brain, neuroimaging, imaging, middleware, platform, network, data sharing, web application, visualization is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: McGill University; Montreal; Canada
is parent organization of: Latin American Brain Mapping Network (LABMAN)
Free nlx_144612 http://www.nitrc.org/projects/cbrain SCR_005513 2026-09-12 12:56:27 30
PRIMEGENS
 
Resource Report
Resource Website
1+ mentions
PRIMEGENS (RRID:SCR_005474) PRIMEGENS analysis service resource, data analysis service, production service resource, service resource, software resource A Web-based Tool for High-throughput Primer and Probe Design. The program has its different utilities available on its web server. A standalone version is also available. Algorithms: * SSPD - Sequence Specific Primer Design: to design primers for each of the specific sequences given by the user in the query input file against any alternate potential hybridization with any of the sequences given in the database input file. * PSPD - Probe Specific Primer Design: to design primers it selects the gene-specific fragments (probes) to design primer pairs for their PCR amplification. * FSPD Fragment Specific Primer Design: primer design algorithm used when there is a very long query sequence for which multiple primers are required for its amplification. * Check Binding Specificity * Probe Design Only: Probe design algorithm could be used to find sequence-specific probes, which doesn''t show any blast hit against database. Such probe design has been used for targeted sequencing like agilent sure-select technology with next-generation sequencing. primer design, high-throughput primer, probe, microarray, analysis, blast, hybridization, primer, probe design, dna methylation is listed by: OMICtools
has parent organization: University of Missouri; Missouri; USA
DOE ;
DOD ;
NIH
PMID:21415011
PMID:18579568
PMID:17951795
PMID:12424113
Free for academic use, Commercial use requires license OMICS_00637, OMICS_02346 http://digbio.missouri.edu/primegens/ SCR_005474 PRIMEGENS-w3, PRIMEGENS - High-throughput Primer and Probe Design, PRIMEGENSw3 2026-09-12 12:56:26 3
VDJ
 
Resource Report
Resource Website
1+ mentions
VDJ (RRID:SCR_005475) software resource Python package for analysing immune receptor sequences (antibodies and T cell receptors). standalone software, python is listed by: OMICtools PMID:24639495 Apache License, v2 OMICS_04064 SCR_005475 2026-09-12 12:56:26 3
Bowtie
 
Resource Report
Resource Website
10000+ mentions
Bowtie (RRID:SCR_005476) alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource Software ultrafast memory efficient tool for aligning sequencing reads. Bowtie is short read aligner. sequence, analysis, long, reference, read, alignment, gap, local, pair, end, rna, rnaseq, bio.tools is used by: deFuse
is used by: Short Read Sequence Typing for Bacterial Pathogens
is used by: TopHat
is used by: BS Seeker
is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is listed by: SoftCite
is related to: Bowtie 2
has parent organization: Johns Hopkins University; Maryland; USA
is required by: RelocaTE
Amazon Web Services in Education Research ;
NHGRI R01 HG006102;
NIGMS R01 GM083873
PMID:19261174
DOI:10.1186/gb-2009-10-3-r25
Free, Available for download, Freely available biotools:bowtie, OMICS_00653 https://github.com/BenLangmead/bowtie, https://bio.tools/bowtie, https://sources.debian.org/src/bowtie/ SCR_005476 2026-09-12 12:56:26 13799
CASHX
 
Resource Report
Resource Website
1+ mentions
CASHX (RRID:SCR_005477) CASHX software resource Software pipeline to parse, map, quantify and manage large quantities of sequence data. CASHX is a set of tools that can be used together, or as independent modules on their own. The reference genome alignment tools can be used with any reference sequence in fasta format. The pipeline was designed and tested using Arabidopsis thaliana small RNA reads generated using an Illumina 1G. is listed by: OMICtools
has parent organization: Oregon State University; Oregon; USA
NSF MCB-1231726;
NIAI AI43288
PMID:19307293 OMICS_00655 SCR_005477 Cache ASsisted Hash Search with Xor logic Pipeline, CASHX Pipeline, Cache ASsisted Hash Search with Xor logic 2026-09-12 12:56:26 4
MicrobesOnline
 
Resource Report
Resource Website
100+ mentions
MicrobesOnline (RRID:SCR_005507) MicrobesOnline analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource, source code MicrobesOnline is designed specifically to facilitate comparative studies on prokaryotic genomes. It is an entry point for operon, regulons, cis-regulatory and network predictions based on comparative analysis of genomes. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html. microbe, genome, bacteria, archaea, fungi, prokaryote, bio.tools, FASEB list is listed by: Debian
is listed by: bio.tools
has parent organization: Lawrence Berkeley National Laboratory
DOE DE-AC02-05CH11231 PMID:19906701 nlx_144607, biotools:microbesonline https://bio.tools/microbesonline SCR_005507 Microbial Genomics Database, Microbes Online 2026-09-12 12:56:27 166
HeadIT
 
Resource Report
Resource Website
1+ mentions
HeadIT (RRID:SCR_005657) HeadIT data or information resource, data repository, data set, service resource, storage service resource Platform for sharing, download, and re-analysis or meta-analysis of sophisticated, fully annotated, human electrophysiological data sets. It uses EEG Study Schema (ESS) files to provide task, data collection, and subject metadata, including Hierarchical Event Descriptor (HED) tag descriptions of all identified experimental events. Visospatial task data also available from, http://sccn.ucsd.edu/eeglab/data/headit.html: A 238-channel, single-subject EEG data set recorded at the Swartz Center, UCSD, by Arnaud Delorme, Julie Onton, and Scott Makeig is al. electrophysiology, data sharing, eeg, visual-auditory cued attention shift paradigm, adult, early adult human, late adult human, memory task, modified sternberg working memory task, visual, auditory, auditory oddball, memory, task uses: HED Tags
is related to: EEGLAB
has parent organization: University of California at San Diego; California; USA
Normal, Healthy, Others possible NIMH R01-MH084819;
NINDS R01-NS047293
Public, Must agree to Data Use Agreement and Terms of Use., Account required for collaboration and to upload data. nlx_149081 http://headit-beta.ucsd.edu/, http://sccn.ucsd.edu/eeglab/data/headit.html http://HeadIT.org SCR_005657 Human Electrophysiology Anatomic Data & Integrated Tools (HeadIT) Resource, Human Electrophysiology Anatomic Data & Integrated Tools Resource, Human Electrophysiology Anatomic Data & Integrated Tools, Human Electrophysiology Anatomic Data and Integrated Tools (HeadIT) Resource 2026-09-12 12:56:29 5
DiProGB
 
Resource Report
Resource Website
1+ mentions
DiProGB (RRID:SCR_005651) DiProGB software resource Genome browser that encodes the genome sequence by physico-chemical dinucleotide properties such as stacking energy, melting temperature or twist angle. Analyses can be performed for the + and ?, as well as for the double strand. genome, browser, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: Dinucleotide Property Database
PMID:19605418 Free, Freely available biotools:diprogb, OMICS_00880 https://bio.tools/diprogb SCR_005651 DiProGB - The Dinucleotide Properties Genome Browser, Dinucleotide Properties Genome Browser 2026-09-12 12:56:29 4
MagicViewer
 
Resource Report
Resource Website
10+ mentions
MagicViewer (RRID:SCR_005648) MagicViewer software resource Software to easily visualize the short reads alignment, identify the genetic variation and associate with the annotation information of reference genome. MagicViewer provides a user-friendly interface in which large-scale short reads and sequencing depth can be easily visualized in zoomable images under user definable color scheme through an operating system-independent manner with the implement of Java language. Meanwhile, it holds a versatile genetic variation annotation and visualization interface, providing details of the query options, functional classifications, subset selection, sequence association and primer design. dna methylation, bisulfite sequencing is listed by: OMICtools
has parent organization: Wenzhou Medical University; Zhejiang; China
PMID:20444865 Free, Public OMICS_00887 SCR_005648 MagicViewer: Integrated Solution for Next-generation Sequencing Data Visualization and Genetic Variation Detection and Annotation 2026-09-12 12:56:29 16
Bambino
 
Resource Report
Resource Website
1+ mentions
Bambino (RRID:SCR_005649) Bambino analysis service resource, data analysis service, production service resource, service resource, software resource A variant detector and graphical alignment viewer for next-generation sequencing data in the SAM/BAM format, which is capable of pooling data from multiple source files. Bambino may be launched online via Java Web Start or downloaded and run locally. java, next-generation sequencing, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: National Cancer Institute
PMID:21278191 Https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/Bambino_Click-thru-agreement-for-executable_final.txt OMICS_00876, biotools:bambino https://bio.tools/bambino SCR_005649 Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format 2026-09-12 12:56:29 5
MATRICS - Measurement And Treatment Research to Improve Cognition in Schizophrenia
 
Resource Report
Resource Website
1+ mentions
MATRICS - Measurement And Treatment Research to Improve Cognition in Schizophrenia (RRID:SCR_005644) MATRICS knowledge environment Cognitive deficits -- including impairments in areas such as memory, attention, and executive function -- are a major determinant and predictor of long-term disability in schizophrenia. Unfortunately, available antipsychotic medications are relatively ineffective in improving cognition. Scientific discoveries during the past decade suggest that there may be opportunities for developing medications that will be effective for improving cognition in schizophrenia. The NIMH has identified obstacles that are likely to interfere with the development of pharmacological agents for treating cognition in schizophrenia. These include: (1) a lack of a consensus as to how cognition in schizophrenia should be measured; (2) differing opinions as to the pharmacological approaches that are most promising; (3) challenges in clinical trial design; (4) concerns in the pharmaceutical industry regarding the US Food and Drug Administration''s (FDA) approaches to drug approval for this indication; and (5) issues in developing a research infrastructure that can carry out clinical trials of promising drugs. The MATRICS program will bring together representatives of academia, industry, and government in a consensus process for addressing all of these obstacles. Specific goals of the NIMH MATRICS are: * To catalyze regulatory acceptance of cognition in schizophrenia as a target for drug registration. * To promote development of novel compounds to enhance cognition in schizophrenia. * Leverage economic research power of industry to focus on important but neglected clinical targets. * Identify lead compounds and if deemed feasible, support human proof of concept trials for cognition in schizophrenia. schizophrenia, cognitive deficit, memory, attention, executive function, disability, cognition, clinical has parent organization: University of California at Los Angeles; California; USA Schizophrenia NIMH nlx_146271 SCR_005644 Measurement And Treatment Research to Improve Cognition in Schizophrenia, Measurement Treatment Research to Improve Cognition in Schizophrenia 2026-09-12 12:56:29 6
WISECONDOR
 
Resource Report
Resource Website
10+ mentions
WISECONDOR (RRID:SCR_005646) WISECONDOR software resource A set of python scripts that detects fetal chromosomal and subchromosomal duplications and deletions in maternal blood samples., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. is listed by: OMICtools
has parent organization: Netherlands Bioinformatics Centre
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_00354 SCR_005646 WIthin-SamplE COpy Number aberration DetectOR 2026-09-12 12:56:29 12
TRANSPATH
 
Resource Report
Resource Website
1+ mentions
TRANSPATH (RRID:SCR_005640) TRANSPATH analysis service resource, data analysis service, data or information resource, database, production service resource, service resource Database on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices. It can either be used as an encyclopedia, for both specific and general information on signal transduction, or can serve as a network analyzer. Cross-references to important sequence and signature databases such as EMBL/GenBank UniProt/Swiss-Prot InterPro or Ensembl EntrezGene RefSeq are provided. The database is equipped with the tools for data visualization and analysis. It has three modules: the first one is the data, which have been manually extracted, mostly from the primary literature; the second is PathwayBuilder, which provides several different types of network visualization and hence facilitates understanding; the third is ArrayAnalyzer, which is particularly suited to gene expression array interpretation, and is able to identify key molecules within signalling networks (potential drug targets). These key molecules could be responsible for the coordinated regulation of downstream events. Manual data extraction focuses on direct reactions between signalling molecules and the experimental evidence for them, including species of genes/proteins used in individual experiments, experimental systems, materials and methods. This combination of materials and methods is used in TRANSPATH to assign a quality value to each experimentally proven reaction, which reflects the probability that this reaction would happen under physiological conditions. Another important feature in TRANSPATH is the inclusion of transcription factor-gene relations, which are transferred from TRANSFAC, a database focused on transcription regulation and transcription factors. Since interactions between molecules are mainly direct, this allows a complete and stepwise pathway reconstruction from ligands to regulated genes. signal transduction, network analyzer, transcriptional regulator, transcription factor, metabolic pathway, signaling pathway, protein-protein interaction, gene-regulatory pathway, signal transduction pathway, complex, signaling molecule, reaction, molecule, gene, pathway, gene expression is related to: TRANSFAC
is related to: GeneTrail
has parent organization: BIOBASE Corporation
BMBF 031U210B;
BMBF 0313092;
European Union FP6 contract LSHG-CT-2004-503568;
European Union MRTN-CT-2004-512285
PMID:18629064
PMID:16381929
PMID:12519957
PMID:11724734
Free for academic use, Free for non-profit use, Account required nif-0000-03580 http://transpath.gbf.de, http://www.gene-regulation.com/pub/databases.html, http://www.biobase.de/pages/products/databases.html SCR_005640 2026-09-12 12:56:29 3
BS Seeker
 
Resource Report
Resource Website
1+ mentions
BS Seeker (RRID:SCR_005641) data analysis software, data processing software, sequence analysis software, software application, software resource Software which performs accurate and fast mapping of bisulfite-treated short reads. Supplementary information and examples are provided on the site. bisulfite sequencing, sequence analysis software, short read, sequence mapping, bio.tools uses: Bowtie
is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: Bs-Seeker2
has parent organization: University of California at Los Angeles; California; USA
PMID:20416082 Free, Available for download, Freely available OMICS_00578, biotools:bs_seeker https://bio.tools/bs_seeker SCR_005641 Bisulfite Sequence Seeker 2026-09-12 12:56:29 3
Internet Analysis Tools Registry
 
Resource Report
Resource Website
1+ mentions
Internet Analysis Tools Registry (RRID:SCR_005638) IATR data processing software, image analysis software, software application, software repository, software resource A centrally available listing of all image analysis tools that are available to the neuroscience community in order to facilitate the development, identification, and sharing of tools. It is hoped that this helps the tool developers to get their tools to a larger user community and to reduce redundancy (or at least utilize tool redundancy to facilitate optimal tool design) in tool development. This also helps tool users in identification of the existing tools for specific problems as they arise. The registry is designed to be self-moderated. This means that all tool entries are owned by some responsible party who enters the tool information, and keeps it up to date via the Web. database, tool, neuroimaging, image, analysis lists: Extensible MATLAB Medical image Analysis
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Harvard Medical School; Massachusetts; USA
Human Brain Project Public Domain nlx_146252 SCR_005638 IATR - Internet Analysis Tools Registry 2026-09-12 12:56:29 1
COBrA
 
Resource Report
Resource Website
1000+ mentions
COBrA (RRID:SCR_005677) COBrA software resource COBrA is a Java-based ontology editor for bio-ontologies that distinguishes itself from other editors by supporting the linking of concepts between two ontologies, and providing sophisticated analysis and verification functions. In addition to the Gene Ontology and Open Biology Ontologies formats, COBrA can import and export ontologies in the Semantic Web formats RDF, RDFS and OWL. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. ontology, anatomy, browser, ontology or annotation browser is listed by: Gene Ontology Tools
is related to: Gene Ontology
is related to: OBO
has parent organization: University of Edinburgh; Scotland; United Kingdom
BBSRC 15/BEP 17046 PMID:15513995 THIS RESOURCE IS NO LONGER IN SERVICE nlx_149117 SCR_005677 COBrA - An Ontology Browser for Anatomy, COBrA: a bio-ontology editor 2026-09-12 12:56:29 1396
Roth Laboratory
 
Resource Report
Resource Website
1+ mentions
Roth Laboratory (RRID:SCR_005711) Roth Lab data or information resource, laboratory portal, organization portal, portal, software resource The Roth Laboratory is designing and interpreting large-scale experiments to understand pathway structure and its relationship to phenotype and human disease. Software for research focused on a specific research goal is available. Current experimental interests: * Exploiting parallel sequencing technology to phenotype all pairwise gene deletion combinations in S. cerevisiae, with initial application to genes involved in transcription. * Generation of S. cerevisiae strains carrying dozens of chosen targeted deletions, with initial application to delete all ABC transporters imparting multidrug resistance. * Targeted insertion of gene sets encoding entire human pathways into S. cerevisiae, with initial application to genes involved in drug metabolism. Current computational interests: * Systematic analysis of genetic interaction to reveal redundant systems and order of action in genetic pathways * Integrating large-scale studies - including phenotype, genetic epistasis, protein-protein and transcription-regulatory interactions and sequence patterns - to quantitatively assign function to genes and guide experimentation and disease association studies. * Alternative splicing and its relationship to protein interaction networks. gene, pathway, phenotype, disease, transcription, drug metabolism, drug, metabolism, protein-protein interaction, transcription-regulatory interaction, protein interaction, protein has parent organization: University of Toronto; Ontario; Canada
has parent organization: Harvard Medical School; Massachusetts; USA
is parent organization of: FuncAssociate: The Gene Set Functionator
nlx_149163 http://llama.med.harvard.edu SCR_005711 2026-09-12 12:56:30 5
GeneMANIA
 
Resource Report
Resource Website
1000+ mentions
GeneMANIA (RRID:SCR_005709) GeneMANIA analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource Data analysis service to predict the function of your favorite genes and gene sets. Indexing 1,421 association networks containing 266,984,699 interactions mapped to 155,238 genes from 7 organisms. GeneMANIA interaction networks are available for download in plain text format. GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input. If members of your gene list make up a protein complex, GeneMANIA will return more potential members of the protein complex. If you enter a gene list, GeneMANIA will return connections between your genes, within the selected datasets. GeneMANIA suggests annotations for genes based on Gene Ontology term enrichment of highly interacting genes with the gene of interest. GeneMANIA is also a gene recommendation system. GeneMANIA is also accessible via a Cytoscape plugin, designed for power users. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible gene, association data, protein interaction, genetic interaction, pathway, co-expression, co-localization, protein, software library, statistical analysis, term enrichment, analysis, browser, gene ontology, gene predicting, gene prioritization, database or data warehouse, other analysis, interaction browser, protein-protein interaction, interaction, FASEB list is listed by: Gene Ontology Tools
is related to: Cytoscape
is related to: Gene Ontology
is related to: PSICQUIC Registry
has parent organization: University of Toronto; Ontario; Canada
Genome Canada ;
Ontario Ministry of Research and Innovation 2007-OGI-TD-05
PMID:20576703
PMID:18613948
PMID:20926419
Open unspecified license, Free for academic use nlx_149159, r3d100013978 https://doi.org/10.17616/R31NJNA2 SCR_005709 2026-09-12 12:56:30 4535

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