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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | |||||||||
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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 | ||||
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The Hamner Institute for Health Sciences: BMDExpress and The multiple-path particle dosimetry Resource Report Resource Website |
The Hamner Institute for Health Sciences: BMDExpress and The multiple-path particle dosimetry (RRID:SCR_005511) | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 24, 2013. BMDExpress is a Java application used to analyze dose-response data from microarray experiments. The program was designed to perform a stepwise analysis on microarray data that combines bench mark dose (BMD) calculations with gene ontology (GO) classification analysis. The combination provides dose estimates at which different cellular processes are altered at a defined increase in risk based on expression levels in the untreated controls. The fitting of the data to the statistical models (linear, 2 polynomial models, 3 polynomial, and power models) is performed using source code borrowed from the U.S. Environmental Protection Agency''''s BMDS software. The MPPD model is a computational model that can be used for estimating human and rat airway particle dosimetry. The model is applicable to risk assessment, research, and education. The MPPD model calculates the deposition and clearance of monodisperse and polydisperse aerosols in the respiratory tracts of rats and human adults and children (deposition only) for particles ranging in size from ultrafine (0.01 m) to coarse (20 m). The models are based on single-path and multiple-path methods for tracking air flow and calculating aerosol deposition in the lung. The single-path method calculates deposition in a typical path per airway generation, while the multiple-path method calculates particle deposition in all airways of the lung and provides lobar-specific and airway-specific information. Within each airway, deposition is calculated using theoretically derived efficiencies for deposition by diffusion, sedimentation, and impaction within the airway or airway bifurcation. Filtration of aerosols by the head is determined using empirical efficiency functions. The MPPD model includes calculations of particle clearance in the lung following deposition. Eight tutorials are provided so that the user can learn to interact with the software. | aerosol, airway, children, dose-response, human, lung, microarray, rat, respiratory tract, risk assessment |
is related to: BMDExpress is related to: Multiple-Path Particle Dosimetry Model |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10456 | SCR_005511 | BMDExpress & MPPD | 2026-09-12 12:56:27 | 0 | ||||||||
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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 | |||||||
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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 | ||||
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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 | ||||||||
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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 | ||||||
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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 | |||||||
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Latin American Brain Mapping Network (LABMAN) Resource Report Resource Website |
Latin American Brain Mapping Network (LABMAN) (RRID:SCR_005509) | LABMAN | community building portal, data or information resource, portal, service resource, training service resource | On March 8, 2008 in Havana, the Latin American Network for Brain Mapping (LABMAN) was created with participants from Argentina, Brazil, Colombia, Cuba and Mexico. The focus of LABMAN is to promote neuroimaging and systems neuroscience in the region through the implementation of training and exchange programs, and to increase public awareness of the Latin American potential to contribute both to basic and applied research in human brain mapping. The immediate LABMAN goals are to: * Train specialists in all major imaging techniques. * Expedite the transfer of new scientific and technical knowledge from abroad. * Increase the scientific productivity of the region. * Drastically increase the awareness of local governments, international organizations and of the general public of brain mapping results on potential. * Organize multinational projects in areas of special relevance to the region, e.g. nutrition, pediatric development, neurodegeneration. Latin American Brain Mapping Network (LABMAN) participants : * Cuban Neuroscience Center * University of Buenos Aires * University of Sao Paulo * Universidad del Valle, Cal��, Colombia * UAM Iztapalapa, Mexico City, Mexico | neuroimaging, systems neuroscience, human, neuroscience, brain mapping |
has parent organization: Max Planck Institute for Biological Cybernetics; Tubingen; Germany has parent organization: CBRAIN |
PMID:19324094 | nlx_144610 | http://ijbem.k.hosei.ac.jp/2006-/volume10/number4/100407.pdf | SCR_005509 | Latin American Brain Mapping Network | 2026-09-12 12:56:27 | 0 | ||||||
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TreQ Resource Report Resource Website |
TreQ (RRID:SCR_005505) | TreQ | software resource | A software read mapper for high-throughput DNA sequencing reads, in particular one to several hundred nucleotides in length, and for large edit distance between sequencing read and match in the reference genome. It can cope particularly well with indels for single-best hit recall of 200nt reads simulated from the human reference genome. TreQ performs best at a running time comparable to BWA at large edit distance settings. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Rutgers University; New Jersey; USA |
PMID:22962448 | GNU General Public License | OMICS_00695, biotools:treq | https://bio.tools/treq | SCR_005505 | TreQ: Indel-tolerant Read Mapper | 2026-09-12 12:56:27 | 0 | |||||
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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 | |||||
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University of Lleida; Lleida; Spain Resource Report Resource Website |
University of Lleida; Lleida; Spain (RRID:SCR_005500) | UdL | university | University based in Lleida, Spain. It was the first university in Catalonia and the whole Crown of Aragon. It was founded in 1300, using the name of Estudi General de Lleida.Leading institution in Spain for research and education in the fields of Agronomy, Food Technology and Forestry. | is related to: Pharma-Planta Consortium | nlx_158307 | http://www.udl.cat/en/udl.html | SCR_005500 | University of Lleida, Universitat de Lleida | 2026-09-12 12:56:27 | 0 | ||||||||
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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 | |||
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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 | |||||
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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 | ||||||
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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 | |||||
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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 | ||||||
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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 | ||||||||
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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 | |||||
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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 |
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