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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Sanford Burnham Prebys Medical Discovery Institute High-content Screening Core Facility Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute High-content Screening Core Facility (RRID:SCR_014869) | HCS | material resource, instrument supplier | Core facility that provides access to the HTS plate and liquid handling infrastructure of the screening center, as well as the screening center�s cell culture facility. Other services include assay development, screening, and data analysis/mining expertise and services for high content screens. Consultation from the team is available for high content image-based screens including sample preparation, image acquisition, image analysis, image data management, and algorithm development. | facility, la jolla, high content screening, assay, phenotype, data mining, analysis, image analysis, development | Commercially available | SCR_014869 | SBP Medical Discovery Institute High-content Screening Core Facility, SBP High-content Screening Core Facility | 2026-08-03 09:35:55 | 0 | |||||||||
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Sanford Burnham Prebys Medical Discovery Institute NMR Facility Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute NMR Facility (RRID:SCR_014861) | material resource, instrument supplier | Facility that acts as a centralized shared resource for NMR studies on proteins, peptides, small molecules, and carbohydrates in solution or in solid state. It provides instrumentation and expertise for NMR data collection. It also provides consultation with investigators on the feasibility of NMR for structural studies of protein candidates, as well as the optimal method to obtain solution structures and binding information by multi-dimensional NMR techniques. It can also train users in basic spectrometer operations, trouble-shoot for instrumental and operational problems, and set up NMR experiments for users as requested. | facility, medical, nmr, protein, peptide, small molecules, carbohydrates, data collection, consultation, spectrometer, linux, software, analysis | Commercially available | SCR_014861 | SBP NMR Facility, SBP Medical Discovery Institute NMR Facility | 2026-08-03 09:35:39 | 0 | ||||||||||
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Sanford Burnham Prebys Medical Discovery Institute Protein Analysis Core Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute Protein Analysis Core (RRID:SCR_014862) | material resource, instrument supplier | Facility that provides a variety of analytical services focused on biophysical characterization of structural and functional properties of proteins in solution, under native, non-denaturing conditions. Examples of services include quality control of protein samples (folding, stability, aggregation); measuring molecular weight of proteins, protein complexes, oligomers and assemblies; charcaterizing protein conformation and shape in solution; determining oligomeric state of protein (including stoichiometry and Kd for self-association) and measuring protein binding to proteins, peptides, small molecules, compounds, metals, nucleotides and other ligands (including determination of equilibrium (Kd) and kinetic rate (kon, koff) constants, stoichiometry, binding enthalpy and entropy). | facility, la jolla, protein, analysis, quality control, molecular weight, stoichiometry | Commercially available | SCR_014862 | SBP Medical Discovery Institute Protein Analysis Core, SBP Protein Analysis Core | 2026-08-03 09:35:54 | 0 | ||||||||||
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regist custom genome Resource Report Resource Website 1+ mentions |
regist custom genome (RRID:SCR_015999) | software resource, source code | One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide.. Regist custom genome software registers custom genomes to Genome Explorer (IN: FASTA). | analysis, pipeline, maser, genome, explorer, fasta, custom, register | Ministry of Education ; Culture ; Sports ; Science and Technology ; Japan |
Restricted | http://cell-innovation.nig.ac.jp/maser_cgi/cip-pl_list_violin_en.cgi | SCR_015999 | Management and Analysis System for Enormous Reads: regist custom genome | 2026-08-03 09:36:16 | 1 | ||||||||
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nSolver Analysis Software Resource Report Resource Website 100+ mentions |
nSolver Analysis Software (RRID:SCR_003420) | nSolver Analysis Software | data processing software, software application, software resource | Data analysis software program that offers nCounter users the ability to QC, normalize, and analyze data without having to purchase additional software packages. | normalization, analysis, ncounter, os x, windows, quality control | is listed by: OMICtools | Restricted | OMICS_02309 | https://nanostring.app.box.com/v/nSolver-AdvancedAnalysis, https://nanostring.com/products/ncounter-analysis-system/ncounter-analysis-solutions/nsolver-data-analysis-support/ | SCR_003420 | 2026-08-04 09:40:54 | 395 | |||||||
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DEAP - Data Exploration and Analysis Portal Resource Report Resource Website 10+ mentions |
DEAP - Data Exploration and Analysis Portal (RRID:SCR_016158) | DEAP | data access protocol, software resource, web service | Web service for data exploration and analysis of the ABCD Study - the largest long-term study of brain development and child health in the United States. | data, exploration, analysis, portal, brain, development, child, health, United, States, long, term, study | is related to: ABCD Study | Free, Available for download | SCR_016158 | DEAP: Data Exploration and Analysis Portal | 2026-08-04 09:43:49 | 18 | ||||||||
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eprime-data-clean Resource Report Resource Website |
eprime-data-clean (RRID:SCR_016020) | data processing software, software application, software resource, data management software | Software to convert E-Prime (software tool for psychology computerized experiment design, data collection, and analysis) generated files to CSV files without errors during conversion. The ABCD project is using E-Prime to run behavioral tests. | convert, data, psychology, computerized, experiment, design, collection, analysis, generate, file, errors, conversion, abcd |
is related to: University of California at San Diego; California; USA works with: ABCD Study |
NIDA U24 DA041123 | Free, Available for download | SCR_016020 | 2026-08-04 09:43:47 | 0 | |||||||||
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Gff2aplot Resource Report Resource Website |
Gff2aplot (RRID:SCR_016128) | data processing software, data visualization software, software application, software resource | Software application to visualize the alignment of two genomic sequences together with their annotations. Used to generate print-quality images for comparative genome sequence analysis. | alignment, pair-wise, plot, genomic, sequence, visualize, together, annotate, analysis, parameter, dataset, |
is listed by: Debian is listed by: OMICtools |
PMID:14668236 | Free, Available for download | OMICS_19949 | https://sources.debian.org/src/gff2aplot/ | SCR_016128 | 2026-08-04 09:43:49 | 0 | |||||||
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Macquarie University Labs and Facilities Resource Report Resource Website |
Macquarie University Labs and Facilities (RRID:SCR_000944) | topical portal, portal, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. Set of facilities based out of Macquarie University in New South Wales. Some facilities provide services such as proteome analysis or resources of various academic departments like engineering, biological sciences, and geography. | proteome, analysis, research, university, biological science, engineering, geography |
is listed by: ScienceExchange is related to: MQ Australian Proteome Analysis Facility is related to: MQ Animal Behaviour Laboratory is related to: MQ Ramaciotti Centre for Gene Function Analysis is related to: MQ BioFocus Research Centre is related to: MQ ARC Centre of Excellence for Engineered Quantum Systems is related to: Macquarie University MQ Research Centre in Quantum Science and Technology is related to: MQ Research Centre for Astronomy Astrophysics and Astrophotnics has parent organization: Macquarie University; Sydney; Australia |
THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_9680 | https://www.mq.edu.au/ | SCR_000944 | Macquarie University Labs Facilities | 2026-08-04 09:40:16 | 0 | |||||||
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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 | 2026-08-05 10:44:20 | 1 | ||||||
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GeneMANIA Resource Report Resource Website 1000+ mentions |
GeneMANIA (RRID:SCR_005709) | GeneMANIA | data or information resource, database, software resource, data analysis service, production service resource, service resource, analysis service 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 | 2026-08-05 10:44:21 | 3358 | |||||
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University of Barcelona Statistics and Bioinformatics Research Group Resource Report Resource Website |
University of Barcelona Statistics and Bioinformatics Research Group (RRID:SCR_005704) | UB Statistics and Bioinformatics Research Group | data or information resource, portal, topical portal, data analysis service, production service resource, service resource, analysis service resource | The Statistics and Bioinformatics research group has as its main objectives the development of methods and tools to deal with problems appearing in the interface between Statistics and Bioinformatics. We started focusing in DNA microarrays but we are also interested in statistical methods for ''omics'' data integration and next generation sequencing (NGS). Our group collaborates with different research groups in the fields of biology and biomedicine, to whom it offers statistical support for problems which are specifically statistic in nature, such as experimental design or microarray data analysis, and also in more general aspects, such as modeling, analysis or data mining. After a first period of collaboration agreements with the Fundaci�� Vall d''Hebr��n Institut de Recerca we contributed to the creation of the Statistics and Bioinformatics Unit (UEB) which provides statistical and bioinformatical support to VHIR researchers. | statistics, bioinformatics, next generation sequencing, dna microarray, dna, microarray, biology, biomedicine, data mining, modeling, analysis | has parent organization: University of Barcelona; Barcelona; Spain | nlx_149154 | SCR_005704 | University of Barcelona Statistics Bioinformatics Research Group | 2026-08-05 10:44:21 | 0 | ||||||||
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go-moose Resource Report Resource Website |
go-moose (RRID:SCR_005666) | go-moose | software resource, data processing software, software application, data analysis software | go-moose is intended as a replacement for the aging go-perl and go-db-perl Perl libraries. It is written using the object oriented Moose libraries. It can be used for performing a number of analyses on GO data, including the remapping of GO annotations to a selected subset of GO terms. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, slimmer-type tool, analysis, gene ontology, other analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: go-perl is related to: go-db-perl has parent organization: SourceForge has parent organization: Berkeley Bioinformatics Open-Source Projects has parent organization: Lawrence Berkeley National Laboratory |
Free for academic use | nlx_149189 | SCR_005666 | 2026-08-05 10:44:18 | 0 | ||||||||
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Onto-Translate Resource Report Resource Website 1+ mentions |
Onto-Translate (RRID:SCR_005725) | Onto-Translate | data or information resource, database, data analysis service, production service resource, service resource, analysis service resource | In the annotation world, the same piece of information can be stored and viewed differently across different databases. For instance, more than one Affymetrix probe ID can refer to the same GenBank sequence (accession number) and more than one nucleotide sequence from GenBank can be grouped in a single UniGene cluster. The result of Onto-Express depends on whether the input list contains Affymetrix probe IDs, GenBank accession numbers or UniGene cluster IDs. The user has to be aware of relations between the different forms of the data in order to interpret correctly the results. Even if the user is aware of the relationships and knows how to convert them, most existing tools allow conversions of individual genes. Onto-Translate is a tool that allows the user to perform easily such translations. Affymetrix probe IDs, etc., translate GO terms into other identifiers like GenBank accession number, Uniprot IDs. User account required. Platform: Online tool | annotation, gene, analysis, database or data warehouse, other analysis, affymetrix probe id, affymetrix, probe id, translate go terms into other identifiers like genbank accession number, genbank accession number, uniprot id, gene ontology, translate |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Wayne State University; Michigan; USA |
PMID:15215428 | Free for academic use | nlx_149182 | SCR_005725 | 2026-08-05 10:44:20 | 3 | |||||||
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GOTaxExplorer Resource Report Resource Website |
GOTaxExplorer (RRID:SCR_005720) | GOTaxExplorer | data or information resource, database, software resource, data analysis service, production service resource, service resource, analysis service resource | GOTaxExplorer presents a new approach to comparative genomics that integrates functional information and families with the taxonomic classification. It integrates UniProt, Gene Ontology, NCBI Taxonomy, Pfam and SMART in one database. GOTaxExplorer provides four different query types: selection of entity sets, comparison of sets of Pfam families, semantic comparison of sets of GO terms, functional comparison of sets of gene products. This permits to select custom sets of GO terms, families or taxonomic groups. For example, it is possible to compare arbitrarily selected organisms or groups of organisms from the taxonomic tree on the basis of the functionality of their genes. Furthermore, it enables to determine the distribution of specific molecular functions or protein families in the taxonomy. The comparison of sets of GO terms allows to assess the semantic similarity of two different GO terms. The functional comparison of gene products makes it possible to identify functionally equivalent and functionally related gene products from two organisms on the basis of GO annotations and a semantic similarity measure for GO. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, molecular function, protein family, taxonomy, visualization, functional similarity, semantic similarity, analysis, comparative genomics analysis, comparative genomics, search engine, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, function, other analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: UniProt is related to: NCBI Taxonomy is related to: Pfam is related to: SMART is related to: FSST - Functional Similarity Search Tool has parent organization: Max-Planck-Institute for Informatics; Saarbrucken; Germany |
German National Genome Research Network ; BMBF 016R0453; DFG KFO 129/1-1; European Union contract LSHG-CT-2003-503265 |
PMID:17346342 | Free for academic use | nlx_149179 | SCR_005720 | 2026-08-05 10:44:19 | 0 | ||||||
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Onto-Miner Resource Report Resource Website |
Onto-Miner (RRID:SCR_005722) | OM | data or information resource, database, data analysis service, production service resource, service resource, analysis service resource | Onto-Miner (OM) provides a single and convenient interface that allows the user to interrogate our databases regarding annotations of known genes. OM will return all known information about a given list of genes. Advantages of OM include the fact it allows queries with multiple genes and allows for scripting. This is unlike GenBank which uses a single gene navigation process. Scripted search of the Onto-Tools database for gene annotations. User account required. Platform: Online tool | gene, annotation, search engine, database, analysis, ontology or annotation search engine, database or data warehouse, other analysis, scripted search of the onto-tools database for gene annotations |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Wayne State University; Michigan; USA |
PMID:15215428 PMID:17584796 |
Free for academic use | nlx_149181 | SCR_005722 | Onto-Miner (OM) | 2026-08-05 10:44:20 | 0 | ||||||
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PRIMEGENS Resource Report Resource Website 1+ mentions |
PRIMEGENS (RRID:SCR_005474) | PRIMEGENS | software resource, data analysis service, production service resource, service resource, analysis service 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 | 2026-08-05 10:44:15 | 3 | ||||
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Bowtie Resource Report Resource Website 10000+ mentions |
Bowtie (RRID:SCR_005476) | data processing software, software application, image analysis software, alignment software, data analysis software, sequence analysis software, 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 |
NHGRI R01 HG006102; NIGMS R01 GM083873; Amazon Web Services in Education Research |
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 | 2026-08-05 10:44:15 | 13226 | ||||||
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InterProScan Resource Report Resource Website 5000+ mentions |
InterProScan (RRID:SCR_005829) | data processing software, web service, data access protocol, software application, data analysis software, software resource, data analysis service, production service resource, service resource, analysis service resource | Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service. | functional, analysis, sequence, protein, nucleotide, predict, presence, domain, site, proteome, genome, metagenome, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: RARTF is related to: InterPro is related to: LegumeIP is related to: UniProtKB has parent organization: European Bioinformatics Institute |
European Union ; Biotechnology and Biological Sciences Research Council ; EMBL |
PMID:15980438 PMID:17202162 PMID:24451626 |
Free, Available for download, Freely available | OMICS_01479, biotools:interproscan_4, nlx_149337 | https://www.ebi.ac.uk/interpro/download.html, https://bio.tools/interproscan_4 | SCR_005829 | InterProScan Sequence Search, InterProScan 2, InterProScan 3, InterProScan 4, InterProScan 5 | 2026-08-05 10:44:21 | 6936 | |||||
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Brede Toolbox Resource Report Resource Website 1+ mentions |
Brede Toolbox (RRID:SCR_006204) | Brede Toolbox | data processing software, image analysis software, software application, software resource, image processing software | A package for neuroinformatics and neuroimaging analysis mostly programmed in Matlab with a few additional programs in Python and Perl. It allows coordinate-based meta-analysis and visualization, neuroimaging analysis of voxel or regional data - not the original data but rather the summary images (e.g., statistical parametric images) and location data in stereotactic space. Among the algorithms implemented are kernel density estimation (for coordinate-based meta-analysis), independent component analysis, non-negative matrix factorization, k-means clustering, singular value decomposition, partial correlation analysis with permutation testing and partial canonical correlation analysis. Visualization of coordinate, surfaces and volumes are possible in 2D and 3D. Generation of HTML for results are possible and algorithms can be accessed from the command line or via a flexible graphical interface. With the Brede Toolbox comes the Brede Database with a small coordinate database from published neuroimaging studies, and ontologies for, e.g., brain function and brain regions. | ontology, database application, independent component analysis, principal component analysis, regression, neuroinformatics, neuroimaging, analysis, matlab, python, perl, coordinate, kernel density estimation, brain function, brain region, visualization, voxel, region |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: Brede Database is related to: Brede Database is related to: Brede Wiki has parent organization: THOR Center for Neuroinformatics |
Free for academic use, Acknowledgement requested | nif-0000-00275 | SCR_006204 | 2026-08-05 10:44:23 | 1 |
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