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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Ponemah Resource Report Resource Website 10+ mentions |
Ponemah (RRID:SCR_017107) | software application, data processing software, data analysis software, data acquisition software, software resource | Software tool for complete physiologic data acquisition and analysis used by physiologists, pharmacologists, and toxicologists to collect, analyze, and summarize preclinical study data. Allows to custom design configuration based on needs, budget and convenience without need for any programming. | Data Sciences International, Inc., physiologic, data, acquisition, analysis, collect, summerize, preclinical, custom, design | Available for purchase | SCR_017107 | 2026-02-17 10:02:48 | 20 | |||||||||||
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ot-tools Resource Report Resource Website 1+ mentions |
ot-tools (RRID:SCR_017191) | data analysis software, software application, data processing software, software resource | Software tools for analysis of cellular cryo-ET data. | analysis, cellular, cryo-ET, data | Free, Available for download, Freely available | SCR_017191 | 2026-02-17 10:02:49 | 5 | |||||||||||
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Gulbenkian Institute of Science Bioinformatics and Computational Unit Core Facility Resource Report Resource Website |
Gulbenkian Institute of Science Bioinformatics and Computational Unit Core Facility (RRID:SCR_017190) | training service resource, data or information resource, production service resource, analysis service resource, access service resource, service resource, core facility, data analysis service | IGC Core in Oeiras, Portugal, promotes use of computational methods in biological research, through training and development of resources and materials, supports biological data analysis using computational methods, conducts research and development in bioinformatics, in particular in data flows, data warehousing and data analyses. | bioinformatics, consulting, data, analysis, management, repository | Open | SCR_017190 | Bioinformatics and Computational Unit, IGC, core facility, Instituto Gulbenkian de Ciencia, Gulbenkian Institute of Science | 2026-02-17 10:03:32 | 0 | ||||||||||
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BSA4Yeast Resource Report Resource Website 1+ mentions |
BSA4Yeast (RRID:SCR_017113) | data access protocol, production service resource, analysis service resource, service resource, software resource, web service, data analysis service | Web application for Quantitative Trait Loci mapping via bulk segregant analysis of yeast sequencing data. Application provides automated data processing, annotations, and web interface to explore identified QTLs. | quantitative, trait, loci, mapping, bulk, segregant, analysis, yeast, sequencing, data, processing, annotation, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Luxembourg; Luxembourg; Luxembourg |
Fonds Nationale de la Recherche (FNR) Luxembourg | Free, Freely available, Registration required | biotools:BSA4Yeast | https://bio.tools/BSA4Yeast | SCR_017113 | Bulk Segregant Analysis for Yeast | 2026-02-17 10:03:31 | 1 | ||||||
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University of Edinburgh College of Medicine and Veterinary Medicine MRC Institute of Genetics and Molecular Medicine Bioinformatics Analysis Core Facility Resource Report Resource Website |
University of Edinburgh College of Medicine and Veterinary Medicine MRC Institute of Genetics and Molecular Medicine Bioinformatics Analysis Core Facility (RRID:SCR_017194) | MRC Institute of Genetics and Molecular Medicine BAC | training service resource, data or information resource, production service resource, analysis service resource, access service resource, service resource, software resource, core facility, data analysis service | Core provides advice, training, provision of computational tools and collaborative expertise to all IGMM researchers. | bioinformatics, data, analysis, sequencing | has parent organization: University of Edinburgh; Scotland; United Kingdom | Restricted | SCR_017194 | The University of Edinburgh, Bioinformatics Analysis, College of Medicine and Veterinary Medicine, College of Medicine & Veterinary Medicine, Core Facility, Institute of Genetics and Molecular Medicine, IGMM, MRC | 2026-02-17 10:03:32 | 0 | ||||||||
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Genome Institute of Singapore Scientific and Research Computing Core Facility Resource Report Resource Website |
Genome Institute of Singapore Scientific and Research Computing Core Facility (RRID:SCR_017193) | GIS Scientific and Research Computing | production service resource, analysis service resource, access service resource, service resource, software resource, core facility, data analysis service | Core provides research computing resources including bioinformatics, application development, data management and IT infrastructure to support next generation sequencing technologies, human genotyping, high throughput screening and computational biology researchers. | bioinformatics, genomic, data, management, next, generation, sequencing, genotyping, analysis | Open | SCR_017193 | Core Facility, GIS, Scientific & Research Computing, Scientific and Research Computing, Genome Institute of Singapore | 2026-02-17 10:03:10 | 0 | |||||||||
|
University of Cambridge Centre for Trophoblast Research Bioinformatics Core Facility Resource Report Resource Website |
University of Cambridge Centre for Trophoblast Research Bioinformatics Core Facility (RRID:SCR_017192) | CTR Bioinformatics Core Facility | training service resource, production service resource, analysis service resource, access service resource, service resource, core facility, data analysis service | Core provides assistance with experimental design, RNA sequencing, whole genome and targeted sequencing, methylation sequencing, protein alignment, microscopy image analysis, and training. | bioinformatics, sequencing, RNA, genome, methylation, protein, alignment, data, image, analysis | has parent organization: University of Cambridge; Cambridge; United Kingdom | Restricted | SCR_017192 | Center for Trophoblast Research, Centre for Trophoblast Research, Bioinformatics Core Facility, University of Cambridge | 2026-02-17 10:03:33 | 0 | ||||||||
|
Brainstorm Resource Report Resource Website 500+ mentions |
Brainstorm (RRID:SCR_001761) | Brainstorm | software application, data processing software, data analysis software, software resource, data visualization software | Software as collaborative, open source application dedicated to analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and animal invasive neurophysiology. User-Friendly Application for MEG/EEG Analysis. | MEG, EEG, data, magnetoencephalography, electroencephalography, visualization, processing, analysis, brain, recording, fNIRS, ECoG, electrophysiology |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: OpenMEEG is related to: Open MEG Archive is related to: MATLAB has parent organization: University of Southern California; Los Angeles; USA |
NIBIB R01 EB002010; NIBIB R01 EB009048; NIBIB R01 EB000473; NIBIB R01 EB026299; CNRS ; McGill University |
PMID:21584256 | Free, Available for download, Freely available | nif-0000-10267 | http://www.nitrc.org/projects/bst https://github.com/brainstorm-tools/brainstorm3 |
SCR_001761 | brainstorm3 | 2026-02-17 09:59:45 | 558 | ||||
|
Mini Analysis Program Resource Report Resource Website 1000+ mentions |
Mini Analysis Program (RRID:SCR_002184) | Mini Analysis | data analysis software, software application, data processing software, software resource | Software tool that detects peaks of any type, any shape, any direction, and any size for neuroscientists who are studying spontaneous activities. Allows detection of virtually any kind of peaks including spontaneous miniature synaptic currents and potentials, action potential spikes, calcium imaging peaks, amperometric peaks, ECG peaks etc. It includes the complex and multiple peak detection algorithm. Has post-detection analyses including essential plots and statistical parameters. Group Analysis provides specialized and detailed analysis options for action potentials, decay fitting, fEPSP/population spikes, amperometry, etc., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Synaptosoft Inc., analysis, peak, spontaneous, activity, synaptic, current, potential, spike, calcium, image, amperometric, ECG, plot, statistical, parameter | THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000143, SCR_014441 | SCR_002184 | Mini Analysis, MiniAnalysis | 2026-02-17 09:59:48 | 1137 | ||||||||
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ChIPSeq Peak Finder Resource Report Resource Website 1+ mentions |
ChIPSeq Peak Finder (RRID:SCR_002081) | data analysis software, software application, data processing software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 12, 2017. A software tool to find peaks from ChIPSeq data generated from the Solexa/Illumina platform., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | chipseq, sequencing, dna, analysis, solexa, illumina |
is listed by: OMICtools is listed by: Debian has parent organization: Genome Institute of Singapore; Singapore; Singapore |
PMID:27863463 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00434 | https://sources.debian.org/src/chip-seq/ | SCR_002081 | ChIPSeq Toolbox | 2026-02-17 09:59:47 | 1 | ||||||
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BrainVision Analyzer Resource Report Resource Website 100+ mentions |
BrainVision Analyzer (RRID:SCR_002356) | BVA | data analysis software, software application, data processing software, software resource | Software to manage the daily work of analyzing various neurophysiological data. Features include a history tree, automated analysis, various data format readers, and more. | Brain Products GmbH, neurophysiology, manage, data, analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Brain Products |
Commercially available | nlx_155717 | http://www.nitrc.org/projects/bva | SCR_002356 | BrainVision Analyzer, BrainVision Analyzer 2 | 2026-02-17 09:59:55 | 449 | ||||||
|
Cistrome Resource Report Resource Website 10+ mentions |
Cistrome (RRID:SCR_000242) | data access protocol, web service, software resource | Web based integrative platform for transcriptional regulation studies. | Transcriptional, regulation, Chip, data, analysis, genome, gene, expression, motif, mining, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy has parent organization: Harvard University; Cambridge; United States |
Dana-Farber Cancer Institute High Tech and Campaign Technology Fund ; National Basic Research Program of China ; NHGRI HG004069; NIDDK DK074967; NIDDK DK062434 |
PMID:21859476 | Free, Freely available | SCR_017663, biotools:cistrome, OMICS_02173 | http://cistrome.org/ap/root https://bio.tools/cistrome |
SCR_000242 | Galaxy Cistrome | 2026-02-17 09:59:25 | 16 | |||||
|
Lasergene's SeqMan Pro Resource Report Resource Website 1+ mentions |
Lasergene's SeqMan Pro (RRID:SCR_000283) | software application, data processing software, data analysis software, software resource, data visualization software | Software for analysis and DNA sequence assembly of Sanger data. It also provides visualizations and analysis of next-gen projects assembled by SeqMan NGen. | dna, sequence, analysis, sanger, snp discovery, data visualization |
is listed by: OMICtools works with: GenVision |
Restricted | OMICS_01810 | SCR_000283 | Lasergenes SeqMan Pro, SeqMan Pro, SeqMan Pro - Software for Contig Assembly and Analysis Including SNP Discovery Coverage Evaluation and Project Annotation, DANSEUR Lasergenes SeqMan Pro | 2026-02-17 09:59:25 | 5 | ||||||||
|
Mini Analysis Guide for Microarrays Resource Report Resource Website 1+ mentions |
Mini Analysis Guide for Microarrays (RRID:SCR_000596) | MAGMA | data or information resource, narrative resource, experimental protocol | A collection of cook-book like manuals for various microarray designs. MAGMA is a collaboration between the Norwegian Microarray Consortium NMC and MolMine AS | microarray design, microarray, manual, guide, array, analysis, j-express, import, data processing, global analysis, differential expression, gene set, co-expressed gene |
is listed by: OMICtools has parent organization: J-Express |
OMICS_00772 | SCR_000596 | 2026-02-17 09:59:28 | 3 | |||||||||
|
EMBL - Bork Group Resource Report Resource Website |
EMBL - Bork Group (RRID:SCR_000810) | EMBL - Bork Group | organization portal, data or information resource, service resource, portal, laboratory portal | The main focus of this Computational Biology group is to predict function and to gain insights into evolution by comparative analysis of complex molecular data. The group currently works on three different scales: * genes and proteins, * protein networks and cellular processes, and * phenotypes and environments. They require both tool development and applications. Some selected projects include comparative gene, genome and metagenome analysis, mapping interactions to proteins and pathways as well as the study of temporal and spatial protein network aspects. All are geared towards the bridging of genotype and phenotype through a better understanding of molecular and cellular processes. The services - resources & tools, developed by Bork Group, are mainly designed and maintained for research & academic purposes. Most of services are published and documented in one or more papers. All our tools can be completely customized and integrated into your existing framework. This service is provided by the company biobyte solutions GmbH. Please visit their tools and services pages for full details and more information. Standard commercial licenses for our tools are also available through biobyte solutions GmbH. The group is partially associated with Max Delbr��ck Center for Molecular Medicine (MDC), Berlin. | computational biology, gene, protein, protein network, cellular process, phenotype, environment, gene, genome, metagenome, analysis, interaction, pathway, temporal, spatial, network, genotype, phenotype, molecular process |
has parent organization: European Molecular Biology Laboratory is parent organization of: SMART is parent organization of: SmashCommunity is parent organization of: Candidate Genes to Inherited Diseases |
European Molecular Biology Laboratory ; Max-Delbruck Center for Molecular Medicine ; European Union ; BMBF ; IBM |
nlx_149173 | SCR_000810 | Bork Group - Comparative Systems Analysis (EMBL) | 2026-02-17 09:59:31 | 0 | |||||||
|
Biometric Research Branch: ArrayTools Resource Report Resource Website 1+ mentions |
Biometric Research Branch: ArrayTools (RRID:SCR_000778) | software application, data processing software, data analysis software, software resource, software toolkit, data visualization software | A software package for the visualization and statistical analysis of DNA microarray gene expression data. The tools have been developed from the R statistical system, in C and fortran programs and Java applications. They are integrated into Excel as an add-in. | visualization, statistic, analysis, dna, microarray, gene, expression, c, java, excel |
is listed by: OMICtools has parent organization: National Cancer Institute has parent organization: National Cancer Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30199 | SCR_000778 | BRB ArrayTools | 2026-02-17 09:59:30 | 6 | ||||||||
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MEGA Resource Report Resource Website 1000+ mentions |
MEGA (RRID:SCR_000667) | MEGA, MEGA6, MEGA4, MEGA 4, MEGA 11 | software application, data processing software, software toolkit, data analysis software, software resource, sequence analysis software | Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny. | comparative, analysis, DNA, protein, sequence, molecular, evolution, pattern, gene, genome, evolution, FASEB list | has parent organization: Pennsylvania State University | Japan Society for the Promotion of Science ; NHGRI HG006039; NHGRI HG002096; Burroughs-Wellcome Fund ; NIGMS R01GM126567; NSF ABI 1661218; NIGMS R35GM139504 |
DOI:10.1093/molbev/msab120 PMID:24132122 PMID:31904846 PMID:22923298 PMID:21546353 PMID:17488738 PMID:15260895 PMID:11751241 PMID:8019868 |
Free, Available for download, Freely available | SCR_023017, nlx_156838 | https://www.megasoftware.net/mega4/ | SCR_000667 | MEGA11, Molecular Evolutionary Genetics Analysis, Molecular Evolutionary Genetics Analysis 6, Molecular Evolutionary Genetics Analysis 4 | 2026-02-17 09:59:30 | 2763 | ||||
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NVM Resource Report Resource Website |
NVM (RRID:SCR_000600) | data visualization software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Software tool for quantitative neuroanatomical measurements in volumetric image data. Used to draw regions of interest for subsequent fMRI analysis. | quantitative, neuroanatomical, measurement, volumetric, image, data, draw, region, fMRI, analysis, morphology, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Neuromorphometrics |
NIMH R43 MH60507; NIMH R44 MH60507; NIMH R43 MH084358 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149080 | http://www.nitrc.org/projects/nvm | SCR_000600 | 2026-02-17 09:59:29 | 0 | |||||||
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University of Colorado at Boulder Labs and Facilities Resource Report Resource Website |
University of Colorado at Boulder Labs and Facilities (RRID:SCR_001054) | data or information resource, material service resource, production service resource, analysis service resource, service resource, portal | A portal for the core labs and facilities at the University of Colorado at Boulder. | electron microprobe, electron microscope, imaging, analysis, portal, labs, facilities, production service resource |
is listed by: ScienceExchange is related to: CU Boulder Electron Microprobe Laboratory is related to: CU Boulder Institute for Behavioral Genetics is related to: Colorado University Boulder BioFrontiers Advanced Light Microscopy Core Facility has parent organization: University of Colorado Boulder; Colorado; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_850 | SCR_001054 | CU Boulder Labs and Facilities, CU Boulder Labs & Facilities, University of Colorado at Boulder Labs & Facilities | 2026-02-17 09:59:35 | 0 | ||||||||
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EZ BioResearch Resource Report Resource Website 1+ mentions |
EZ BioResearch (RRID:SCR_001050) | material service resource, production service resource, reagent manufacture, service resource | A biotechnology company that develops, manufactures and distributes molecular biology tool kits and laboratory consumable products. Services include DNA and RNA microarrays, PCR and transgenic genotyping, and DNA/RNA analysis and quality control. | molecular biology, tool kit, dna, rna, microarray, pcr, transgenic, genotyping, analysis, biotechnology | is listed by: ScienceExchange | Commercial | SciEx_571 | http://www.scienceexchange.com/facilities/ez-bioresearch | SCR_001050 | EZ BioResearch LLC | 2026-02-17 09:59:35 | 3 |
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