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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Silver Lab Microscopy Software Resource Report Resource Website 1+ mentions |
Silver Lab Microscopy Software (RRID:SCR_017456) | data acquisition software, data processing software, data visualization software, software application, software resource | Software for use with compact Acousto-Optic Lens Microscope (AOLM) developed in the Silver Lab at UCL. Written in LabVIEW. Performs multiple imaging modes and protocols including Z-stacks, multi-plane, single-plane, sub-volume, patches and points. It comes with tools for visualising data acquired with system. | Imaging, visualising, electrophysiological, data, acousto, optic, lens, microscope, Silver Lab, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: University College London; London; United Kingdom |
NINDS NS099689 | Free, Available for download, Freely available | http://silverlab.org/software-resources/ | SCR_017456 | 2026-09-03 04:54:34 | 2 | ||||||||
|
vbSPT Resource Report Resource Website 1+ mentions |
vbSPT (RRID:SCR_017554) | data analysis software, data processing software, software application, software resource | Software package for analysis of single particle diffusion trajectories, where diffusion constants switch randomly according to Markov process. Analytical tool to combine information from thousands of short single-molecule trajectories of intracellularly diffusing proteins. Has ability to learn number of diffusive states directly from data, in addition to model parameters such as transition rates and diffusion constants. | Analysis, single, particle, diffusion, trajectory, Markov, short, molecule, intracellularly, protein, data, transition, state | PMID:23396281 | Free, Available for download, Freely available | https://sourceforge.net/projects/vbspt/files/latest/download?source=files | SCR_017554 | variational Bayes single particle tracking | 2026-09-03 04:54:38 | 3 | ||||||||
|
LabChart Reader Resource Report Resource Website 100+ mentions |
LabChart Reader (RRID:SCR_017551) | data analysis software, data processing software, software application, software resource | LabChart data analysis software creates a platform for all of your recording devices to work together, allowing you to acquire biological signals from multiple sources simultaneously and apply advanced calculations and plots as your experiment unfolds. LabChart Reader is free version of software that allows to analyse with some limitations. LabChart Reader doesn’t allow saving of data - export image only. Has data pad for analysis. | Adinstruments, LabChart, data, analysis, calculation, plot | is related to: LabChart | https://www.adinstruments.com/products/labchart/versions-and-licenses | SCR_017551 | LabChart Reader software 8.1, LabChart Reader software | 2026-09-03 04:54:31 | 144 | |||||||||
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Wellcome Trust Sanger Institute; Hinxton; United Kingdom Resource Report Resource Website 500+ mentions |
Wellcome Trust Sanger Institute; Hinxton; United Kingdom (RRID:SCR_011784) | WTSI, Sanger | institution | Non profit research organization for genome sequences to advance understanding of biology of humans and pathogens in order to improve human health globally. Provides data which can be translated for diagnostics, treatments or therapies including over 100 finished genomes, which can be downloaded. Data are publicly available on limited basis, and provided more extensively upon request. | research, genome, sequence, human, health, project, global, data, treatment, therapy |
is listed by: re3data.org is affiliated with: Open Targets is related to: Clonalframe is related to: ClonalOrigin is related to: TraCeR is parent organization of: ILLUMINUS is parent organization of: ARNIE is parent organization of: Sequence Search and Alignment by Hashing Algorithm is parent organization of: Sequencing of Idd regions in the NOD mouse genome is parent organization of: CAROL is parent organization of: DINDEL is parent organization of: Wellcome Trust Case Control Consortium is parent organization of: OLORIN is parent organization of: Exomiser is parent organization of: COSMIC - Catalogue Of Somatic Mutations In Cancer is parent organization of: GeneDB is parent organization of: Breast Cancer Somatic Genetics Study is parent organization of: Artemis: Genome Browser and Annotation Tool is parent organization of: ACT: Artemis Comparison Tool is parent organization of: Alien hunter is parent organization of: Pfam is parent organization of: DNAPlotter is parent organization of: VAGrENT is parent organization of: SMALT is parent organization of: LookSeq is parent organization of: ZMP is parent organization of: Deciphering Developmental Disorders is parent organization of: Sanger Mouse Resources Portal is parent organization of: SpliceDB is parent organization of: DECIPHER is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: Genes to Cognition: Neuroscience Research Programme is parent organization of: MEROPS is parent organization of: Rfam is parent organization of: VEGA is parent organization of: Bacterial Genomes is parent organization of: Caenorhabditis Genome Sequencing Projects is parent organization of: D. rerio Blast Server is parent organization of: Fungi Sequencing Projects is parent organization of: PEER is parent organization of: Alfresco - FRont-End for Sequence COmparison is parent organization of: AutoCSA (Automatic Comparative Sequence Analysis) is parent organization of: AceDB is parent organization of: CnD is parent organization of: Genomics of Drug Sensitivity in Cancer is parent organization of: Zebrafish Genome Project is parent organization of: Tree families database is parent organization of: Ensembl is parent organization of: BamView is parent organization of: SVMerge is parent organization of: RetroSeq is parent organization of: Consensus CDS is parent organization of: WormBase is parent organization of: Belvu is parent organization of: Bio-tradis is parent organization of: Blixem is parent organization of: Dotter is parent organization of: Exonerate is parent organization of: Fastaq is parent organization of: Gubbins is parent organization of: CellPhoneDB is parent organization of: Ensembl Metazoa is parent organization of: Scmap is parent organization of: Scfind is parent organization of: Recognition of Errors in Assemblies using Paired Reads is parent organization of: SAMTOOLS is parent organization of: Cell Model Passports |
Wellcome Trust | ISNI: 0000 0004 0606 5382, nlx_91258, grid.10306.34, Wikidata: Q1142544 | https://ror.org/05cy4wa09 | SCR_011784 | Wellcome Trust Sanger Institute, Genome Research Limited, The Wellcome Sanger Institute, Sanger Institute, Wellcome Trust Sanger Institute Genome Research Limited | 2026-09-03 04:51:21 | 543 | ||||||
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The Immunology Database and Analysis Portal (ImmPort) Resource Report Resource Website 1000+ mentions |
The Immunology Database and Analysis Portal (ImmPort) (RRID:SCR_012804) | ImmPort | controlled vocabulary, data or information resource, data repository, database, disease-related portal, ontology, portal, service resource, storage service resource, topical portal | Data sharing repository of clinical trials, associated mechanistic studies, and other basic and applied immunology research programs. Platform to store, analyze, and exchange datasets for immune mediated diseases. Data supplied by NIAID/DAIT funded investigators and genomic, proteomic, and other data relevant to research of these programs extracted from public databases. Provides data analysis tools and immunology focused ontology to advance research in basic and clinical immunology. | immunology, basic, clinical, data, share, store, analyze, exchange, dataset, immune, mediated, disease, analysis, tool, FASEB list |
is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: NIDDK Research Resources is affiliated with: Cytokine Registry is related to: MetaCyto is related to: The 10000 Immunomes is related to: NIAID |
Immune mediated disease | DAIT ; NIAID ; NIAID HHSN266200400076C; NIAID HHSN272201200028C; NIH |
PMID:24791905 | nlx_152691, r3d100012529 | http://www.immport.org/immport-open/public/home/home, http://www.immport.org/ | http://www.immport.org | SCR_012804 | Immunology Data and Analysis Portal, ImmPort system, ImmPort, Immunology Database and Analysis Portal | 2026-09-03 04:51:53 | 1383 | |||
|
Autogrid Resource Report Resource Website 1000+ mentions |
Autogrid (RRID:SCR_015982) | data analysis software, data processing software, simulation software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software for automated docking analysis to precalculate the set of grids describing the target protein. It is a part of automated molecular modeling simulation software AutoDock. | software, automated, docking, analysis, tool, precalculate, set, grid, ligand, protein, target, molecular, simulation, modeling, protein-ligand interaction, data |
is listed by: SoftCite is related to: AutoDock has parent organization: The Scripps Research Institute Labs and Facilities |
The Scripps Research Institute ; San Diego ; California |
PMID:16862531 | THIS RESOURCE IS NO LONGER IN SERVICE | http://mgl.scripps.edu/forum | SCR_015982 | Autogrid toolkit, Autogrid: automated grid | 2026-09-03 04:53:29 | 1261 | ||||||
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Bamtools Resource Report Resource Website 100+ mentions |
Bamtools (RRID:SCR_015987) | data analysis software, data management software, data processing software, software application, software resource, software toolkit | Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies. | c++, api, sam, bam genome, sequence, alignment, data, analysis, management, command, manipulation, binary, map, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG004719; NHGRI RC2 HG005552 |
PMID:21493652 DOI:10.1093/bioinformatics/btr174 |
biotools:bamtools, OMICS_11315 | https://bio.tools/bamtools, https://sources.debian.org/src/bamtools/ | SCR_015987 | API:Application Programming Interface, BAM:Binary Alignment Map, SAM:Sequence Alignment Map | 2026-09-03 04:53:29 | 344 | ||||||
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Blixem Resource Report Resource Website 1+ mentions |
Blixem (RRID:SCR_015994) | alignment software, data processing software, image analysis software, software application, software resource | Software for sequence alignments that displays multiple match sequences aligned against a single genomic reference sequence. It can be used for manipulation, display and annotation of genomic data, to check the quality of an alignment, to find missing/misaligned sequence, and to identify splice sites and polyA sites. | software, sequence, alignment, annotation, genomic, reference, data, display, manipulation, DNA |
is related to: SEQtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
NHGRI U54 HG00455; Wellcome Trust Grant 098051 |
PMID:26801397 | Free, Available for download | SCR_015994 | SEQtools Blixem | 2026-09-03 04:53:23 | 2 | |||||||
|
auto-scoring Resource Report Resource Website |
auto-scoring (RRID:SCR_016015) | data processing software, data visualization software, software application, software resource | Visualization software that calculates derived scores for the electronic record system REDCap (Research Electronic Data Capture) to build and manage online surveys and databases. Used in the ABCD-STUDY (Adolescent Brain Cognitive Development - STUDY) report framework. | visual, data, processing, calculate, derived, score, electronic, record, system, data, capture, research | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016015 | 2026-09-03 04:53:30 | 0 | |||||||||
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little-man-task Resource Report Resource Website |
little-man-task (RRID:SCR_016018) | data management software, data processing software, data transfer software, software application, software resource | Software tool to manage data and derived results. It is used for import of derived measures into REDCap (Research Electronic Data Capture). | capture, data, manage, derive, measure, abcd, study | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016018 | 2026-09-03 04:53:43 | 0 | |||||||||
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redcap-completion Resource Report Resource Website |
redcap-completion (RRID:SCR_016019) | data management software, software application, software resource | Software to measure item level completion in a large REDCap project. It provides a web-interface to review data and it is used in the ABCD project to assess data collection sites for the reached level of completion. | measure, item, level, completion, large, electronic, data, capture, research, review, data, collection |
is related to: University of California at San Diego; California; USA works with: REDCap |
NIDA U24 DA041123 | Free, Available for download | SCR_016019 | 2026-09-03 04:53:30 | 0 | |||||||||
|
aux-file-upload Resource Report Resource Website |
aux-file-upload (RRID:SCR_016026) | data management software, data processing software, data transfer software, software application, software resource | Software application to upload functional MR imaging runs produce auxilary data that can be collected centrally. Connects to a subject database research electronic data capture (REDCap). | upload, data, transmitted, addition, basic, calculation, subject, database, research, electronic, capture, imaging, session, abcd |
is related to: University of California at San Diego; California; USA works with: ABCD Study works with: REDCap |
NIDA U24 DA041123 | Free, Available for download | SCR_016026 | 2026-09-03 04:53:44 | 0 | |||||||||
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FIONA-QC-PHANTOM Resource Report Resource Website 1+ mentions |
FIONA-QC-PHANTOM (RRID:SCR_016024) | data analysis software, data processing software, software application, software resource | Software for online quality control operations performed on Phantom MRI data. It checks the accuracy and reproducibility of data. | application, quality, control, operation, phantom, MRI, data, accurate, reproducible, online, qc |
is related to: University of California at San Diego; California; USA is related to: ABCD Study works with: Diffusion MRI - In-vivo and Phantom Data |
NIDA U24 DA041123 | Free, Available for download | SCR_016024 | 2026-09-03 04:53:24 | 1 | |||||||||
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nih-ipad-app-end-point Resource Report Resource Website |
nih-ipad-app-end-point (RRID:SCR_016029) | data acquisition software, data processing software, data storage software, software application, software resource | Data collection software for centrally and securely storing data from the NIH iPad application. It allows users to capture results from multiple iPads at a central location. | abcd, collect, tool, central, storing, data, NIH, iPad, application, secure, capture, result, multiple, location | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016029 | 2026-09-03 04:53:20 | 0 | |||||||||
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DIAMOND Resource Report Resource Website 100+ mentions |
DIAMOND (RRID:SCR_016071) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search. | sequence, aligner, high, performance, analysis, big, data, protein, DNA, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools has parent organization: University of Tubingen; Tubingen; Germany |
PMID:25402007 DOI:10.1038/nmeth.3176 |
Free, Available for download | OMICS_08011, biotools:diamond | https://bio.tools/diamond, https://sources.debian.org/src/diamond-aligner/ | SCR_016071 | 2026-09-03 04:53:46 | 489 | |||||||
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Datamash Resource Report Resource Website 1+ mentions |
Datamash (RRID:SCR_016067) | data analysis software, data processing software, software application, software resource | Software for a command-line interface which performs basic numeric, textual and statistical operations on input textual data files. It is designed to aid researchers in automating analysis pipelines, without writing code or short scripts. | command-line, interface, basic, numerical, textual, statistical, operation, input, data, files, automate, analysis, pipelines | is listed by: Debian | Free Software Foundation (FSF) | Free, Available for download | https://sources.debian.org/src/datamash/ | SCR_016067 | GNU Datamash | 2026-09-03 04:53:32 | 4 | |||||||
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GARLI Resource Report Resource Website 100+ mentions |
GARLI (RRID:SCR_016117) | GARLI | data analysis software, data processing software, software application, software resource | Software application for inferring phylogenetic trees and analysis of molecular sequence data using the maximum-likelihood criterion. It implements nucleotide, amino acid and codon-based models of sequence evolution. | inference, phylogenetic, tree, analysis, molecular, sequence, data, maximum, likelihood, criterion, nucleotide, amino acid, codon, model, evolution |
is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_04234 | https://code.google.com/archive/p/garli/, https://sources.debian.org/src/garli/ | SCR_016117 | Genetic Algorithm for Rapid Likelihood Inference | 2026-09-03 04:53:47 | 280 | ||||||
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gdpc Resource Report Resource Website |
gdpc (RRID:SCR_016119) | data processing software, data visualization software, software application, software resource | Software application for visualizing output data from molecular dynamics simulations. It can be customized to read almost any input file format, animate it, and output images of each frame. | visualizing, output, data, molecular, dynamic, simulation, animation, visualization |
is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_19946 | https://sources.debian.org/src/gdpc/ | http://www.frantz.fi/software/gdpc.php, https://directory.fsf.org/wiki/Gdpc | SCR_016119 | 2026-09-03 04:53:34 | 0 | |||||||
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bioSyntax Resource Report Resource Website 1+ mentions |
bioSyntax (RRID:SCR_016207) | data management software, software application, software resource | Software for syntax highlighting for computational biology. | computation, syntax, language, code, scientific, data, workflow, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
DOI:10.1186/s12859-018-2315-y | Free, Available for download | biotools:biosyntax, OMICS_25594 | https://github.com/bioSyntax/bioSyntax, https://bio.tools/biosyntax, https://sources.debian.org/src/biosyntax/ | SCR_016207 | 2026-09-03 04:53:27 | 2 | |||||||
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PhonBank Resource Report Resource Website 1+ mentions |
PhonBank (RRID:SCR_016312) | data repository, service resource, storage service resource | Database for study of early phonological development using Phon program. Child phonology component of TalkBank system. | Data, early, phonological, development, Phon, program, child |
is recommended by: National Library of Medicine is related to: TalkBank |
NICHD R01 HD051698 | Free, Freely available | SCR_016312 | 2026-09-03 04:53:34 | 2 |
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