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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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SOURCE Resource Report Resource Website 50+ mentions |
SOURCE (RRID:SCR_005799) | SOURCE | data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | SOURCE compiles information from several publicly accessible databases, including UniGene, dbEST, UniProt Knowledgebase, GeneMap99, RHdb, GeneCards and LocusLink. GO terms associated with LocusLink entries appear in SOURCE. The mission of SOURCE is to provide a unique scientific resource that pools publicly available data commonly sought after for any clone, GenBank accession number, or gene. SOURCE is specifically designed to facilitate the analysis of large sets of data that biologists can now produce using genome-scale experimental approaches Platform: Online tool | genomic, functional annotation, ontology, gene expression, gene, genome, statistical analysis, bio.tools, FASEB list |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: SMD |
NIGMS ; NCI CA85129-04; NIGMS GM07365 |
PMID:12519986 | Restricted | biotools:source, nlx_149287 | https://login.stanford.edu/idp/profile/SAML2/Redirect/SSO?execution=e1s1 https://bio.tools/source |
SCR_005799 | 2026-02-16 09:46:41 | 69 | |||||
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IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature Resource Report Resource Website 10+ mentions |
IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature (RRID:SCR_006027) | IDEAL | data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | IDEAL, Intrinsically Disordered proteins with Extensive Annotations and Literature, is a collection of knowledge on experimentally verified intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). IDEAL contains manually curated annotations on IDPs in locations, structures, and functional sites such as protein binding regions and posttranslational modification sites together with references and structural domain assignments. Protean segment One of the unique phenomena seen in IDPs is so-called the coupled folding and binding, where a short flexible segment can bind to its binding partner with forming a specific structure to act as a molecular recognition element. IDEAL explicitly annotates these regions as protean segment (ProS) when unstructured and structured information are both available in the region. Access to the data All the entries are tabulated in the list and individual entries can be retrieved by using the search tool at the upper-right corner in this page. IDEAL also provides the BLAST search, which can find homologs in IDEAL. All the information in IDEAL can be downloaded in the XML file. | intrinsically disordered protein, protein, intrinsically disordered region, region, location, structure, functional site, protein binding region, binding region, posttranslational modification site, reference, structural domain assignment, blast, homolog, simian virus 40, epstein-barr virus, human herpesvirus 1, residue, protean segment, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Nagoya University; Nagoya; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:22067451 | biotools:ideal, nlx_151427 | https://bio.tools/ideal | SCR_006027 | IDEAL - Intrinsically Disordered proteins with Extensive Annotations Literature, Intrinsically Disordered proteins with Extensive Annotations and Literature | 2026-02-16 09:46:36 | 10 | |||||
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Pathbase Resource Report Resource Website 10+ mentions |
Pathbase (RRID:SCR_006141) | Pathbase | web service, controlled vocabulary, image repository, data access protocol, image collection, data repository, database, storage service resource, software resource, ontology, service resource, data or information resource | Database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice. The database currently holds more than 1000 images of lesions from mutant mice and their inbred backgrounds and further images are being added continuously. Images can be retrieved by searching for specific lesions or class of lesion, by genetic locus, or by a wide set of parameters shown on the Advanced Search Interface. Its two key aims are: * To provide a searchable database of histopathology images derived from experimental manipulation of the mouse genome or experiments conducted on genetically manipulated mice. * A reference / didactic resource covering all aspects of mouse pathology Lesions are described according to the Pathbase pathology ontology developed by the Pathbase European Consortium, and are available at the site or on the Gene Ontology Consortium site - OBO. As this is a community resource, they encourage everyone to upload their own images, contribute comments to images and send them their feedback. Please feel free to use any of the SOAP/WSDL web services. (under development) | histopathology, photomicrograph, macroscopic, mutant, genetically manipulated, pathology, transgenic, rodent, mpath ontology, mouse pathology ontology, skinbase, genotype, skin, gene, tissue, hair, mutant mouse strain, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: University of Cambridge; Cambridge; United Kingdom is parent organization of: Mouse Pathology Ontology |
Lesion, Mutant mouse strain, Inbred mouse strain | North American Hair Research Society ; Ellison Medical Foundation ; European Union QLRI-1999-00320; European Union LSHG-CT-2006-037188; NCI CA089713; NCRR RR17436; NIH AR49288 |
PMID:20587689 PMID:15623888 PMID:14681470 |
Except where otherwise noted, Creative Commons Attribution-NonCommercial-ShareAlike License, v3 Unported, Images on the database remain the property of the persons generously allowing their images to be used and are acknowledged within each record. Images should not be modified, Reproduced or disseminated without the express permission of the submitter. | biotools:pathbase, nlx_151637 | https://bio.tools/pathbase | SCR_006141 | Pathbase - European mutant mouse pathology database | 2026-02-16 09:46:38 | 11 | |||
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DARC - Database for Aligned Ribosomal Complexes Resource Report Resource Website 10+ mentions |
DARC - Database for Aligned Ribosomal Complexes (RRID:SCR_006932) | DARC | model, data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | A database for aligned ribosomal complexes that provides a resource for directly comparing the structures. A collection of files deposited in the RCSB protein data bank and the Electron Microscopy Data Bank have been aligned so as to make direct comparison of the structures possible. An easy-to-use, searchable interface allows users to access and download >130 cryo-EM maps and >300 atomic models in the format of brix and pdb files, respectively. The aligned coordinate system substantially simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors. | ribosomal complex, cryo-electron microscopy, ribosomal particle, atomic model, ribosome, x-ray crystallography, structure, bio.tools |
uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) uses: Electron Microscopy Data Bank at PDBe (MSD-EBI) is listed by: Debian is listed by: bio.tools has parent organization: Ludwig-Maximilians-University; Munich; Germany |
DFG SFB594; DFG SFB646; DFG WI3285/1-1 |
PMID:22009674 | biotools:darc_site, nlx_149452 | https://bio.tools/darc_site | SCR_006932 | The DARC site, Database for Aligned Ribosomal Complexes, Database for Aligned Ribosomal Complexes (DARC), DARC site | 2026-02-16 09:46:50 | 27 | |||||
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PLEXdb - Plant Expression Database Resource Report Resource Website 10+ mentions |
PLEXdb - Plant Expression Database (RRID:SCR_006963) | PLEXdb | data analysis service, analysis service resource, data repository, database, storage service resource, topical portal, portal, production service resource, service resource, data or information resource | PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data. The integrated tools of PLEXdb allow investigators to use commonalities in plant biology for a comparative approach to functional genomics through use of large-scale expression profiling data sets. | gene expression, plant, plant pathogen, genotype, phenotype, genetic, physical, pathway, plant biology, compare, functional genomics, expression profiling, expression atlas, pathogen, genome, anova, cluster, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: FuncExpression has parent organization: Iowa State University; Iowa; USA |
UniNSF DBI-0543441; NSF IOS-0922746; USDA 3625-21000-049-00D |
PMID:22084198 | biotools:plexdb, r3d100011516, nlx_149236 | https://bio.tools/plexdb https://doi.org/10.17616/R39D13 |
SCR_006963 | PLEXdb - Gene expression resources for plants and plant pathogens, Plant Expression Database | 2026-02-16 09:46:51 | 21 | |||||
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MUSCLE Resource Report Resource Website 10000+ mentions |
MUSCLE (RRID:SCR_011812) | MUSCLE | software application, data processing software, data analysis software, data analysis service, analysis service resource, image analysis software, software resource, production service resource, service resource, alignment software | Multiple sequence alignment method with reduced time and space complexity.Multiple sequence alignment with high accuracy and high throughput. Data analysis service for multiple sequence comparison by log- expectation. | bio.tools |
is used by: TranslatorX is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: PREFAB has parent organization: European Bioinformatics Institute |
PMID:15034147 PMID:15318951 DOI:10.1093/nar/gkh340 |
biotools:muscle, OMICS_00982 | https://bio.tools/muscle http://www.drive5.com/muscle/ https://www.drive5.com/muscle/manual/ https://www.drive5 http://bioconductor.org/packages/release/bioc/html/muscle.html.com/muscle/manual/install.html https://sources.debian.org/src/muscle/ |
SCR_011812 | MUltiple Sequence Comparison by Log- Expectation | 2026-02-16 09:47:59 | 16137 | ||||||
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neXtProt Resource Report Resource Website 100+ mentions |
neXtProt (RRID:SCR_008911) | database, data or information resource, topical portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2025. Human protein knowledge platform. Knowledge platform for human proteins selects and filters high throughput data pertinent to human proteins from UniProtKB. Extends UniProtKB/Swiss-Prot annotations for human proteins to include several new data types. | Protein, proteomics, sirna, 3d, pathway, variant, protein-protein interaction, protein-drug interaction, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: UniProtKB has parent organization: SIB Swiss Institute of Bioinformatics |
Swiss Commission for Technology and Innovation ; SIB |
PMID:22139911 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:nextprot, nlx_151482 | https://bio.tools/nextprot | SCR_008911 | 2026-02-16 09:47:18 | 166 | ||||||
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PASA Resource Report Resource Website 500+ mentions |
PASA (RRID:SCR_014656) | software application, data processing software, sequence analysis software, data analysis software, software resource | Gene structure annotation and analysis tool that uses spliced alignments of expressed transcript sequences to automatically model gene structures. It also incorporates gene structures based on transcript alignments into existing gene structure annotations. It is one component of a larger eukayotic annotation pipeline implemented at the Broad Institute. | gene structure, annotation, gene structure analysis tool, spliced alignment, transcript sequence, bio.tools |
is used by: BRO_annotation is listed by: Debian is listed by: bio.tools |
DOI:10.1093/nar/gkg770 | Available for download | biotools:PASA | https://bio.tools/PASA | SCR_014656 | Program to Assemble Spliced Alignments (PASA), Program to Assemble Spliced Alignments | 2026-02-16 09:48:36 | 999 | ||||||
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Molecular Dynamics Workflow (BioKepler) Resource Report Resource Website 1+ mentions |
Molecular Dynamics Workflow (BioKepler) (RRID:SCR_014389) | data processing software, software application, software resource, workflow software | A workflow for running molecular dynamics simulations. It can be used for all-atom molecular dynamic simulations, which involve five steps of minimization, one step of heating, three steps of equilibration, and one or more instances of production. The input is a set of directories that include the MD simulation input scripts, system topology and coordinate files. Output files are list of plots, simulation trajectories, intermediate files, restart files, and the like. | workflow, MD, molecular dynamics, simulation, software, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: bioKepler has parent organization: University of California at San Diego; California; USA |
NIGMS P41GM103426 | Requires Linux | biotools:ambergpumdsimulation | http://nbcr.ucsd.edu/data/downloads/workflows/ https://bio.tools/ambergpumdsimulation |
SCR_014389 | Molecular Dynamics Workflow, AmberGPUMDSimulation, Molecular Dynamics Workflow Software, Amber GPUMD Simulation | 2026-02-16 09:48:38 | 1 | ||||||
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Populations Resource Report Resource Website |
Populations (RRID:SCR_024175) | software resource, software toolkit, software library | Population genetic software for individuals or populations distances based on allelic frequencies, phylogenetic trees, file conversions. | Population genetic, individuals or populations distances, allelic frequencies, phylogenetic trees, file conversions, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_29592 | https://sources.debian.org/src/populations/ | SCR_024175 | populations | 2026-02-16 09:50:39 | 0 | |||||||
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quicktree Resource Report Resource Website 10+ mentions |
quicktree (RRID:SCR_024205) | software resource, software toolkit, software library | Software application as implementation of Neighbor-Joining algorithm, capable of reconstructing phylogenies from huge alignments. | Neighbor-Joining algorithm, reconstructing phylogenies from huge alignments, | is listed by: Debian | PMID:3447015 | Free, Available for download, Freely available, | https://sources.debian.org/src/quicktree/ | SCR_024205 | 2026-02-16 09:50:48 | 12 | ||||||||
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python-airr Resource Report Resource Website |
python-airr (RRID:SCR_024187) | software resource, software toolkit, software library | Software airr reference library provides basic functions and classes for interacting with AIRR Community Data Representation Standards, including tools for read, write and validation. | airr reference library, functions and classes for interacting with AIRR Community Data Representation Standards, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/python3-airr/ | SCR_024187 | 2026-02-16 09:50:54 | 0 | |||||||||
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Tab2MAGE Resource Report Resource Website |
Tab2MAGE (RRID:SCR_024101) | software resource, software toolkit, software library | Software package written and supported by the ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets.Tab2MAGE uses flexible spreadsheet format for MIAME annotation of microarray experiments.Spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange. | ArrayExpress, submitting large microarray experiment datasets, spreadsheet format for MIAME annotation of microarray experiments, | is listed by: Debian | Free, Available for download, Freely available, | https://tab2mage.sourceforge.net/ | https://sources.debian.org/src/mage2tab/ | SCR_024101 | mage2tab, ArrayExpress Tab2MAGE | 2026-02-16 09:50:38 | 0 | |||||||
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Mapsembler2 Resource Report Resource Website 1+ mentions |
Mapsembler2 (RRID:SCR_024102) | software resource, software toolkit, software library | Targeted assembly software. It takes as input any number of NGS raw read sets and starter set of input sequences.May be used to Validate assembled sequence, Check if known enzyme is present in metagenomic NGS read set, Enrich unmappable reads by extending them, Check what happens at the extremities of a contig, Check the presence / absence and quantify RNA seq splicing events, Check presence/absence of SNPs or structural variants. | Targeted assembly, NGS raw read, input sequences, | is listed by: Debian | PMID:22443449 | Free, Available for download, Freely available, | OMICS_18310 | https://sources.debian.org/src/mapsembler2/ | SCR_024102 | mapsembler2, Mapsembler | 2026-02-16 09:50:45 | 1 | ||||||
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affyio Resource Report Resource Website |
affyio (RRID:SCR_024223) | software resource, software toolkit, software library | Software R package as routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing CEL and CDF file formats. | parsing Affymetrix data files, accessing CEL and CDF file formats, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_29381 | https://sources.debian.org/src/r-bioc-affyio/ | SCR_024223 | 2026-02-16 09:50:48 | 0 | ||||||||
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MAXFLOW Resource Report Resource Website |
MAXFLOW (RRID:SCR_024103) | software resource, software toolkit, software library | Software library that implements the maxflow-mincut algorithm.Used for computing mincut/maxflow in a graph. | computing mincut/maxflow in a graph, | is listed by: Debian | DOI:10.1109/TPAMI.2004.60 | Free, Available for download, Freely available, | https://sources.debian.org/src/maxflow/ | SCR_024103 | maxflow | 2026-02-16 09:50:47 | 0 | |||||||
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pssh2 Resource Report Resource Website |
pssh2 (RRID:SCR_024181) | software resource, software toolkit, software library | Software tools for creating the sequence-to-structure alignment database PSSH2. | creating sequence-to-structure alignment database, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/pssh2/ | SCR_024181 | 2026-02-16 09:50:40 | 0 | |||||||||
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pyepl Resource Report Resource Website 1+ mentions |
pyepl (RRID:SCR_024182) | software resource, software toolkit, software library | Software library for coding psychology experiments in Python.Supports presentation of both visual and auditory stimuli, and supports both manual and sound input as responses. | coding psychology experiments, Python | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/python-pyepl/ | SCR_024182 | Python Experiment-Programming Library | 2026-02-16 09:50:47 | 3 | ||||||||
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pbcopper Resource Report Resource Website |
pbcopper (RRID:SCR_024152) | software resource, software toolkit, software library | Software library provides suite of data structures, algorithms, and utilities for PacBio C++ applications. | data structures, algorithms, utilities for PacBio C++ applications, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/pbcopper/ | SCR_024152 | 2026-02-16 09:50:46 | 0 | |||||||||
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Parsnp Resource Report Resource Website 10+ mentions |
Parsnp (RRID:SCR_024153) | software resource, software toolkit, software library | Software to align the core genome of hundreds to thousands of bacterial genomes. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction. | align core genome, bacterial genomes, | is listed by: Debian | PMID:25410596 | Free, Available for download, Freely available, | OMICS_21461 | https://sources.debian.org/src/parsnp/ https://github.com/marbl/parsnp |
SCR_024153 | parsnp | 2026-02-16 09:50:48 | 39 |
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