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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ComplexHeatmap Resource Report Resource Website 1000+ mentions |
ComplexHeatmap (RRID:SCR_017270) | data processing software, software application, data visualization software, data analysis software, software resource | Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns. | arrange, multiple, heatmap, visualize, data, pattern, genomic, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools |
German Cancer Research Center-Heidelberg Center for Personalized Oncology ; BMBF |
PMID:27207943 | Free, Available for download, Freely available | biotools:complexheatmap | https://github.com/jokergoo/ComplexHeatmap, https://bio.tools/complexheatmap | SCR_017270 | 2026-08-05 10:46:45 | 3266 | ||||||
|
SWISS-MODEL Resource Report Resource Website 1000+ mentions |
SWISS-MODEL (RRID:SCR_018123) | data or information resource, data access protocol, software resource, service resource, web service | Software tool as fully automated protein structure homology modeling server, accessible via ExPASy web server, or from program DeepView Swiss Pdb-Viewer. Structural bioinformatics web-server dedicated to homology modeling of 3D protein structures. Used to make protein modelling accessible to all biochemists and molecular biologists. | 3D protein structure, homology modeling server, protein modeling, structural bioinformatics, automated comparative modeling, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: ExPASy Bioinformatics Resource Portal is related to: Swiss-PdbViewerDeepViewv4.0 has parent organization: University of Basel; Basel; Switzerland provides: SWISS-MODEL Repository |
PMID:12824332 | Free, Freely available | biotools:swiss-model_workspace, biotools:swiss_model | https://bio.tools/swiss_model, https://bio.tools/swiss-model_workspace | SCR_018123 | 2026-08-05 10:46:56 | 2796 | |||||||
|
SIGNOR Resource Report Resource Website 10+ mentions |
SIGNOR (RRID:SCR_018485) | data or information resource, data repository, database, storage service resource, service resource | Software application to organize and store in structured format signaling information published in scientific literature. Information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. Each relationship is linked to literature reporting experimental evidence. Each node is annotated with chemical inhibitors that modulate its activity. Signaling information is mapped to human proteome. SIGNOR 2.0 stores manually annotated causal relationships between proteins and other biologically relevant entities including chemicals, phenotypes, complexes, etc with compliance to FAIR data principles. | Signal transduction data, signaling information, published data collection, activity flow, chemical inhibitor, human proteome, manually annotated data, protein, protein relationship, FAIR data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: REDIportal |
Italian Association for Cancer Research ; ELIXIR-IIB ; Italian Node of the European ELIXIR infrastructure ; EMBL-EBI |
PMID:31665520 | Free, Available for download, Freely available | biotools:signor | https://bio.tools/signor | SCR_018485 | SIGnaling Network Open Resource, SIGNOR 2.0 | 2026-08-05 10:47:01 | 40 | |||||
|
FaceSync project Resource Report Resource Website |
FaceSync project (RRID:SCR_021393) | data or information resource, project portal, instrument resource, portal | Project related to emotions and facial expressions. Includes open source guide to building affordable head mount for camera to maintain high temporal and spatial resolution of face throughout duration of experiment. Device is paired with FaceSync, Python toolbox which automatically synchronizes recorded facial expressions to videos and events such as social interactions. | Automatically synchronize videos, manually align audio, plot facial landmark movements, graph data, head mounted camera setup, 3D blueprints, recording facial expressions, OpenBehavior, Bio.Tools, Instrument |
is listed by: OpenBehavior is related to: FaceSync |
PMID:32185017 | Free, Freely available | SCR_021393 | 2026-08-05 10:47:25 | 0 | |||||||||
|
EvidenceFinder Resource Report Resource Website 1+ mentions |
EvidenceFinder (RRID:SCR_013764) | software resource, web application | A web application to assist in the identification of articles and research related to literature search terms. The search covers full text articles in the Europe PMC repository. Relevant papers are suggested to users based on the scientific term searched and the selection of questions, generated by the application, relevant to term searched. | web application, software resource, literature search, bio.tools |
is used by: Europe PubMed Central is listed by: Connected Researchers is listed by: Debian is listed by: bio.tools is related to: Connected Researchers is related to: Europe PubMed Central has parent organization: Europe PubMed Central |
Wellcome Trust 098231 | DOI:10.1093/nar/gku1061 | Free, Public | biotools:evidence_finder | https://bio.tools/evidence_finder | SCR_013764 | 2026-08-05 10:46:03 | 3 | ||||||
|
Mspire-Simulator Resource Report Resource Website 1+ mentions |
Mspire-Simulator (RRID:SCR_001431) | software application, simulation software, standalone software, software resource | A free, open-source shotgun proteomic simulator that goes beyond previous simulation attempts by generating LC-MS features with realistic m/z and intensity variance along with other noise components. | standalone software, shotgun, proteomic, simulation software, bio.tools |
uses: mzML is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian has parent organization: Brigham Young University; Utah; USA |
PMID:24090032 | Free, Freely Available | biotools:mspire-simulator, OMICS_03359 | https://bio.tools/mspire-simulator | SCR_001431 | 2026-08-05 10:43:22 | 1 | |||||||
|
IMG System Resource Report Resource Website 100+ mentions |
IMG System (RRID:SCR_002965) | IMG, IMG/M | data or information resource, portal | Resource for analysis and annotation of genome and metagenome datasets in comprehensive comparative context. IMG provides users with tools for analyzing publicly available genome datasets and metagenome datasets. | microbiome, microbial genetics, genome and metagenome datasets analysis, genome and metagenome datasets, genome, metagenomics, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: Human Microbiome Project has parent organization: DOE Joint Genome Institute |
PMID:17932063 PMID:22086953 |
Free, Freely available | nif-0000-03010, OMICS_01478, SCR_014605, biotools:img_m | http://img.jgi.doe.gov/m, https://bio.tools/img_m | SCR_002965 | Integrated Microbial Genomes System | 2026-08-05 10:43:44 | 199 | |||||
|
EchoBASE Resource Report Resource Website 1+ mentions |
EchoBASE (RRID:SCR_002430) | EchoBASE | data or information resource, database | A database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655. It has been created to integrate information from post-genomic experiments into a single resource with the aim of providing functional predictions for the 1500 or so gene products for which we have no knowledge of their physiological function. While EchoBASE provides a basic annotation of the genome, taken from other databases, its novelty is in the curation of post-genomic experiments and their linkage to genes of unknown function. Experiments published on E. coli are curated to one of two levels. Papers dealing with the determination of function of a single gene are briefly described, while larger dataset are actually included in the database and can be searched and manipulated. This includes data for proteomics studies, protein-protein interaction studies, microarray data, functional genomic approaches (looking at multiple deletion strains for novel phenotypes) and a wide range of predictions that come out of in silico bioinformatic approaches. The aim of the database is to provide hypothesis for the functions of uncharacterized gene products that may be used by the E. coli research community to further our knowledge of this model bacterium. | gene, bio.tools |
is listed by: bio.tools is listed by: Debian |
GlaxoSmithKline ; BBSRC |
PMID:15608209 | nif-0000-02781, biotools:echobase, r3d100011646 | https://bio.tools/echobase, https://doi.org/10.17616/R38W6H | SCR_002430 | EchoBASE: an integrated post-genomic database for Escherichia coli | 2026-08-05 10:43:37 | 6 | |||||
|
Autophagy Database Resource Report Resource Website 10+ mentions |
Autophagy Database (RRID:SCR_002671) | Autophagy DB, AutophagyDB | data or information resource, database | Database that provides basic, up-to-date information on relevant literature, and a list of autophagy-related proteins and their homologs in eukaryotes. | autophagy, protein, homolog, ortholog, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tokyo; Tokyo; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:20972215 | Free, Available for download, Freely available | OMICS_03306, biotools:the_autophagy_database, r3d100012565 | https://bio.tools/the_autophagy_database, https://doi.org/10.17616/R3J786 | SCR_002671 | 2026-08-05 10:43:39 | 17 | |||||
|
DOMINE: Database of Protein Interactions Resource Report Resource Website 1+ mentions |
DOMINE: Database of Protein Interactions (RRID:SCR_002399) | DOMINE | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026. Database of known and predicted protein domain (domain-domain) interactions containing interactions inferred from PDB entries, and those that are predicted by 8 different computational approaches using Pfam domain definitions. DOMINE contains a total of 26,219 domain-domain interactions (among 5,410 domains) out of which 6,634 are inferred from PDB entries, and 21,620 are predicted by at least one computational approach. Of the 21,620 computational predictions, 2,989 interactions are high-confidence predictions (HCPs), 2,537 interactions are medium-confidence predictions (MCPs), and the remaining 16,094 are low-confidence predictions (LCPs). (May 2014) | domain-domain interaction, prediction, protein domain, interaction, protein domain interaction, protein, domain, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Pfam has parent organization: University of Texas at Dallas; Texas; USA |
PMID:21113022 PMID:17913741 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01906, nif-0000-02758, biotools:domine | https://bio.tools/domine | SCR_002399 | Database of Protein Domain Interactions | 2026-08-05 10:43:38 | 1 | |||||
|
VIPERdb Resource Report Resource Website 50+ mentions |
VIPERdb (RRID:SCR_002853) | data or information resource, database | Database for icosahedral virus capsid structures. The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. In addition, all virus capsids are placed in a single icosahedral orientation convention, facilitating comparison between different structures. The web site includes powerful search utilities , links to other relevant databases, background information on virus capsid structure, and useful database interface tools. It is an information source for the analysis of high resolution virus structures. VIPERdb is a one-stop site dedicated to helping users around the world examine the many icosahedral virus structures contained within the Protein Data Bank (PDB) by providing them with an easy to use database containing current data and a variety of analytical tools. Sponsors: VIPERdb is funded by the NIH., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | exploration, analysis, capsid, computational, convention, database, icosahedral, structural, structure, system, virus, visual, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Scripps Research Institute |
PMID:33313778 PMID:30265627 |
Free, Freely available | nif-0000-25311, r3d100012362, nif-0000-03630, biotools:viperdb, SCR_007970 | https://bio.tools/viperdb, https://doi.org/10.17616/R3HT0Q | SCR_002853 | Virus Particle ExploreR | 2026-08-05 10:43:42 | 59 | ||||||
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Human Gene Connectome Server Resource Report Resource Website 1+ mentions |
Human Gene Connectome Server (RRID:SCR_002627) | HGCS | data analysis service, production service resource, service resource, analysis service resource | An interactive web server that enables researchers to prioritize any list of genes by their biological proximity to defined core genes (i.e. genes that are known to be associated with the phenotype), and to predict novel gene pathways. | gene, disease, phenotype, genome, connectome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Human Gene Connectome |
PMID:23509278 | Free | nlx_156049, biotools:hgcs | https://bio.tools/hgcs | SCR_002627 | 2026-08-05 10:43:39 | 5 | ||||||
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Nucleic Acid Database Resource Report Resource Website 10+ mentions |
Nucleic Acid Database (RRID:SCR_003255) | NDB | data or information resource, database | A database of three-dimensional structural information about nucleic acids and their complexes. In addition to primary data, it contains derived geometric data, classifications of structures and motifs, standards for describing nucleic acid features, as well as tools and software for the analysis of nucleic acids. A variety of search capabilities are available, as are many different types of reports. NDB maintains the macromolecular Crystallographic Information File (mmCIF). | nucleic acid, dna, nucleopeptide, nucleoprotein, nucleotide, rna, transfection, sequence, structure, function, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: MINAS - Metal Ions in Nucleic AcidS is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: Jenalib: Jena Library of Biological Macromolecules has parent organization: Rutgers University; New Jersey; USA |
NSF ; DOE ; NIH |
PMID:24185695 PMID:1384741 |
Free, Available for download, Freely available | nif-0000-03184, biotools:ndb, r3d100010415 | https://bio.tools/ndb, https://doi.org/10.17616/R3531R | SCR_003255 | 2026-08-05 10:43:48 | 36 | |||||
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RefSeq Resource Report Resource Website 10000+ mentions |
RefSeq (RRID:SCR_003496) | data or information resource, database | Collection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases. | reference sequence, transcript, protein, dna, rna, plasmid, organelle, virus, genome, nucleic acid, ortholog, paralog, haplotype, nucleotide sequence, gene expression, blast, gold standard, bio.tools |
is listed by: OMICtools is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: BeetleBase is related to: EcoGene is related to: INSDC is related to: HFV Database is related to: RefSeqGene is related to: NCBI Protein Database is related to: RefSeqGene is related to: UniParc at the EBI is related to: NCBI Nucleotide is related to: UniParc is related to: ProRepeat is related to: NCBI Virus is related to: Codon and Codon-Pair Usage Tables is related to: RefSeq non-redundant proteins has parent organization: NCBI |
PMID:24316578 PMID:24259432 PMID:22121212 PMID:18927115 PMID:17130148 PMID:15608248 |
Free, Available for download, Freely available | SCR_016579, nif-0000-03397, OMICS_01659, biotools:refseq, r3d100011306 | ftp://ftp.ncbi.nlm.nih.gov/refseq, https://bio.tools/refseq, https://doi.org/10.17616/R3HP70 | SCR_003496 | RefSeq, , Reference Sequence Database, Reference Sequence, Reference Sequences, NCBI | 2026-08-05 10:43:51 | 18049 | ||||||
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MutDB Resource Report Resource Website 10+ mentions |
MutDB (RRID:SCR_003251) | data or information resource, database | Database with annotations for human variation data with protein structural information and other functionally relevant information, if available. The mutations are organized by gene. | web database, annotation database, human genome, human protein, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Buck Institute; California; USA |
PMID:15980479 | Free, Freely available | biotools:mutdb, nif-0000-03173 | https://bio.tools/mutdb | SCR_003251 | 2026-08-05 10:43:48 | 10 | |||||||
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Proteome Analyst Specialized Subcellular Localization Server Resource Report Resource Website 1+ mentions |
Proteome Analyst Specialized Subcellular Localization Server (RRID:SCR_003143) | PA-SUB | data analysis service, production service resource, service resource, analysis service resource | Web server specialized to predict the subcellular localization of proteins using established machine learning techniques. | subcellular localization, protein, machine learning, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Alberta; Alberta; Canada |
PMID:14990451 | Free, Available for download, Freely available | biotools:pa-sub, OMICS_01631 | https://psort.org/#:~:text=Proteome%20Analyst's%20Subcellular%20Localization%20Server, proteins%20to%20many%20localization%20sites. | SCR_003143 | 2026-08-05 10:43:46 | 1 | ||||||
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PolymiRTS Resource Report Resource Website 100+ mentions |
PolymiRTS (RRID:SCR_003389) | PolymiRTS | data or information resource, database | Database of naturally occurring DNA variations in microRNA (miRNA) seed regions and miRNA target sites. MicroRNAs pair to the transcripts of protein-coding genes and cause translational repression or mRNA destabilization. SNPs and INDELs in miRNAs and their target sites may affect miRNA-mRNA interaction, and hence affect miRNA-mediated gene repression. The PolymiRTS database was created by scanning 3'UTRs of mRNAs in human and mouse for SNPs and INDELs in miRNA target sites. Then, the potential downstream effects of these polymorphisms on gene expression and higher-order phenotypes are identified. Specifically, genes containing PolymiRTSs, cis-acting expression QTLs, and physiological QTLs in mouse and the results of genome-wide association studies (GWAS) of human traits and diseases are linked in the database. The PolymiRTS database also includes polymorphisms in target sites that have been supported by a variety of experimental methods and polymorphisms in miRNA seed regions. | polymorphism, microrna, human, disease, trait, snp, indel, pathway, genetic variant, gene expression, phenotype, chromosome, chromosome location, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
PhRMA Foundation ; UT Center for Integrative and Translational Genomics ; NICHD HD052472; NIAAA AA014425; NIDA DA021131; NINR NR009270; NIAID AI081050; NIAID AI019782; American Heart Association 0830134N; United States Department of Defense W81XHW-05-01-0227 |
PMID:24163105 PMID:22080514 |
Free, Available for download, Freely available | nif-0000-03324, biotools:polymirts, OMICS_00391 | https://bio.tools/polymirts | http://compbio.utmem.edu/miRSNP/ | SCR_003389 | Polymorphism in microRNA Target Site, PolymiRTS Database, Polymorphism in microRNAs and their TargetSites | 2026-08-05 10:43:50 | 149 | |||
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FastSNP Resource Report Resource Website 50+ mentions |
FastSNP (RRID:SCR_003140) | data analysis service, production service resource, service resource, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 9, 2016. A web server that allows users to efficiently identify and prioritize high-risk SNPs according to their phenotypic risks and putative functional effects. A unique feature is that the functional effect information used for SNP prioritization is always up-to-date, because FASTSNP extracts the information from 11 external web servers at query time using a team of web wrapper agents. Moreover, FASTSNP is extendable by deploying more Web wrapper agents. FASTSNP provides three options for users to submit requests. If users already have some candidate SNPs on a candidate gene, they may use Query by Candidate Gene to select the specific SNPs on the gene to perform prioritization. If users have a specified SNP or a list of SNP rsid's needs to be prioritized, they can use Query by SNP option and upload the SNP list in an Excel-format file. Finally, if users have a novel SNP sequence, FASTSNP provides Novel SNP analysis. FASTSNP will generate a SNP Function Report for each SNP. Users can export SNP data to an excel file for further genotyping processes. Other features of FASTSNP include SNP quality checking and haplotype LD information. | single nucleotide polymorphism, function, phenotype, transcript, prioritize, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Academia Sinica; Taipei; Taiwan |
National Research Program in Genomic Medicine ; National Science Council Taiwan NSC93-3112-B-001-008-Y; National Science Council Taiwan NSC93-3112-B-001-018-Y |
PMID:16845089 | Free, Freely available | biotools:fastsnp, OMICS_00173, nif-0000-30566 | https://bio.tools/fastsnp | http://fastsnp.ibms.sinica.edu.tw/pages/input_CandidateGeneSearch.jsp | SCR_003140 | FastSNP: A Functional Analysis and Selection Tool for SNP in Large Scale Association Study, Function Analysis and Selection Tool for Single Nucleotide Polymorphisms, A Functional Analysis and Selection Tool for SNP in Large Scale Association Study | 2026-08-05 10:43:46 | 62 | ||||
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PHI-base Resource Report Resource Website 100+ mentions |
PHI-base (RRID:SCR_003331) | PHI-base | data or information resource, database | Database that catalogs experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. It is an invaluable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. In collaboration with the FRAC team, it also includes antifungal compounds and their target genes. Each entry is curated by domain experts and is supported by strong experimental evidence (gene disruption experiments, STM etc), as well as literature references in which the original experiments are described. Each gene is presented with its nucleotide and deduced amino acid sequence, as well as a detailed description of the predicted protein's function during the host infection process. To facilitate data interoperability, genes have been annotated using controlled vocabularies and links to external sources (Gene Ontology terms, EC Numbers, NCBI taxonomy, EMBL, PubMed and FRAC). | gene expression, pathogenic bacteria, virulence, infection, target site, gene, pathogen-host interaction, interaction, phenotype, pathogen, disease, host, anti-infective, nucleotide sequence, amino acid sequence, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian |
BBSRC BB/1000488/1 | PMID:17942425 PMID:17153929 PMID:16381911 |
Free, Freely available | nif-0000-03276, r3d100011301, biotools:phi-base | https://bio.tools/phi-base, https://doi.org/10.17616/R35D1V | http://www4.rothamsted.bbsrc.ac.uk/phibase/ | SCR_003331 | Pathogen Host Interaction base, Pathogen Host Interaction, Pathogen Host Interaction-Base | 2026-08-05 10:43:49 | 198 | |||
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T-profiler Resource Report Resource Website 10+ mentions |
T-profiler (RRID:SCR_003452) | T-profiler | data analysis service, production service resource, service resource, analysis service resource | One of the key challenges in the analysis of gene expression data is how to relate the expression level of individual genes to the underlying transcriptional programs and cellular state. The T-profiler tool hosted on this website uses the t-test to score changes in the average activity of pre-defined groups of genes. The gene groups are defined based on Gene Ontology categorization, ChIP-chip experiments, upstream matches to a consensus transcription factor binding motif, and location on the same chromosome, respectively. If desired, an iterative procedure can be used to select a single, optimal representative from sets of overlapping gene groups. A jack-knife procedure is used to make calculations more robust against outliers. T-profiler makes it possible to interpret microarray data in a way that is both intuitive and statistically rigorous, without the need to combine experiments or choose parameters. Currently, gene expression data from Saccharomyces cerevisiae and Candida albicans are supported. Users can submit their microarray data for analysis by clicking on one of the two organism-specific tabs above. Platform: Online tool | expression, gene, binding, cellular, transcriptional, gene expression, microarray, gene ontology, transcription factor, binding motif, chip-chip, chip, motif, t-test, statistical analysis, transcriptome, bio.tools |
is listed by: Biositemaps is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Columbia University; New York; USA has parent organization: University of Amsterdam; Amsterdam; Netherlands |
Netherlands Foundation for Technical Research APB.5504; NHGRI R01HG003008 |
PMID:15980543 | Free for academic use | nif-0000-33354, biotools:t-profiler | https://bio.tools/t-profiler | SCR_003452 | T-profiler: Scoring the Activity of Pre-defined Groups of Genes Using Gene Expression Data | 2026-08-05 10:43:51 | 11 |
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