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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
MIMOSA
 
Resource Report
Resource Website
MIMOSA (RRID:SCR_000184) software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for modeling count data using Dirichlet-multinomial and beta-binomial mixtures with applications to single-cell assays. software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Bioconductor
PMID:23887981 THIS RESOURCE IS NO LONGER IN SERVICE biotools:mimosa, OMICS_05642 https://bio.tools/mimosa SCR_000184 MIMOSA - Mixture Models for Single-Cell Assays, MIMOSA: Mixture Models For Single Cell Assays 2026-09-05 06:24:13 0
MODENT - A Tool For Reconstructing Gene Regulatory Networks
 
Resource Report
Resource Website
1+ mentions
MODENT - A Tool For Reconstructing Gene Regulatory Networks (RRID:SCR_000220) ModEnt software resource A computational tool that reconstructs gene regulatory networks from high throughput experimental data. gene regulatory network, experimental data, computation, computational tool, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Tel Aviv University; Ramat Aviv; Israel
PMID:22216865 Free, Available for download, Freely available biotools:modent, OMICS_01685 https://bio.tools/modent SCR_000220 2026-09-05 06:24:14 1
GENIE3
 
Resource Report
Resource Website
10+ mentions
GENIE3 (RRID:SCR_000217) GENIE3 software resource An algorithm for the inference of gene regulatory networks from expression data. javascript, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
PMID:20927193 Free, Available for download, Freely available biotools:genie3, OMICS_01683 https://bio.tools/genie3 http://www.montefiore.ulg.ac.be/~huynh-thu/software.html SCR_000217 2026-09-05 06:24:14 10
GraBCas
 
Resource Report
Resource Website
GraBCas (RRID:SCR_000205) GraBCas software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software tool for predicting granzyme B and caspase cleavage sites. matlab, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
PMID:15980455 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01674, biotools:grabcas https://bio.tools/grabcas SCR_000205 2026-09-05 06:24:16 0
Hyper Cell Line Database
 
Resource Report
Resource Website
Hyper Cell Line Database (RRID:SCR_007730) HyperCLDB biomaterial supply resource, material resource, tissue bank Hypertext on cell culture availability extracted from the Cell Line Data Base of the Interlab Project. HyperCLDB includes links to records of OMIM, the Online Mendelian Inheritance in Man Catalogue, and now also links to the PubMed, database of bibliographic biomedical references, which are drawn primarily from MEDLINE and PREMEDLINE. cell, cell line, tumor, tissue, organ, blood, bodily fluid, ascitic fluid, brain, bone marrow, cancer, transforming agent, software, bio.tools is listed by: One Mind Biospecimen Bank Listing
is listed by: 3DVC
is listed by: Debian
is listed by: bio.tools
is related to: ATCC
is related to: Cell Line Knowledge Base
has parent organization: IST National Institute for Cancer Research; Genoa; Italy
Cancer, Etc. PMID:18927105 nif-0000-03004, biotools:hypercldb https://bio.tools/hypercldb SCR_007730 2026-09-05 06:31:44 0
Genome Reviews
 
Resource Report
Resource Website
1+ mentions
Genome Reviews (RRID:SCR_007685) data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE, documented April 24, 2017. The Genome Reviews database provides an up-to-date, standardized and comprehensively annotated view of the genomic sequence of organisms with completely deciphered genomes. Currently, Genome Reviews contains the genomes of archaea, bacteria, bacteriophages and selected eukaryota. Genome Reviews is available as a MySQL relational database, or a flat file format derived from that in the EMBL Nucleotide Sequence Database. An Ensembl-style browser is now available for Genome Reviews, providing a zoomable graphical view of all chromosomes and plasmids represented in the database. The location and structure of all genes is shown and the distribution of features throughout the sequence is displayed. complete genome sequence, genome sequence, nucleotides, gold standard, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: European Bioinformatics Institute
European Union FELICS contract 021902 (RII3);
European Union TEMBLOR contract QLRI- CT-2001000015
PMID:16901215
PMID:15608201
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-02899, biotools:genomereviews https://bio.tools/genomereviews SCR_007685 Genome Reviews Database 2026-09-05 06:31:42 4
FireDB
 
Resource Report
Resource Website
1+ mentions
FireDB (RRID:SCR_007655) FireDB data or information resource, database A database of Protein Data Bank structures, ligands and annotated functional site residues. The database can be accessed by PDB codes or UniProt accession numbers as well as keywords. FireDB contains information on every chemical compound in the PDB, including their descriptions, the PDB structures in which the compounds are found and the amino acids that are in contact with the ligand. protein, protein structure, pdb, bio.tools uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
is listed by: bio.tools
is listed by: Debian
has parent organization: Spanish National Cancer Research Center
nif-0000-02839, biotools:firedb https://bio.tools/firedb SCR_007655 2026-09-05 06:31:42 7
MfunGD - MIPS Mouse Functional Genome Database
 
Resource Report
Resource Website
50+ mentions
MfunGD - MIPS Mouse Functional Genome Database (RRID:SCR_007783) MfunGD data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2019.Database for annotated mouse proteins and their occurrence in protein networks. It contains cDNA and protein sequences, annotation, gene models and mapping, FunCat, UCSC Genome Viewer, SIMAP, pseudogenes (Genome Viewer Track), InterPro, and splice variants. Protein function annotation is performed using the Functional Catalogue (FunCat) annotation scheme, which is a hierarchically structured classification system. To provide up-to-date similarity search results and InterPro domain analyses, the protein entries are interconnected with the SIMAP database. The gene models are based on the RefSeq mouse cDNAs. The work of our group is focussed on the annotation of biological systems. Therefore, results from the Mammalian Protein-Protein Interaction Database and the Comprehensive Resource of Mammalian Protein Complexes are linked to the MfunGD dataset. Links to external resources are also provided. MfunGD is implemented in GenRE, a J2EE based component oriented multi-tier architecture. bio.tools is listed by: Debian
is listed by: bio.tools
GSF National Research Center for Environment and Health ;
German Federal Ministry of Research and Education
PMID:16381934 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-03121, biotools:mfungd https://bio.tools/mfungd SCR_007783 Mouse Functional Genome Database 2026-09-05 06:31:45 90
IRESite
 
Resource Report
Resource Website
50+ mentions
IRESite (RRID:SCR_007753) data or information resource, database Database of experimentally verified IRES structures. Presents information about experimentally studied Internal Ribosome Entry Site segments. bio.tools, experimentally verified IRES structures, Internal Ribosome Entry Site segments, IRES structures, IRES segments is listed by: bio.tools
is listed by: Debian
has parent organization: Charles University; Prague; Czech Republic
nif-0000-03047, nif-0000-03046, SCR_007754, biotools:iresite https://bio.tools/iresite http://ifr31w3.toulouse.inserm.fr/IRESdatabase/ SCR_007753 IRESdb, , IRESdb - the Internal Ribosome Entry Site database, Internal Ribosome Entry Site 2026-09-05 06:31:44 52
Integr8 : Access to complete genomes and proteomes
 
Resource Report
Resource Website
50+ mentions
Integr8 : Access to complete genomes and proteomes (RRID:SCR_007740) data or information resource, database The Integr8 web portal provides easy access to integrated information about deciphered genomes and their corresponding proteomes. Available data includes DNA sequences (from databases including the EMBL Nucleotide Sequence Database, Genome Reviews, and Ensembl); protein sequences (from databases including the UniProt Knowledgebase and IPI); statistical genome and proteome analysis (performed using InterPro, CluSTr, and GOA); and information about orthology, paralogy, and synteny. bio.tools is listed by: bio.tools
is listed by: Debian
is related to: InteroPorc
has parent organization: European Bioinformatics Institute
nif-0000-03027, biotools:intergr8 https://bio.tools/intergr8 SCR_007740 Integr8 2026-09-05 06:31:44 52
TAndem Splice Site DataBase
 
Resource Report
Resource Website
1+ mentions
TAndem Splice Site DataBase (RRID:SCR_007961) data or information resource, database TassDB stores extensive data about alternative splice events at GYNGYN donors and NAGNAG acceptors. Currently, 114,554 tandem splice sites of eight species are contained in the database, 5,209 of which have EST/mRNA evidence for alternative splicing. Users can search by Transcript Accession Number and Gene Symbol, SQL Query, and Tandem Donor/Tandem Acceptor pairs. bio.tools is listed by: bio.tools
is listed by: Debian
nif-0000-03536, biotools:tassdb https://bio.tools/tassdb http://helios.informatik.uni-freiburg.de/TassDB/ SCR_007961 TassDB 2026-09-05 06:31:49 6
SISYPHUS
 
Resource Report
Resource Website
1+ mentions
SISYPHUS (RRID:SCR_007930) data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A collection of manually curated protein structural alignments and their interrelationships. Each multiple alignment within the SISYPHUS database consists of structurally similar regions common to a group of proteins. These regions range from oligomeric biological units, or individual domains to fragments of different size representing either internal structural repeats or motifs common to structurally distinct proteins. The SISYPHUS multiple alignments are displayed with SPICE, a browser that provides an integrated view of protein sequences, structures and their annotations. bio.tools is listed by: bio.tools
is listed by: Debian
THIS RESOURCE IS NO LONGER IN SERVICE biotools:sisyphus https://bio.tools/sisyphus SCR_007930 SISYPHUS 2026-09-05 06:31:48 3
SilkDB
 
Resource Report
Resource Website
100+ mentions
SilkDB (RRID:SCR_007926) data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 20,2019.A database of integrated genome resources for the silkworm, Bombyx mori. This database provides access to not only genomic data including functional annotation of genes, gene products and chromosomal mapping, but also extensive biological information such as microarray expression data, ESTs and corresponding references. SilkDB will be useful for the silkworm research community as well as comparative genomics. Recently, an international collaboration has been launched to assemble a complete silkworm genome sequence, which is based on the 6� and 3� draft genome sequences created by Chinese group and Japanese group in 2004 (Mita et al., 2004; Xia et al., 2004), respectively. The genome assembly quality has been greatly improved. Base on a high density SNP genetic map, over 80% of genome sequence could be mapped on 28 chromosomes of the silkworm. The first version of SilkDB was released in 2004. Since that time, the silkworm has become a focus in insect research community and the study of silkworm has been greatly accelerated. Now, we are happy to announce the release of a new version of SilkDB, which updated all of the data, added new information of genome sequence and genes, and provides new tools to facilitate use of the genome database. bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Southwest University; Chongqing; China
THIS RESOURCE IS NO LONGER IN SERVICE r3d100012187, biotools:silkdb https://bio.tools/silkdb, https://doi.org/10.17616/R3435Z, https://doi.org/10.17616/R3435Z SCR_007926 SilkDB 2026-09-05 06:31:48 161
Athena
 
Resource Report
Resource Website
100+ mentions
Athena (RRID:SCR_008110) data or information resource, database Athena is a web-based application that warehouses disparate datatypes related to the control of gene expression. Athena provides several features to enable exploration of the regulatory mechanisms of Arabidopsis gene control. The first main tool we provide is visualization of promoter domains of selected genes. Database crossreference for these transcription factors is provided as well as a statistical test for enrichment of binding activity within the set of selected promoters. The data mining tools in Athena allow for selection of sets of genes based on two different factors. -Genes can be select by specifying a set of binding factors whose putative sites must be present within all of those genes'' promoter regions. -Alternatively, genes can be selected using Gene Ontology annotations. Both GO (Gene Ontology) Slim terms and Gene Ontology terms are available. One can select a set of genes by either choosing a union of the genes annotated by a selected set of Slim terms or Gene Ontology terms. The selected gene''s putative binding factors are listed, including enrichment data. Furthermore, enriched presence of Gene Ontology terms is given. The analysis suite provides both enhanced data mining tools for selecting genes as well as several data displays., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. gene control, gene expression, arabidopsis, binding factor, regulatory mechanism, ontology, bio.tools, FASEB list is listed by: bio.tools
is listed by: Debian
has parent organization: Washington State University; Washington; USA
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-20815, biotools:Athena https://bio.tools/Athena SCR_008110 Athena 2026-09-05 06:31:50 495
LitMiner
 
Resource Report
Resource Website
1+ mentions
LitMiner (RRID:SCR_008200) data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The LitMiner software is a literature data-mining tool that facilitates the identification of major gene regulation key players related to a user-defined field of interest in PubMed abstracts. The prediction of gene-regulatory relationships is based on co-occurrence analysis of key terms within the abstracts. LitMiner predicts relationships between key terms from the biomedical domain in four categories (genes, chemical compounds, diseases and tissues). The usefulness of the LitMiner system has been demonstrated recently in a study that reconstructed disease-related regulatory networks by promoter modeling that was initiated by a LitMiner generated primary gene list. To overcome the limitations and to verify and improve the data, we developed WikiGene, a Wiki-based curation tool that allows revision of the data by expert users over the Internet. It is based on the annotation of key terms in article abstracts followed by statistical co-citation analysis of annotated key terms in order to predict relationships. Key terms belonging to four different categories are used for the annotation process: -Genes: Names of genes and gene products. Gene name recognition is based on Ensembl . Synonyms and aliases are resolved. -Chemical Compounds: Names of chemical compounds and their respective aliases. -Diseases and Phenotypes: Names of diseases and phenotypes -Tissues and Organs: Names of tissues and organs LitMiner uses a database of disease and phenotype terms for literature annotation. Currently, there are 2225 diseases or phenotypes, 801 tissues and organs, and 10477 compounds in the database. gene, biomedical, chemical, compound, disease, identification, literature, medline interfaces, mining, modeling, phenotype, promoter, regulation, regulatory, relationship, tissue, tool, bio.tools is listed by: bio.tools
is listed by: Debian
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-21241, biotools:litminer https://bio.tools/litminer SCR_008200 LitMiner 2026-09-05 06:31:51 2
Homologous Sequences in Ensembl Animal Genomes
 
Resource Report
Resource Website
1+ mentions
Homologous Sequences in Ensembl Animal Genomes (RRID:SCR_008356) HOMOLENS data or information resource, database Database of homologous genes from Ensembl organisms, structured under ACNUC sequence database management system. It allows to select sets of homologous genes among species, and to visualize multiple alignments and phylogenetic trees. It is possible to search for orthologous genes in a wide range of taxons. HOMOLENS is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies. More generally, HOMOLENS gives an overall view of what is known about a peculiar gene family. Note that HOMOLENS is split into two databases on this server: HOMOLENS contains the protein sequences while HOMOLENSDNA contains the nucleotide sequences. Protein sequences of HOMOLENS have been generated by translating the CDS of HOMOLENSDNA and using associated cross-references to generate the annotations. ensembl, evolution, gene, alignment, comparative, homologous, molecular, nucleotide, organism, phylogenetic, phylogeny, protein, sequence, specie, structure, taxon, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Claude Bernard University Lyon 1; Lyon; France
biotools:homolens, nif-0000-25424 https://bio.tools/homolens SCR_008356 2026-09-05 06:31:52 3
Regulatory Sequence Analysis Tools
 
Resource Report
Resource Website
100+ mentions
Regulatory Sequence Analysis Tools (RRID:SCR_008560) data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Retrieve-ensembl-seq is included in the software suite regulatory sequence analysis tools (RSAT), allowing instant submission of retrieved sequences to further analysis tools. AVAILABILITY: retrieve-ensembl-seq is integrated in the RSAT suite: http://rsat.ulb.ac.be/rsat. Web site: http://rsat.ulb.ac.be/rsat/retrieve-ensembl-seq_form.cgi. Web services: http://rsat.ulb.ac.be/rsat/web_services/RSATWS.wsdl. Stand-alone distribution: freely available under an academic licence to download from the RSAT web site. The complete manual, a convenient tutorial and demos are available from the RSAT website. Additional help can be found on the RSAT public forum. bio.tools, FASEB list is listed by: Debian
is listed by: bio.tools
is related to: Yeast Search for Transcriptional Regulators And Consensus Tracking
DOI:10.1093/nar/gkv362 THIS RESOURCE IS NO LONGER IN SERVICE biotools:rsat, nif-0000-31437, OMICS_08097 https://bio.tools/rsat https://sources.debian.org/src/rsat/ SCR_008560 RSAT 2026-09-05 06:31:53 108
Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD)
 
Resource Report
Resource Website
10+ mentions
Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD) (RRID:SCR_008621) SNPSpD analysis service resource, data analysis service, production service resource, service resource SNPSpD is a method of correcting for non-independance of single nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with each other, on the basis of the spectral decomposition (SpD) of matrices of LD between SNP''s. Additionally, output from SNPSpD includes eigenvalues, principal-component coefficients, and factor loadings after varimax rotation, enabling the selection of a subset of SNPs that optimize the information in a genomic region. bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: Queensland Institute of Medical Research
National Health and MRC Australia 241916 PMID:14997420 biotools:snpspd, nif-0000-31985 https://bio.tools/snpspd http://genepi.qimr.edu.au/general/daleN/SNPSp SCR_008621 Single Nucleotide Polymorphism Spectral Decomposition 2026-09-05 06:31:53 18
Webproanalyst
 
Resource Report
Resource Website
Webproanalyst (RRID:SCR_008348) analysis service resource, data analysis service, production service resource, service resource WebProAnalyst provides web-accessible analysis for scanning the quantitative structure-activity relationships in protein families. It searches for a sequence region, whose substitutions are correlated with variations in the activities of a homologous protein set, the so-called activity modulating sites. WebProAnalyst allows users to search for the key physicochemical characteristics of the sites that affect the changes in protein activities. It enables the building of multiple linear regression and neural networks models that relate these characteristics to protein activities. WebProAnalyst implements multiple linear regression analysis, back propagation neural networks and the Structure-Activity Correlation/Determination Coefficient (SACC/SADC). A back propagation neural network is implemented as a two-layered network, one layer as input, the other as output (Rumelhart et al, 1986). WebProAnalyst uses alignment of amino acid sequences and data on protein activity (pK, Km, ED50, among others). The input data are the numerical values for the physicochemical characteristics of a site in the multiple alignment given by a slide window. The output data are the predicted activity values. The current version of WebProAnalyst handles a single activity for a single protein. The SACC/SADC may be defined as an estimate of the strongest multiple correlation between the physicochemical characteristics of a site in a multiple alignment and protein activities. The SACC/SADC coefficient makes possible the calculation of the possible highest correlation achievable for the quantitative relationship between the physicochemical properties of sites and protein activities. The SACC/SADC is a convenient means for an arrangement of positions by their functional significance. WebProAnalyst outputs a list of multiple alignment positions, the respective correlation values, also regression analysis parameters for the relationships between the amino acid physicochemical characteristics at these positions and the protein activity values. family, functional, activity, alignment, amino acid, homologous, modulating site, neural, physicochemical, propagation, protein, quantitative, region, relationship, scan, sequence, structure, substitution, variation, bio.tools is listed by: bio.tools
is listed by: Debian
nif-0000-25212, biotools:webproanalyst https://bio.tools/webproanalyst SCR_008348 Webproanalyst 2026-09-05 06:31:52 0
GeneSeeker
 
Resource Report
Resource Website
1+ mentions
GeneSeeker (RRID:SCR_008347) data or information resource, database The GeneSeeker allows you to search across different databases simultaneously, given a known human genetic location and expression/phenotypic pattern. The GeneSeeker returns any found gene names which are located on the specified location and expressed in the specified tissue. To search for more expression location in one search, just enter them in the textbox for the expression location and separate them with logical operators (and, or, not). You can specify as many tissues as you want, the program starts 20 queries simultaneously, and then waits for a query to finish before starting another query, to keep server loads to a minimum. You can also search only for expression, just leave the cytogenetic location fields blank, and do the query. If you only want to look for one cytogenetic location, only fill in the first location field, and the GeneSeeker will search with only this one. Housekeeping genes , found in Swissprot can be excluded, or genes that are to be excluded can be specified. Human chromosome localizations are translated with an oxford-grid to mouse chromosome localizations, and then submitted to the Mgd. Sponsors: GeneSeeker is a service provided by the Centre for Molecular and Biomolecular Informatics (CMBI). expression, federated database, gene, genetic, biomolecular, chromosome, cytogenetic, database, human, localization, location, molecular, pattern, phenotypic, tissue, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Radboud University; Nijmegen; The Netherlands
biotools:geneseeker, nif-0000-25211 https://bio.tools/geneseeker SCR_008347 GeneSeeker 2026-09-05 06:31:52 5

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