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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
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 2026-09-03 05:02:19 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 2026-09-03 05:02:43 90
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 2026-09-03 05:02:42 0
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 2026-09-03 05:02:31 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 2026-09-03 05:02:30 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 2026-09-03 05:02:36 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 2026-09-03 05:02:48 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 2026-09-03 05:02:53 161
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 2026-09-03 05:02:55 495
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 2026-09-03 05:02:39 2
RightField
 
Resource Report
Resource Website
1+ mentions
RightField (RRID:SCR_002649) RightField software application, software resource An open-source tool for adding ontology term selection to Excel spreadsheets. It is used by a "Template Creator" to create semantically aware Excel spreadsheet templates. The Excel templates are then reused by Scientists to collect and annotate their data; without any need to understand, or even be aware of, RightField or the ontologies used. For each annotation field, RightField can specify a range of allowed terms from a chosen ontology (subclasses, individuals or combinations). The resulting spreadsheet presents these terms to the users as a simple drop-down list. This reduces the adoption barrier for using community ontologies as the annotation is made by the scientist that generated the data rather than a third party, and the annotation is collected at the time of data collection. RightField is a standalone Java application which uses Apache-POI for interacting with Microsoft documents. It enables users to import Excel spreadsheets, or generate new ones from scratch. Ontologies can either be imported from their local file systems, or from the BioPortal ontology repository. Individual cells, or whole columns or rows can be marked with the required ranges of ontology terms and an individual spreadsheet can be annotated with terms from multiple ontologies. annotation, semantic, ontology, term selection, excel, java, bio.tools is listed by: BioPortal
is listed by: FORCE11
is listed by: bio.tools
is listed by: Debian
is related to: SEEK
is related to: Workflow4Ever
has parent organization: University of Manchester; Manchester; United Kingdom
has parent organization: Heidelberg Institute for Theoretical Studies; Heidelberg; Germany
PMID:21622664 Free, Available for download, Freely available biotools:rightfield, nlx_156077 https://bio.tools/rightfield SCR_002649 2026-09-03 05:04:02 3
AltAnalyze - Alternative Splicing Analysis Tool
 
Resource Report
Resource Website
50+ mentions
AltAnalyze - Alternative Splicing Analysis Tool (RRID:SCR_002951) AltAnalyze software application, software resource Software application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), it will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, it provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichement and more). AltAnalyze can be run through an intuitive graphical user interface or command-line and requires no advanced knowledge of bioinformatics programs or scripting. Alternative regulated exons can be subsequently visualized in the context of proteins, domains and microRNA binding sites with the Cytoscape Plugin DomainGraph. analysis, alternative splicing, microarray, calculate, pathway, ontology, domain, microrna, targeting, splicing, microarry, rna-seq, metabolomics, mac osx, windows, ubuntu, cross platform, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: Cytoscape
has parent organization: University of California at San Francisco; California; USA
PMID:20513647 Free, Available for download, Freely available nif-0000-30083, OMICS_02250, biotools:altanalyze https://bio.tools/altanalyze SCR_002951 Alternative Splicing Analysis Tool 2026-09-03 05:03:54 86
cortex
 
Resource Report
Resource Website
100+ mentions
cortex (RRID:SCR_002467) cortex software application, software resource Software package with functions that will help researchers plan how many subjects per group need to be included in an MRI-based cortical thickness study to ensure a thickness difference is detected. The package requires cortical thickness mapping and co-registration to be carried out using Freesurfer. The power analyses are implemented in the R software package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. clinical neuroinformatics, mgh/mgz, magnetic resonance, r, surface analysis, thickness, mri, cortical thickness, morphometry, neuroimaging, power analysis, study design, bio.tools is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: bio.tools
is listed by: Debian
has parent organization: Brain Research Institute
PMID:22807270 THIS RESOURCE IS NO LONGER IN SERVICE nlx_155842, biotools:cortex http://brain.org.au/software/cortex/power, http://www.nitrc.org/projects/cortex, https://bio.tools/cortex SCR_002467 Sample Size Estimates for Well-Powered Cross-Sectional Cortical Thickness Studies 2026-09-03 05:03:52 374
MAKER
 
Resource Report
Resource Website
1000+ mentions
MAKER (RRID:SCR_005309) software resource, software toolkit Software genome annotation pipeline. Portable and easily configurable genome annotation pipeline. Used to allow smaller eukaryotic and prokaryotic genomeprojects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence based quality values. gene prediction, genome annotation, identifies repeats, aligns ESTs and proteins to genome, data management, genome annotation, annotation, curation, bio.tools, FASEB list is listed by: bio.tools
is listed by: Debian
is related to: MAKER Web Annotation Service
has parent organization: University of Utah; Utah; USA
PMID:25501943 SCR_023883, nlx_144363, biotools:maker https://bio.tools/maker, https://github.com/Yandell-Lab/maker SCR_005309 Maker2, maker 2026-09-03 05:04:04 1519
Unipro UGENE
 
Resource Report
Resource Website
100+ mentions
Unipro UGENE (RRID:SCR_005579) UGENE software resource, software toolkit A multiplatform open-source software to assist molecular biologists without much expertise in bioinformatics to manage, analyze and visualize their data. UGENE integrates widely used bioinformatics tools within a common user interface. The toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees and 3D structures. Most of the integrated algorithms are tuned for maximum performance by the usage of multithreading and special processor instructions. UGENE includes a visual environment for creating reusable workflows that can be launched on local resources or in a High Performance Computing (HPC) environment. UGENE is written in C++ using the Qt framework. The built-in plugin system and structured UGENE API make it possible to extend the toolkit with new functionality. c++, windows, mac os, linux, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
PMID:22368248
DOI:10.1093/bioinformatics/bts091
GNU General Public License, v2, Acknowledgement requested OMICS_01022, biotools:ugene https://bio.tools/ugene, https://sources.debian.org/src/ugene/ SCR_005579 2026-09-03 05:04:05 183
Yabi
 
Resource Report
Resource Website
Yabi (RRID:SCR_005359) Yabi service resource, software resource A web-based analytical environment framework for bioinformatics applications that can be customized for a diverse range of -omics applications. The software system is adaptable to a range of both pluggable execution and data backends in an open source implementation. Enabling seamless and transparent access to heterogenous HPC environments at its core, it then provides an analysis workflow environment that can create and reuse workflows as well as manage large amounts of both raw and processed data in a secure and flexible way across geographically distributed compute resources. Yabi can be used via a web-based environment to drag-and-drop tools to create sophisticated workflows. It can also be accessed through the Yabi command line which is designed for users that are more comfortable with writing scripts or for enabling external workflow environments to leverage the features in Yabi. Configuring tools can be a significant overhead in workflow environments. Yabi greatly simplifies this task by enabling system administrators to configure as well as manage running tools via a web-based environment and without the need to write or edit software programs or scripts. grid computing, high performance computing, cloud computing, bioinformatics, pipeline, workflow, command line, python, linux, storage, compute, genomics, transcriptomics, proteomics, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Murdoch University; Perth; Australia
PMID:22333270 GNU General Public License, v3 OMICS_01148, biotools:yabi https://bio.tools/yabi SCR_005359 2026-09-03 05:04:27 0
HAPLOCLUSTERS
 
Resource Report
Resource Website
HAPLOCLUSTERS (RRID:SCR_007439) HAPLOCLUSTERS software application, software resource Software program designed to detect excess haplotypes sharing in datasets consisting of case and control haplotypes. Excess haplotype sharing can be seen around disease loci in case samples since LD persists longer here than in the controls where LD is persisting only according to the relatedness of the individuals in the population, i.e. the age of the population. (entry from Genetic Analysis Software) gene, genetic, genomic, bio.tools is listed by: Genetic Analysis Software
is listed by: bio.tools
is listed by: Debian
Aging nlx_154014, biotools:haploclusters https://bio.tools/haploclusters SCR_007439 2026-09-03 05:03:51 0
LINKAGE
 
Resource Report
Resource Website
LINKAGE (RRID:SCR_007033) software application, software resource Standard software package for genetic linkage called LINKAGE. Genetic linkage analysis is statistical technique used to map genes and find approximate location of disease genes. Genetic linkage analysis, map genes, find location, disease, genes is listed by: Genetic Analysis Software
is listed by: bio.tools
is listed by: Debian
is related to: FASTLINK
nlx_154346, biotools:linkage https://bio.tools/linkage, https://gaow.github.io/genetic-analysis-software/l/lcp/, https://gaow.github.io/genetic-analysis-software/l/linkage-general-pedigrees/ http://www.jurgott.org/linkage/LinkagePC SCR_007033 , Linkage Control Program 2026-09-03 05:04:22 0
PubCrawler
 
Resource Report
Resource Website
10+ mentions
PubCrawler (RRID:SCR_008235) service resource, software resource PubCrawler is a free alerting service that scans daily updates to the NCBI Medline (PubMed) and GenBank databases. PubCrawler helps keeping scientists informed of the current contents of Medline and GenBank, by listing new database entries that match their research interests. The free PubCrawler web service has been operating for five years and so far has brought literature and sequence updates to over 22 000 users. It provides information on a personalized web page whenever new articles appear in PubMed or when new sequences are found in GenBank that are specific to customized queries. The server also acts as an automatic alerting system by sending out short notifications or emails with the latest updates as soon as they become available. PubCrawler searches the NCBI PubMed (Medline) and Entrez (GenBank) databases daily using search parameters (keywords, author names, etc.) specified by the user. There is no limit on the number of searches that can be carried out. Previous search hits are stored and only the newest PubMed or GenBank records are shown each day. The results are presented as an HTML Web page, similar to the results of an NCBI PubMed or Entrez query. This Web page can be located on our computer (the PubCrawler WWW-Service), on your computer (the stand-alone program), or you can receive it via e-mail (set this up using the PubCrawler WWW-Service). The Web page sorts the results into groups of PubMed/GenBank entries that are zero-days-old, 1-day-old, 2-days-old, etc., up to a user-specified age limit. Sponsors: Development of PubCrawler was supported by EMBnet training tools, bio.tools is listed by: 3DVC
is listed by: bio.tools
is listed by: Debian
biotools:pubcrawler, nif-0000-21345 https://bio.tools/pubcrawler SCR_008235 PubCrawler 2026-09-03 05:04:33 10
MULTIMAP
 
Resource Report
Resource Website
10+ mentions
MULTIMAP (RRID:SCR_007168) MULTIMAP software application, software resource Software program for automated construction of genetic maps (entry from Genetic Analysis Software) gene, genetic, genomic, lisp, unix, (sun/compaq-alpha/hp..), bio.tools is listed by: Genetic Analysis Software
is listed by: bio.tools
is listed by: Debian
biotools:multimap, nlx_154013 https://bio.tools/multimap http://compgen.rutgers.edu/Multimap/ SCR_007168 2026-09-03 05:04:11 31

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