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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ApiDB CryptoDB Resource Report Resource Website 10+ mentions |
ApiDB CryptoDB (RRID:SCR_013455) | ApiDB CryptoDB | data or information resource, database | An integrated genomic and functional genomic database for the parasite Cryptosporidium. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining. Organisms included in CryptoDB are Cryptosporidium parvum, Cryptosporidium hominis, Cryptosporidium muris and environmental isolate sequences from numerous species. CryptoDB is allied with the databases PlasmoDB and ToxoDB via ApiDB, an NIH/NIAID-funded Bioinformatics Resource Center. Tools include: * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Cryptosporidium Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * CryptoCyc: Explore Automatically Defined Metabolic Pathways * Searches via Web Services: Web service access to our data | cryptosporidium parvum, cryptosporidium, cryptosporidium genome, cryptosporidium orf, cryptosporidium sage tag alignments, cryptosporidium snp, genomic sequence, dna motif, snp, est, orf, data set, bio.tools |
uses: SynView is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Eukaryotic Pathogen Database Resources |
NIAID contract HHSN266200400037C | PMID:16381902 | nif-0000-02698, biotools:cryptodb | https://bio.tools/cryptodb | http://cryptodb.org/ | SCR_013455 | CryptoDB, Cryptosporidium Genomics Resource | 2026-02-14 02:06:43 | 25 | ||||
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Open Trials Resource Report Resource Website 1+ mentions |
Open Trials (RRID:SCR_015570) | data or information resource, database | Database that contains data such as registry entries, portions of regulatory documents describing individual trials, structured data on methods and results, and researchers and papers from and/or related to clinical trials. The initiative aims to locate, match, and share all publicly accessible data and documents, on all trials conducted, on all medicines and other treatments, globally. | clinical trial, clinical trial database, clinical trial data, open database, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Oxford; Oxford; United Kingdom |
Laura and John Arnold Foundation ; Wellcome Trust ; World Health Organisation ; West of England Academic Health Science Network |
Open source | biotools:opentrials | https://bio.tools/opentrials | SCR_015570 | 2026-02-14 02:06:46 | 3 | |||||||
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lncRNAdb Resource Report Resource Website 100+ mentions |
lncRNAdb (RRID:SCR_015491) | data or information resource, database | Searchable database of comprehensive annotations of eukaryotic long non-coding RNAs. Entries are manually curated from referenced literature. | reference database, eukaryotic annotation, annotation database, eukaryotic long non coding rna database, functional long noncoding rnas, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
Open source, Acknowledgement requested, The community can contribute to this resource | biotools:lncrnadb | https://bio.tools/lncrnadb | SCR_015491 | lncRNAdb v2.0, Long Noncoding RNA Database, Long Noncoding RNA Database v2.0 | 2026-02-14 02:06:22 | 163 | |||||||
|
ExPASy ABCD database Resource Report Resource Website 10+ mentions |
ExPASy ABCD database (RRID:SCR_017401) | ABCD ExPASy, The ABCD database | data or information resource, database | Repository of sequenced antibodies, integrating curated information about antibody and its antigen with cross links to standardized databases of chemical and protein entities. Manually curated repository of sequenced antibodies, developed by Geneva Antibody Facility at University of Geneva, in collaboration with CALIPHO and Swiss Prot groups at SIB Swiss Institute of Bioinformatics. Database provides list of sequenced antibodies with their known targets. Each antibody is assigned unique ID number that can be used in academic publications to increase reproducibility of experiments. | Sequenced antibody, manually curated, known target, ExPASy, repository, chemically defined antibodies, antibody, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: ExPASy Bioinformatics Resource Portal is related to: SIB Swiss Institute of Bioinformatics has parent organization: University of Geneva; Geneva; Switzerland |
University of Geneva ; ProCare Foundation ; Swiss National Science Foundation |
PMID:31410491 | Free, Freely available | SCR_019000, biotools:AbCD_database | https://bio.tools/ABCD_database | SCR_017401 | ExPASy ABCD (AntiBodies Chemically Defined) Database, The ABCD database, AntiBodies Chemically Defined, AntiBodies Chemically Defined Expert Protein Analysis System database, ExPASy ABCD Database, The AntiBodies Chemically Defined Database | 2026-02-14 02:06:54 | 10 | ||||
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Signaling Pathways Project Resource Report Resource Website 10+ mentions |
Signaling Pathways Project (RRID:SCR_018412) | SPP | data or information resource, database | Web multi omics knowledgebase based upon public, manually curated transcriptomic and cistromic datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Integrated omics knowledgebase for mammalian cellular signaling pathways. Web browser interface was designed to accommodate numerous routine data mining strategies. Datasets are biocurated versions of publically archived datasets and are formatted according to recommendations of the FORCE11 Joint Declaration on Data Citation Principles73, and are made available under Creative Commons CC 3.0 BY license. Original datasets are available. | Data integration, genetic database, gene regulatory network, cell signalling, cellular signalling network, transcriptomic data, manualy curated, cistromic data, cellular receptor, enzyme, transcrptomic factor, mammalian cellular signaling pathway, data mining strategy, dataset, , bio.tools |
is used by: Hypothesis Center is listed by: Debian is listed by: bio.tools works with: Gene Expression Omnibus (GEO) works with: NCBI Sequence Read Archive (SRA) |
NIDDK DK097771; NIDDK DK097748; NIDDK DK48807; NIDDK DK107535; NIDDK DK56338; NIDDK DK095686; NIDDK DK105126; NCI CA125123; NHLBI HL127624; Dan L. Duncan NCI Comprehensive Cancer Center at Baylor College of Medicine ; CPRIT RP150578 |
PMID:31672983 | Free, Freely available | r3d100013650, biotools:Signaling_Pathways_Project | https://bio.tools/Signaling_Pathways_Project https://doi.org/10.17616/R31NJN0Y |
https://www.signalingpathways.org | SCR_018412 | 2026-02-14 02:06:25 | 30 | ||||
|
FATCAT Resource Report Resource Website 100+ mentions |
FATCAT (RRID:SCR_014631) | web application, software resource | Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | web server, protein, comparison, structure, flexible protein structure, protein structure comparison, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: FATCAT Flexible Structural Neighborhood |
NIGMS GM101457; NIGMS GM63208; NIGMS GM076221; NSF DBI-0349600 |
PMID:14534198 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fatcat | https://bio.tools/fatcat | SCR_014631 | (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists, (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists (FATCAT) | 2026-02-15 09:21:06 | 139 | |||||
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Vienna RNA Resource Report Resource Website 100+ mentions |
Vienna RNA (RRID:SCR_008550) | data or information resource, database, software resource | This server provides programs, web services, and databases, related to our work on RNA secondary structures. For general information and other offerings from our group see the main TBI web server. With the 1st of May 2009 we updated our servers to the Vienna RNA package version 1.8.2! The Vienna RNA Servers: * RNAfold server predicts minimum free energy structures and base pair probabilities from single RNA or DNA sequences. * RNAalifold server predicts consensus secondary structures from an alignment of several related RNA or DNA sequences. You need to upload an alignment. * RNAinverse server allows you to design RNA sequences for any desired target secondary structure. * RNAcofold server allows you to predict the secondary structure of a dimer. * RNAup server allows you to predict the accessibility of a target region. * LocARNA server generates structural alignments from a set of sequences. In collaboration with the Bioinformatics Group Freiburg. * barriers server allows you to get insights into RNA folding kinetics. * RNAz server will assist you in detecting thermodynamically stable and evolutionarily conserved RNA secondary structures in multiple sequence alignments. * Structure conservation analysis server will assist you in detecting evolutionarily conserved RNA secondary structures in multiple sequence alignments. * RNAstrand server allows you to predict the reading direction of evolutionarily conserved RNA secondary structures. * RNAxs server assists you in siRNA design. * Bcheck predicts rnpB genes Downloads Get the Source code for: * the Vienna RNA Package, our basic RNA secondary structure analysis software. * The ALIDOT package for finding conserved structure motifs (add-on) * The barriers program for analysis of RNA folding landscapes. Databases * Atlas of conserved Viral RNA Structures found by ALIDOT | bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: ANNOgesic has parent organization: University of Vienna; Vienna; Austria |
DOI:10.1186/1748-7188-6-26 | biotools:vienna_rna_package, nif-0000-31411, OMICS_09351 | https://bio.tools/vienna_rna_package https://sources.debian.org/src/vienna-rna/ |
SCR_008550 | Vienna RNA | 2026-02-15 09:19:51 | 404 | |||||||
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BARS Resource Report Resource Website 10+ mentions |
BARS (RRID:SCR_009123) | BARS | software application, software resource | Software application that is a statistical method that bridges the gap between single-locus and haplotype-based tests of association. It is based on the non-parametric regression techniques embodied by Bayesian Adaptive Regression Splines. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, r, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154204, biotools:bars, nlx_154228, SCR_009106 | https://bio.tools/bars | SCR_009123 | Bayesian Adaptive Regression Splines | 2026-02-15 09:19:57 | 39 | ||||||
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Sybil Resource Report Resource Website 10+ mentions |
Sybil (RRID:SCR_005593) | Sybil | data or information resource, database, software resource | A web-based software package for comparative genomics. | comparative genomics, genome, synteny, protein cluster, protein, gene, genomic region, synteny gradient, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22121156 | OMICS_00945, biotools:sybil | https://bio.tools/sybil | SCR_005593 | Sybil: Web-based software for comparative genomics | 2026-02-15 09:19:00 | 37 | ||||||
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Database of Secondary Structure Assignments Resource Report Resource Website 50+ mentions |
Database of Secondary Structure Assignments (RRID:SCR_002725) | DSSP | data or information resource, database, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB) and the program that calculates DSSP entries from PDB entries. DSSP is distributed on a basis of trust and instructions are available on the site. * Precompiled executables are also available for Linux and Windows. (The Windows .exe file was compiled under Linux using Mingw32, has never seen a Windows environment and should thus be virus-free. Download the source if you want to be 100% sure.) Under Windows the DSSP output does not make it to the console, so redirect it to a file instead: dsspcmbi source.pdb destination.dssp > messages.txt * Several changes have been made to the DSSP program to solve problems with recent PDB files. These are documented in the source code. * FTP access to the DSSP files resides at the CMBI: ftp.cmbi.kun.nl/pub/molbio/data/dssp or ftp://ftp.ebi.ac.uk/pub/databases/dssp/. If you have problems downloading the DSSP files, it is likely that your FTP program is not able to handle tens of thousands of files in one directory. In this case, install a proper FTP program, for example NCFTP. However, it is recommended that you download DSSP files with the rsync command. | amino acid sequence, hydrogen bonding, protein conformation, proteins, gold standard, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: Radboud University; Nijmegen; The Netherlands |
PMID:6667333 PMID:21071423 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-23901, biotools:dssp, OMICS_06247 | http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+LibInfo+-lib+DSSP https://bio.tools/dssp https://sources.debian.org/src/dssp/ |
http://www.sander.ebi.ac.uk/dssp/ | SCR_002725 | 2026-02-15 09:18:23 | 59 | |||||
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ProP Server Resource Report Resource Website 50+ mentions |
ProP Server (RRID:SCR_014936) | web application, software resource | Web application which predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase prediction. | web application, prediction, arginine, lysine, cleavage, propeptide, eukaryotic, protein, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1093/protein/gzh013 | Open source | biotools:prop, BioTools:prop | https://bio.tools/prop https://bio.tools/prop https://bio.tools/prop |
SCR_014936 | ProP, ProP 1.0 Server, ProP 1.0 | 2026-02-15 09:21:13 | 75 | ||||||
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Composition Profiler Resource Report Resource Website 10+ mentions |
Composition Profiler (RRID:SCR_014630) | web application, software resource | Web tool for discovery and visualization of differences in amino acid composition. Two samples of amino acid sequences serve as input and a bar chart composed of twenty data points is output. | web tool, web application, amino acid, amino acid composition, sequence, bar chart, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:17578581 | Source code available, Acknowledgement requested | biotools:composition_profiler | https://bio.tools/composition_profiler | SCR_014630 | 2026-02-15 09:20:57 | 32 | |||||||
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GeneWise Resource Report Resource Website 1000+ mentions |
GeneWise (RRID:SCR_015054) | web application, software resource | Gene alignment tool from the EBI which predicts gene structure using similar protein sequences. See also the associated GenomeWise tool. | gene alignment, dna sequence, protein sequence, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: European Bioinformatics Institute |
PMID:15123596 | Freely available, Available for download | biotools:wise | https://bio.tools/wise | SCR_015054 | 2026-02-15 09:20:48 | 1017 | |||||||
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Telescope Resource Report Resource Website 1+ mentions |
Telescope (RRID:SCR_017626) | web application, software resource | Open source web application that tracks progress of jobs submitted to remote servers using Sun Grid Engine (SGE) on-demand scheduling system. Allows remote scheduling of pre-defined pipelines, as well as re-scheduling queued jobs. Telescope does not assume anything from the remote server, except for SSH connection. The connection is established using SSH key pairs that are stored after encrypted. | Track, progress, remote, server, scheduling, system, on demand, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of California at Los Angeles; California; USA |
Free, Freely available | biotools:telescope | https://bio.tools/Telescope | SCR_017626 | 2026-02-15 09:22:10 | 2 | ||||||||
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SimVascular Resource Report Resource Website 50+ mentions |
SimVascular (RRID:SCR_002686) | software application, software resource, simulation software | Open source software suite for cardiovascular simulation. It includes code for reading 3D images, segmenting structures, generating models and meshes, and modeling blood flow in deformable vessels. The suite also includes tools for physiologic boundary conditions, fluid structure interaction, and an accurate and efficient finite element Navier-Stokes solver. Commercial components have been used in the simulation process, and for these components, the project attempts to provide interfaces that allow substitution of open source components. The SimVascular project is derived from the ASPIRE2 software project and includes modified portions of PHASTA from RPI/SCOREC. | simulation software, fluid dynamics, blood flow, cardiovascular, image-based geometric modeling, image segmentation, mesh generation, vascular, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Simtk.org |
PMID:31446517 | Free, Available for download, Freely available | nif-0000-23311, BioTools:SimVascular, biotools:SimVascular | https://bio.tools/SimVascular https://bio.tools/SimVascular https://bio.tools/SimVascular |
SCR_002686 | SimVascular: Cardiovascular Modeling and Simulation | 2026-02-16 09:45:48 | 70 | ||||||
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Protein Information Resource Resource Report Resource Website 50+ mentions |
Protein Information Resource (RRID:SCR_002837) | PIR | data or information resource, topical portal, portal | Integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies. Provides databases and protein sequence analysis tools to scientific community, including Protein Sequence Database which grew out from the Atlas of Protein Sequence and Structure. Conducts research in biomedical text mining and ontology, computational systems biology, and bioinformatics cyberinfrastructure. In 2002 PIR, along with its international partners, EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics), were awarded a grant from NIH to create UniProt, a single worldwide database of protein sequence and function, by unifying the PIR-PSD, Swiss-Prot, and TrEMBL databases. Currently, PIR major activities include: i) UniProt (Universal Protein Resource) development, ii) iProClass protein data integration and ID mapping, iii) PRO protein ontology, and iv) iProLINK protein literature mining and ontology development. The FTP site provides free download for iProClass, PIRSF, and PRO. | annotation, genomic, mining, protein, protein bioinformatics, proteomic, research, sequence, structure, systems biology, gold standard, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: NCBI Protein Database has parent organization: University of Delaware; Delaware; USA has parent organization: Georgetown University; Washington D.C.; USA is parent organization of: PRO is parent organization of: PIRSF is parent organization of: PR is parent organization of: UniProt |
NLM P41 LM05798 | PMID:12520019 | Free, Freely available | biotools:pir, nif-0000-21327, nif-0000-00143, SCR_008229 | https://bio.tools/pir http://pir.georgetown.edu/ |
SCR_002837 | PIR - Protein Information Resource | 2026-02-16 09:45:53 | 83 | ||||
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NEST Simulator Resource Report Resource Website 100+ mentions |
NEST Simulator (RRID:SCR_002963) | NEST | software application, software resource, simulation software | Software tool as simulator for spiking neural network models that focuses on dynamics, size and structure of neural systems rather than on exact morphology of individual neurons. Used for any size spiking neurons networks including models of information processing, models of network activity dynamics, models of learning and plasticity. | simulation, neuron, spiking, neural network, model, neural system, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: MUlti SImulation Coordinator has parent organization: NEST Initiative |
DOI:10.1007/978-1-4614-7320-6_258-5 | Free, Available for download, Freely available | nif-0000-00162, biotools:nest | https://github.com/nest/nest-simulator https://bio.tools/nest |
SCR_002963 | Neural Simulation Tool, NEural Simulation Tool, nest, nest-simulator | 2026-02-16 09:45:53 | 175 | |||||
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lsa_slurm Resource Report Resource Website 1+ mentions |
lsa_slurm (RRID:SCR_018134) | source code, software resource | Software tool to implement pre-assembly binning scheme leveraging sparse dictionary learning and matrix factorization to solve sparse decomposition problems arising in field of metagenomics. | Sparse dictionary learning, pre-assembly binning scheme, matrix factorization, sparse decomposition, metagenomic, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:Metagenomic_read_binning_using_sparse_coding | https://bio.tools/Metagenomic_read_binning_using_sparse_coding | SCR_018134 | Metagenomic_read_binning_using_sparse_coding | 2026-02-15 09:22:18 | 1 | |||||||
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QGene Resource Report Resource Website 100+ mentions |
QGene (RRID:SCR_003209) | QGene | software application, data processing software, data analysis software, source code, software resource, simulation software | A free, open-source, computationally efficient Java program for comparative analyses of QTL mapping data and population simulation that runs on any computer operating system. (entry from Genetic Analysis Software) It is written with a plug-in architecture for ready extensibility. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Source code is available on request. | gene, genetic, genomic, java, qtl mapping, trait analysis, trait, population, simulation, map, quantitative trait locus, comparison, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Kansas State University; Kansas; USA |
NSF DBI 0109879; USDA-NRI Applied Plant Genomics Program 2004-35317-14867 |
PMID:18940826 | Free, Available for download, Freely available | biotools:qgene, nif-0000-31383 | https://bio.tools/qgene | http://coding.plantpath.ksu.edu/qgene | SCR_003209 | QGene - Software for QTL data exploration | 2026-02-16 09:46:02 | 126 | |||
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MOSCPHASER Resource Report Resource Website |
MOSCPHASER (RRID:SCR_009092) | MOSCPHASER | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Software application for inferring haplotypes composed of both CNV alleles and SNP alleles. | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools |
PMID:18492685 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154109, biotools:mocsphaser | https://bio.tools/mocsphaser | http://emu.src.riken.jp/MOCSphase/MOSCphaser.zip | SCR_009092 | Mixture Of Cnv-Snp PHASER | 2026-02-15 09:19:57 | 0 |
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