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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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precrec Resource Report Resource Website 1+ mentions |
precrec (RRID:SCR_018659) | software application, software resource, data analytics software, software toolkit | Software R package for fast and accurate precision recall and ROC curve calculations. Calculates accurate precision recall and Receiver Operator Characteristics curves. | Precision recall, receiver operator characteristics, receiver operator characteristics curve, curve calculations, precision recall calculation, , bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CRAN |
DOI:10.1093/bioinformatics/btw570 | Free, Freely available | biotools:precrec | https://bio.tools/precrec | SCR_018659 | 2026-02-16 09:49:30 | 1 | |||||||
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Gmove Resource Report Resource Website 1+ mentions |
Gmove (RRID:SCR_019132) | software application, software resource, simulation software | Software tool for genome annotation. Eukaryotic gene prediction tool focused on evidence supported by expressed sequences like transcripts and conserved proteins alignments. Can be used to reannotate genomes, to do comparative gene prediction and improve existing genome annotation. Can predict gene models with canonical and non-canonical splice sites. | Expressed sequences, RNAseq, conserved proteins, conserved proteins alignment, genome annotation, Eukaryotic gene prediction, gene prediction, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:gmove | https://github.com/institut-de-genomique/gmove https://bio.tools/gmove |
SCR_019132 | Gene MOdeling using Various Evidence | 2026-02-16 09:49:40 | 3 | |||||||
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asSeq Resource Report Resource Website 1+ mentions |
asSeq (RRID:SCR_001625) | asSeq | software application, data processing software, data analysis software, source code, software resource | Software that establishes a statistical framework for future developments of eQTL (expression quantitative trait locus) mapping methods using RNA-seq data (e.g., linkage-based eQTL mapping), and the joint study of multiple genetic markers and/or multiple genes. This R package has been submitted to R/bioconductor. It will be available on bioconductor soon. It is recommended to install this R package from bioconductor. You can also install this R package from the source code by yourself. Since the R package contains C code, a C complier is required for installation. With both R and appropriate c complier installed, this R package can be installed using the following command (in Mac Terminal window or Windows command window) R CMD INSTALL asSeq | r, rna-seq, expression quantitative trait locus, total read count, allele-specific expression, allele-specific gene expression, gene expression quantitative trait locus, rna isoform, gene expression, genetic marker, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Bioconductor has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:21838806 | Free, Available for download, Freely available | OMICS_01948, nlx_153893, biotools:asseq | https://bio.tools/asseq | SCR_001625 | 2026-02-16 09:45:32 | 6 | ||||||
|
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 | |||
|
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 | |||||||
|
STEPS Resource Report Resource Website 100+ mentions |
STEPS (RRID:SCR_008742) | STEPS | software application, software resource, simulation software | STEPS is a package for exact stochastic simulation of reaction-diffusion systems in realistic, complex 3D geometries. Our core simulation algorithm is an efficient implementation of a variation on Gillespie''s SSA, extended to deal with diffusion of molecules over the elements of a 3D tetrahedral mesh. While it was mainly developed for simulating detailed models of neuronal signaling pathways in dendrites and around synapses, it is a general tool and can be used for studying any biochemical pathway in which spatial gradients and morphology are thought to play a role. We have implemented STEPS as a set of Python modules, which means STEPS users can use Python scripts to control all aspects of setting up the model, generating a mesh, controlling the simulation and generating and analyzing output. The core computational routines are still implemented as C/C++ extension modules for maximal speed of execution. | reaction-diffusion, stochastic, signaling, molecular, python, software, simulator, reaction kinetics, 3d diffusion, signaling pathway, scripting, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Okinawa Institute of Science and Technology has parent organization: University of Antwerp; Antwerp; Belgium |
GOA ; UA Belgium ; Human Frontier Science Program ; Okinawa Institute of Science and Technology |
biotools:steps, nlx_143852 | https://bio.tools/steps | http://steps.sourceforge.net/STEPS/Home.html | SCR_008742 | STochastic Engine For Pathway Simulation | 2026-02-16 09:47:15 | 336 | |||||
|
FusionHunter Resource Report Resource Website 1+ mentions |
FusionHunter (RRID:SCR_011895) | FusionHunter | source code, software resource | Software for identifying fusion transcripts using paired-end RNA-seq. | perl, annotation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01350, biotools:fusionhunter | https://bio.tools/fusionhunter | SCR_011895 | FusionHunter: identifying fusion transcripts using paired-end RNA-seq | 2026-02-15 09:20:28 | 8 | |||||||
|
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 | ||||
|
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 | |||||
|
ReadqPCR Resource Report Resource Website |
ReadqPCR (RRID:SCR_000030) | software application, software resource, standalone software | A software package that provides functions to read raw RT-qPCR data of different platforms. | standalone software, mac os x, unix/linux, windows, r, data import, gene expression, microtitre plate assay, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: University College London; London; United Kingdom |
PMID:22748112 | Free, Available for download, Freely available | biotools:readqpcr, OMICS_03936 | https://bio.tools/readqpcr | SCR_000030 | ReadqPCR - Read qPCR data | 2026-02-16 09:45:10 | 0 | ||||||
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mzMatch Resource Report Resource Website 1+ mentions |
mzMatch (RRID:SCR_000543) | software resource, software toolkit | A software to provide small tools for common processing tasks for LC/MS data. It is an extension to the metabolomics analysis pipeline mzMatch.R. The software is modular, open source, platform independent and written in Java. | metabolomics, analysis, java, tool, peak extraction, filtering, normalization, derivative detection, identification, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23162054 | Free, Available for download, Freely available, | biotools:mzmatch, OMICS_02642 | https://bio.tools/mzmatch | SCR_000543 | 2026-02-16 09:45:17 | 5 | |||||||
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metabnorm Resource Report Resource Website |
metabnorm (RRID:SCR_001266) | software application, software resource, standalone software | Software tool as mixed model normalization method for metabolomics data.Uses normalization approach based on mixed model, with simultaneous estimation of correlation matrix. | Metabolomics datasets, corelation, normalization, identifying metabolites, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
Cancer Research UK Cambridge Institute ; Erik and Edith Fernström foundation ; Cancer Research UK |
PMID:24711654 | Free, Available for download, Freely available | OMICS_03548, biotools:metabnorm | https://bio.tools/metabnorm | SCR_001266 | 2026-02-16 09:45:27 | 0 | ||||||
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Bioinformatics Toolkit Resource Report Resource Website 100+ mentions |
Bioinformatics Toolkit (RRID:SCR_010277) | software resource, software toolkit | A platform that integrates a great variety of tools for protein sequence analysis. Many tools are developed in-house, and serveral public tools are offered with extended functionality. Most frequently used tools HHpred Sensitive protein homology detection and structure prediction by HMM-HMM-comparison. Starting from a query sequence, HHpred builds a multiple sequence alignment using HHblits and turns it into a profile HMM. This is then compared it with a database of HMMs representing proteins with known structure (e.g. PDB, SCOP) or annotated protein families (e.g. PFAM, SMART, CDD, COGs, KOGs). The output is a list of closest homologs with alignments. HHpred can also build 3d homology models using the identified templates in the PDB database. It can optimize template picking and query-template alignments for homology modeling. The HHblits software is part of the open source package HHsuite. HHblits Remote homology detection method based on iterative HMM-HMM comparison. HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM and iteratively searches through uniprot20 or nr20 databases by adding significantly similar sequences from the previous search to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is faster, up to twice as sensitive and produces more accurate alignments. The HHblits software is part of the open source package HHsuite. Quick2d Quick2D gives you an overview of secondary structure features like alpha-helices, extended beta-sheets, coiled coils, transmembrane helices and disorder regions. Predictions by PSIPRED, JNET, Prof(Rost), Prof(Ouali), Coils, MEMSAT2, HMMTOP, DISOPRED2 and VSL2. Modeller A Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. Coils/PCoils This server compares a single sequence (COILS) or a sequence alignment (PCOILS) to a database of known coiled-coils and derives a similarity score. The program then calculates the probability that the sequence will adopt a coiled-coil conformation. PSI-Blast Search with an amino acid sequence against protein databases for locally similar sequences. Similar to ProteinBLAST but more sensitive. PSI-BLAST first performs a BLAST search and builds an alignment from the best local hits. This alignment is then used as a query for the next round of search. After each successive round the search alignment is updated. | bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
DOI:10.1038/NMETH.1818 | nlx_156936, OMICS_28407, biotools:bioinformatics_toolkit | https://bio.tools/bioinformatics_toolkit https://sources.debian.org/src/hhsuite/ |
SCR_010277 | 2026-02-16 09:47:46 | 235 | ||||||||
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e-Driver Resource Report Resource Website 1+ mentions |
e-Driver (RRID:SCR_002674) | software application, software resource, standalone software | Software tool to identify cancer driver genes based on linear annotations of biological regions such as protein domains.Uses information on three-dimensional structures of mutated proteins to identify specific structural features. Then algorithm analyzes whether these features are enriched in cancer somatic mutations and are candidate driver genes. | Identify cancer driver genes, candidate driver genes, perl, protein, mutated proteins, cancer somatic mutations, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Cancer | PMID:25064568 | Free, Available for download, Freely available | biotools:e-Driver, OMICS_05288 | https://bio.tools/e-Driver | SCR_002674 | 2026-02-16 09:45:57 | 5 | ||||||
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NetNGlyc Resource Report Resource Website 1000+ mentions |
NetNGlyc (RRID:SCR_001570) | NetNGlyc | software application, production service resource, analysis service resource, service resource, software resource, data analysis service | Server that predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons. NetNGlyc 1.0 is also available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for the most common UNIX platforms. | predict, n-glycosylation site, human, protein, neural network, sequence, asn-xaa-ser/thr sequon, glycoprotein, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: CBS Prediction Servers |
Free, Freely available | nlx_153863, biotools:netnglyc | https://bio.tools/netnglyc | SCR_001570 | NetNGlyc Server | 2026-02-17 09:59:38 | 1753 | ||||||
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YinOYang Resource Report Resource Website 100+ mentions |
YinOYang (RRID:SCR_001605) | YinOYang | software application, production service resource, analysis service resource, service resource, software resource, data analysis service | Server that produces neural network predictions for O-beta-GlcNAc attachment sites in eukaryotic protein sequences. This server can also use NetPhos, to mark possible phosphorylated sites and hence identify Yin-Yang sites. YinOYang 1.2 is available as a stand-alone software package, with the same functionality. Ready-to-ship packages exist for the most common UNIX platforms. | neural network, prediction, o-beta-glcnac attachment site, protein sequence, protein, sequence, glycosylation site, proteome, post-translational modification, protein function, glycoprotein, bio.tools |
uses: NetPhos is listed by: bio.tools is listed by: Debian has parent organization: CBS Prediction Servers |
Danish National Research Foundation | PMID:11928486 | Free, Freely available | nlx_153865, biotools:yinoyang | https://bio.tools/yinoyang | SCR_001605 | 2026-02-17 09:59:43 | 111 | |||||
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MatrixDB Resource Report Resource Website 50+ mentions |
MatrixDB (RRID:SCR_001727) | MatrixDB | data or information resource, production service resource, database, service resource | Freely available database focused on interactions established by extracellular proteins and polysaccharides, taking into account the multimeric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data. It includes interaction data extracted from the literature by manual curation, and offers access to relevant data involving extracellular proteins provided by the IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database. The database reports mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. Interactions with lipids and cations are also reported. MatrixDB is focused on mammalian interactions, but aims to integrate interaction datasets of model organisms when available. MatrixDB provides direct links to databases recapitulating mutations in genes encoding extracellular proteins, to UniGene and to the Human Protein Atlas that shows expression and localization of proteins in a large variety of normal human tissues and cells. MatrixDB allows researchers to perform customized queries and to build tissue- and disease-specific interaction networks that can be visualized and analyzed with Cytoscape or Medusa. Statistics (2013): 2283 extracellular matrix interactions including 2095 protein-protein and 169 protein-glycosaminoglycan interactions. | extracellular, protein fragment, biomolecule, cation, cleavage, collagen, glycosaminoglycan, human, interaction, laminin, lipid, mammalian, matricryptin, matrikin, matrix, molecule, monomer, mulimerization, multimer, polysaccharide, protein, protein-carbohydrate interaction, protein-protein interaction, recognition, thrombospondin, interactome, extracellular protein, protein-polysaccharide interaction, extracellular interaction, molecular interaction, model organism, inorganic, small molecule-protein, small molecule, extracellular matrix protein, protein-glycosaminoglycan interaction, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: IMEx - The International Molecular Exchange Consortium is related to: Gene Ontology is related to: PSI-MI is related to: HPRD - Human Protein Reference Database is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: IMEx - The International Molecular Exchange Consortium is related to: PSICQUIC Registry is related to: IntAct has parent organization: Claude Bernard University Lyon 1; Lyon; France |
European Union contract FP7-HEALTH-2007-223411 | PMID:20852260 PMID:19147664 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:matrixdb, r3d100010672, nif-0000-10226 | https://bio.tools/matrixdb https://doi.org/10.17616/R3M03H |
http://matrixdb.ibcp.fr/ | SCR_001727 | MatrixDB: Extracellular Matrix Interactions Database, Extracellular Matrix Interactions Database | 2026-02-17 09:59:45 | 86 | |||
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Biocatalogue - The Life Science Web Services Registry Resource Report Resource Website 1+ mentions |
Biocatalogue - The Life Science Web Services Registry (RRID:SCR_001679) | BioCatalogue | data access protocol, data or information resource, database, software resource, web service | Crowd-curated catalog of life sciences Web services with over 2400 service entries, thereby enabling users (people and programs) to discover and use these services easily. It provides a platform with several (standardized) interfaces and a suite of tools for registration of services by the community of users as well as empowers the community to extend and enhance the system. BioCatalogue provides a centralized biological web services market place which is accessible to the world as it is searchable and indexable to search engines. Additionally, it provides a quality of service standard for biological web services thereby enabling services to be classified and checked for availability, reliability and other quality measures. Primary goals: * Provide a single registration point for Web Service providers and a single search site for scientists and developers. * Providers, Expert curators and Users will provide oversight, monitor the catalog and provide high quality annotations for services. * BioCatalogue is a place where the community can find contacts and meet the experts and maintainers of these services. | biological, web, life science, programmatic access, bioinformatics, registry, annotation, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: MetaLocGramN is related to: myExperiment is related to: bioDBcore has parent organization: European Bioinformatics Institute has parent organization: University of Manchester; Manchester; United Kingdom |
European Union LHSG-CT-2004-512092; EMBO ASTF 338.00-2009 |
PMID:20484378 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:biocatalogue, nif-0000-10167 | https://bio.tools/biocatalogue | SCR_001679 | Biocatalog | 2026-02-17 09:59:41 | 7 | ||||
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Clustal Omega Resource Report Resource Website 5000+ mentions |
Clustal Omega (RRID:SCR_001591) | Clustal Omega, Clustalo | software application, data processing software, software resource, service resource, image analysis software, alignment software | Software package as multiple sequence alignment tool that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. Accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/Clustal, GCG/MSF, RSF. | multiple, sequence, alignment, DNA, RNA, protein, generate, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Clustal W2 is related to: Clustal W2 is related to: Clustal 2 has parent organization: European Bioinformatics Institute has parent organization: University College Dublin; Dublin; Ireland |
Science Foundation Ireland | PMID:21988835 PMID:20439314 DOI:10.1038/msb.2011.75 |
Free, Available for download, Freely available | OMICS_00972, SCR_016062, biotools:clustalo, nlx_153836 | https://sources.debian.org/src/clustalo/ http://www.clustal.org/omega/ http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::clustalO-multialign https://bio.tools/clustalo https://sources.debian.org/src/clustalo/ |
SCR_001591 | 2026-02-17 09:59:42 | 9956 |
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