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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Visualization and Analysis of Networks containing Experimental Data (VANTED) Resource Report Resource Website 10+ mentions |
Visualization and Analysis of Networks containing Experimental Data (VANTED) (RRID:SCR_001138) | VANTED | software application, data analysis software, software resource, data processing software, data visualization software | Software tool for extendable network visualization and analysis for the life sciences. It is Java-based and allows users to create, edit and map data onto existing or new networks. Experimental datasets can be visualized on network elements as graphical charts to show time series data or data of different treatments, as well as environmental conditions in the context of the underlying biological processes. Users can utilize built-in statistical algorithms to evaluate mapped data. | binary executable, simulation software, signal processing software, java, network visualization, statistical analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:23140568 | Open source | biotools:vanted, nif-0000-00373 | https://bitbucket.org/vanted-dev/vanted/src, https://bio.tools/vanted | http://vanted.ipk-gatersleben.de/ | SCR_001138 | Visualization and Analysis of Networks containing Experimental Data, VANTED v2 | 2026-07-28 09:40:08 | 14 | ||||
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NetNGlyc Resource Report Resource Website 1000+ mentions |
NetNGlyc (RRID:SCR_001570) | NetNGlyc | software application, service resource, data analysis service, software resource, production service resource, analysis service resource | 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 | 2026-07-28 09:40:19 | 1753 | ||||||
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YinOYang Resource Report Resource Website 100+ mentions |
YinOYang (RRID:SCR_001605) | YinOYang | software application, service resource, data analysis service, software resource, production service resource, analysis service resource | 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 | 2026-07-28 09:40:13 | 111 | |||||
|
Clustal Omega Resource Report Resource Website 5000+ mentions |
Clustal Omega (RRID:SCR_001591) | Clustal Omega, Clustalo | software application, service resource, software resource, data processing software, alignment software, image analysis 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 | 2026-07-28 09:40:19 | 9956 | |||||
|
asSeq Resource Report Resource Website 1+ mentions |
asSeq (RRID:SCR_001625) | asSeq | software application, data analysis software, source code, software resource, data processing software | 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 | 2026-07-28 09:40:14 | 6 | ||||||
|
MatrixDB Resource Report Resource Website 50+ mentions |
MatrixDB (RRID:SCR_001727) | MatrixDB | data or information resource, service resource, database, production 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 | 2026-07-28 09:40:15 | 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 or information resource, database, data access protocol, 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 | 2026-07-28 09:40:14 | 7 | ||||
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PhosphoSitePlus: Protein Modification Site Resource Report Resource Website 500+ mentions |
PhosphoSitePlus: Protein Modification Site (RRID:SCR_001837) | PSP | knowledge environment resource, data or information resource, portal | A freely accessible on-line systems biology resource devoted to all aspects of protein modification, as well as other post-translational modifications. It provides valuable and unique tools for both cell biologists and mass spectroscopists. PhosphoSite is a human- and mouse-centric database. It includes features such as: viewing the locations of modified residues on molecular models; browsing and searching MS2 records by disease, tissue, and cell line; submitting lists of peptides to identify previously reported genes; searching by sub-cellular localization, treatment, tissues, cell types, cell lines and diseases, and protein types and protein domains; searching for experimentally-verified kinase substrates and viewing preferred substrate motifs; and viewing MS2 spectra for peptides and sites not previously published. | portal, mass spectroscopist, molecular model, mouse, post translational, subcellular localization, protein modification, post-translational modification, protein phosphorylation, protein structure, protein function, ubiquitinylation, acetylation, cellular component, cell type, visualization, data repository, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: Cytoscape is related to: ConsensusPathDB has parent organization: Cell Signaling Technology |
NCI ; NIAAA R44 AA014848; NIGMS R43 GM65768 |
PMID:22135298 | Free, Freely available | biotools:phosphositeplus, nif-0000-10399 | https://bio.tools/phosphositeplus | SCR_001837 | PhosphoSitePlus, PhosphoSite | 2026-07-28 09:40:26 | 903 | ||||
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biospytial Resource Report Resource Website 1+ mentions |
biospytial (RRID:SCR_018226) | software application, data analysis software, software resource, data management software, data processing software, data visualization software, software toolkit | Software package as spatial graph based computing engine for ecological big data. Modular open source knowledge engine designed to import, organize, analyse and visualize big spatial ecological datasets using power of graph theory. Handles species occurrences and their taxonomic classification for performing ecological analysis on biodiversity and species distributions. Data are linked with relationships that are stored in graph database, while tabular and geospatial data are stored in relational database management system. | spatial data infrastructure, biodiversity informatics, ecological knowledge engine, ecological data analysis, biodiversity, taxonomic classification, bio.tools |
is listed by: Debian is listed by: bio.tools |
CONACyT ; GBIF ; Lancaster University |
DOI:10.5524/100723 | Free, Available for download, Freely available | biotools:biospytial | https://bio.tools/biospytial | SCR_018226 | 2026-07-28 09:44:42 | 2 | ||||||
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NetMHCpan Server Resource Report Resource Website 100+ mentions |
NetMHCpan Server (RRID:SCR_018182) | software resource, data access protocol, web service | Web server for quantitative prediction of peptide binding to any MHC molecule of known sequence using artificial neural networks. Characterizes binding specificity of given major histocompatibility complex molecule and predicts peptide length profile and peptide binding affinity. NetMHCpan 3.0 is improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets. NetMHCpan 4.0 is trained on naturally eluted ligands and on peptide binding affinity data. NetMHCpan-4.1 server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs). | Quantitative prediction, peptide binding, MHC molecule, artificial neural network, Major Histocompatibilty Complex, peptide length, peptide binding affinity, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Agencia Nacional de Promoción Científica y Tecnológica ; Argentina ; NIAID |
PMID:19002680 PMID:28978689 |
Free, Available for download, Freely Available | biotools:netmhcpan | https://bio.tools/netmhcpan, https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/ | SCR_018182 | NetMHCpan 1.0, NetMHCpan 3.0, NetMHCpan 2.0, NetMHCpan 4.1, NetMHCpan 4.0, NetMHCpan | 2026-07-28 09:44:42 | 138 | |||||
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Mousebytes Resource Report Resource Website 1+ mentions |
Mousebytes (RRID:SCR_017904) | service resource, data or information resource, data repository, database, storage service resource | Open access database for all cognitive data collected from touchscreen related tasks. Performs data comparison and interactive data visualization for any data uploaded onto the site. There are also guidelines and video tutorials available. | Data, mouse, cognition, imaging, genomics, integration, bio.tools, OpenBehavior |
is listed by: Debian is listed by: bio.tools is listed by: OpenBehavior has parent organization: Western University; Ontario; Canada |
Weston Brain Institute (Canada) ; Canadian Institute of Health Research ; NSERC ; Alzheimer’s Society of Canada ; Canadian First Research Excellence Fund (BrainsCAN) ; Brain Canada |
PMID:31825307 | Free, Freely available | SCR_021549, SCR_021598, r3d100013886, biotools:Mousebytes | https://bio.tools/MouseBytes, https://edspace.american.edu/openbehavior/project/touchscreen-cognition-mousebytes/, https://doi.org/10.17616/R31NJN7I | SCR_017904 | MouseBytes | 2026-07-28 09:44:35 | 4 | |||||
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Mesquite Resource Report Resource Website 100+ mentions |
Mesquite (RRID:SCR_017994) | software application, software resource, data analysis software, data processing software | Software tool as modular system for evolutionary analysis. Software for evolutionary biology, designed to organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Analyses available depend on modules installed. Comes with many packages already installed. | Modular, evolutionary, analysis, organize, comparative data, organism, phylogenetic, population genetic, non-pylogenetic | is listed by: Debian | NSF DEB 1258220; David and Lucile Packard Foundation ; NSERC Discovery grant ; NSF |
Free, Available for download, Freely available | https://sources.debian.org/src/mesquite/ | SCR_017994 | Mesquite 3.04, Mesquite 3.61 | 2026-07-28 09:44:40 | 151 | |||||||
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4See Resource Report Resource Website 1+ mentions |
4See (RRID:SCR_018014) | data visualization software, software resource, software application, data processing software | Software tool to visualize 4C data. | Visualize, 4C data, bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.3389/fgene.2019.01372 | Free, Available for download, Freely available | biotools:4see | https://bio.tools/4see | SCR_018014 | 2026-07-28 09:44:41 | 1 | |||||||
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NeuroChaT Resource Report Resource Website 1+ mentions |
NeuroChaT (RRID:SCR_018020) | software application, data analysis software, software resource, data processing software, software toolkit | Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories. | Neuronal signal, analysis, freely behaving animal, spatial coding, behavioural neurophysiology, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Wellcome Trust | DOI:12688/wellcomeopenres.15533.1 | Free, Available for download, Freely available | biotools:NeuroChat | https://bio.tools/NeuroChaT | SCR_018020 | Neuron Characterisation Toolbox | 2026-07-28 09:44:41 | 2 | |||||
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Online Peri-Event Time Histogram for Open Ephys Resource Report Resource Website 1+ mentions |
Online Peri-Event Time Histogram for Open Ephys (RRID:SCR_018022) | OPETH | data visualization software, software resource, software application, data processing software | Software tool to enable flexible online visualization of action potential alignment to external events. Performs spike detection based on raw Open Ephys data exported via ZeroMQ. Requires triggers from Open Ephys for histogram display as spikes are detected around them. | Open source, open ephys, optogenetics, behavior, electrophysiology data, neuroscience experiment, spike detection, behavior tagging, neuron, histogram, bio.tools |
is listed by: Debian is listed by: bio.tools |
Hungarian Academy of Sciences Lendület Program LP2015-2/2015; European Research Council Starting Grant 715043; Generalitat Valenciana Postdoctoral Fellowship Program APOSTD/2019/003 |
DOI:10.1101/783688 | Free, Available for download, Freely available | biotools:OPEtH | https://bio.tools/OPETH | SCR_018022 | Online Peri-Event Time Histogram | 2026-07-28 09:44:49 | 4 | ||||
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ΔG prediction server Resource Report Resource Website 10+ mentions |
ΔG prediction server (RRID:SCR_018191) | service resource, software resource, data access protocol, web service | Web server to predict ΔGapp for membrane insertion of potential TM helix. Given amino acid sequence of putative transmembrane helix, server gives prediction of corresponding apparent free energy difference for insertion of this sequence into Endoplasmic Reticulum membrane by means of Sec61 translocon. | Amino acid sequence, putative transmembrane helix, free energy difference, sequence insertion, endoplasmic reticulum membrane, potential TM helix, predict energy difference, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Stockholm University; Stockholm; Sweden |
Free, Freely available | biotools:deltag_prediction | http://dgpred.cbr.su.se/index.php?p=TMpred, https://bio.tools/deltag_prediction | SCR_018191 | ΔG prediction server v1.0 | 2026-07-28 09:44:38 | 12 | |||||||
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Multi-omics Visualization Platform Resource Report Resource Website 1+ mentions |
Multi-omics Visualization Platform (RRID:SCR_018077) | MVP | software application, data analysis software, software resource, data processing software, data visualization software | Software tool as plugin to enable viewing of results produced from workflows integrating genomic sequencing data and mass spectrometry proteomics data. Plugin to Galaxy bioinformatics workbench which enables visualization of mass spectrometry-based proteomics data integrated with genomic and/or transcriptomic sequencing data. Useful for verifying quality of results and characterizing novel peptide sequences identified using multi-omic proteogenomic approach. | Proteogenomics, data, multi-omics, mass spectrometry, proteomics, genomics, transcriptomics, Galaxy Project, data visualization, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIH U24 CA199347 | Free, Available for download, Freely available | biotools:mvp_a | http://galaxyp.org, https://bio.tools/mvp_a | SCR_018077 | Multi-omics Visualization Platform, Galaxy MVP | 2026-07-28 09:44:37 | 1 | |||||
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DichroWeb Resource Report Resource Website 50+ mentions |
DichroWeb (RRID:SCR_018125) | service resource, data analysis service, data access protocol, software resource, production service resource, web service, analysis service resource | Web server for analysis of protein circular dichroism spectra. Provides access to circular dichroism secondary structure calculation algorithms and reference databases. Used in analysis of protein secondary structures. | Analysis, protein, circular dichroism spectra, secondary structure, reference database, algorithm, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of London; London; United Kingdom |
BBSRC | PMID:17896349 PMID:15215473 |
Restricted | biotools:dichroweb | https://bio.tools/dichroweb | SCR_018125 | 2026-07-28 09:44:37 | 62 | ||||||
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ProtParam Tool Resource Report Resource Website 5000+ mentions |
ProtParam Tool (RRID:SCR_018087) | software application, service resource, data analysis software, sequence analysis software, data processing software, software resource, production service resource, analysis service resource | Software tool to calculate various physicochemical parameters for given protein stored in Swiss-Prot or TrEMBL or for user entered protein sequence. Protein can either be pecified as Swiss-Prot/TrEMBL accession number or ID, or in form of raw sequence. Computed parameters include molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity. | Calculate phycicochemical parameter, protein, Swiss-Prot, TrEMBL, protein sequence, molecular weight, theortical pl, amino acid composition, atomic composition, extinction coefficient, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: ExPASy Bioinformatics Resource Portal |
NHGRI U01 HG02712; Swiss Federal Government through Federal Office of Education and Science |
PMID:10027275 | Free, Freely available | biotools:protparam | https://bio.tools/protparam | SCR_018087 | ProtParam | 2026-07-28 09:44:49 | 5406 | |||||
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Plant Co-expression Annotation Resource Resource Report Resource Website 1+ mentions |
Plant Co-expression Annotation Resource (RRID:SCR_018429) | Plantannot | service resource, data or information resource, data access protocol, software resource, web service | Webserver for identifying targets for genetically modified crop breeding pipelines. Used to find proteins that have no annotation or function assigned and could be related to molecular mechanisms regarding abiotic stresses in plants. System aggregates orthology, coexpression networks and genomic data to filter genomes of plants downloaded from Phytozome and NCBI and select candidate proteins in that regard. | Omics, plant, annotation, function, breeding, genetically modified crops, abiotic stress in plant, plant genome, plant genomic data, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Phytozome is related to: NCBI is related to: Machado |
Embrapa | DOI:10.1101/2020.05.22.110510 | Free, Freely available | biotools:plantannot | https://www.machado.cnptia.embrapa.br/plantannot2, https://bio.tools/plantannot | SCR_018429 | Plantannot v2 | 2026-07-28 09:44:56 | 1 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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