BionocularsLife science search engine providing access to 80M+ articles, from PubMed and OpenAlex, through complementary search pathways.
Combines classical keyword search with AI-assisted exploration, including semantic keyword grouping, knowledge graph visualization, and AI-driven summarization. All AI-generated insights are traceable to source articles. Designed to support transparent, user-steered literature exploration for biology and biomedical research. Currently in early access.https://www.bionoculars.com/bionocularsbiotools:bionocularsRRID:SCR_028217rridWeb applicationWeb servicehttp://edamontology.org/topic_3344Biomedical sciencehttp://edamontology.org/topic_3303Medicinehttp://edamontology.org/topic_3070Biologyhttp://edamontology.org/topic_0218Natural language processinghttp://edamontology.org/topic_0089Ontology and terminologyhttp://edamontology.org/topic_3068Literature and languageMacLinuxWindowsProprietaryEmergingCommercialOpen access (with restrictions)http://edamontology.org/operation_0305Literature searchhttp://edamontology.org/operation_0224Query and retrievalhttps://www.bionoculars.com/tutorialQuick start guidehttps://www.bionoculars.com/blog/early-accessRelease notesbio.toolsThe community registry of computational tools and data resources for biosciences.https://bio.toolsbio.toolsbiotools:bio.toolsRRID:SCR_014695rridWeb APIDatabase portalWeb applicationhttp://edamontology.org/topic_0089Ontology and terminologyhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0219Data curation and archivalhttp://edamontology.org/topic_3307Computational biologyJavaScriptPythonGPL-3.0EmergingFree of chargeOpen accessToolsDenmarkhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/data_3671Texthttp://edamontology.org/format_1964plain text format (unformatted)https://biotools.readthedocs.io/en/latest/support.html?highlight=helpHelpdeskhttps://github.com/bio-tools/biotoolsregistry/issuesIssue trackerhttps://biotools.readthedocs.io/en/latest/contributors_guide.html#mailing-listMailing listhttps://github.com/bio-tools/biotoolsregistry/Repositoryhttps://github.com/bio-tools/biotoolsRegistrySource codehttps://biotools.readthedocs.io/en/latest/api_usage_guide.htmlAPI documentationAPI usage guidehttps://biotools.readthedocs.io/en/latest/api_reference.htmlAPI documentationAPI Referencehttps://biotools.readthedocs.io/en/latest/publications.html#citationCitation instructionshttps://biotools.readthedocs.io/en/latest/contributors_guide.htmlContributions policyhttps://biotools.readthedocs.io/en/latest/Generalhttps://biotools.readthedocs.io/en/latest/governance.htmlGovernancehttps://biotools.readthedocs.io/en/latest/curators_guide.htmlUser manualCurators Guide10.1093/nar/gkv1116Primary10.12688/f1000research.12974.1Other10.1093/gigascience/gix022Other10.1007/s10009-015-0392-zOtherContributorshttps://biotools.readthedocs.io/en/latest/contributors.htmlPersonRandom Number LabAn interactive set of tools including randomization of data (even stratified random sampling) and random assignments for studies, generation of random numbers following specific probability distributions, generation of random and quasi-random point distributions and sampling patterns, noise in one or two dimensions with adjustable spectral properties, random walks and Lévy flights. Own data tables can be provided for random sampling in a privacy-friendly way, as data processing takes place directly in the browser and no data is transferred to anywhere else. The Random Number Lab also offers some educational material and worksheets and can be used for scientific and educational purposes.https://randomnumberlab.orgrandom_number_labbiotools:random_number_labRRID:SCR_028010rridWeb applicationhttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_3678Experimental design and studiesLinuxiOSMacAndroidWindowsJavaScriptMatureFree of chargehttp://edamontology.org/operation_0364Random sequence generationGeneration of sequences of random numbers or elements, spatial point patterns, random walkshttp://edamontology.org/operation_0337VisualisationVisualization of random distributions and random processeshttp://edamontology.org/operation_2409Data handlingRandomization and permutation of data in a privacy-preserving wayThomas Amthorhello@randomnumberlab.orghttps://orcid.org/0000-0002-1456-6131PersonDeveloperMaintainerPSIPREDThe PSIPRED Protein Analysis Workbench unites many available analysis tools into a single web based framework. An excellent tool for prediction of secondary structure, with access to GenTHREADER for protein fold recognition and MEMSAT-2 transmembrane topology prediction.http://bioinf.cs.ucl.ac.uk/psipred/psipredbiotools:psipredRRID:SCR_018546rridWeb applicationhttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_0736Protein folds and structural domainshttp://edamontology.org/topic_3542Protein secondary structurehttp://edamontology.org/topic_0130Protein folding, stability and designhttp://edamontology.org/topic_2814Protein structure analysisLinuxWindowsMachttp://edamontology.org/operation_0469Protein secondary structure prediction (turns)http://edamontology.org/operation_0303Protein fold recognitionhttp://edamontology.org/operation_0267Protein secondary structure predictionhttp://bioinf.cs.ucl.ac.uk/index.php?id=779General10.1093/bioinformatics/16.4.4041086904110.1006/jmbi.1999.30911049386810.1093/nar/gkt38123748958PMC3692098psipred teampsipred@cs.ucl.ac.ukPersonPrimary contactSWISS-2DPAGEData on proteins identified on various 2-D PAGE and SDS-PAGE reference maps.http://www.expasy.org/ch2d/swiss-2dpagebiotools:swiss-2dpageRRID:SCR_006946rridDatabase portalhttp://edamontology.org/topic_0121ProteomicsLinuxWindowsMacProteomicshttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_0989Protein identifierhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_2374Spot serial numberhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_2791Reference map name (SWISS-2DPAGE)http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_2791Reference map name (SWISS-2DPAGE)http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_2374Spot serial numberhttp://world-2dpage.expasy.org/swiss-2dpage/docs/manch2d.htmlGeneral10.1002/pmic.20030083015274128PrimarySIB Swiss Institute of BioinformaticsInstituteContributorhttp://world-2dpage.expasy.org/contactPersonPrimary contactnf-core-proteinfamiliesnf-core/proteinfamilies is a bioinformatics pipeline that generates protein families from amino acid sequences and/or updates existing families with new sequences. It takes a protein fasta file as input, clusters the sequences and then generates protein family Hiden Markov Models (HMMs) along with their multiple sequence alignments (MSAs). Optionally, paths to existing family HMMs and MSAs can be given (must have matching base filenames one-to-one) in order to update with new sequences in case of matching hits.https://github.com/nf-core/proteinfamiliesnf-core_proteinfamiliesbiotools:nf-core_proteinfamilies2.0.02.1.02.2.0RRID:SCR_027374rrid1.3.0Workflowhttp://edamontology.org/topic_0623Gene and protein familiesGroovyMITnf-coreMatureFree of chargeOpen accesshttps://github.com/nf-core/proteinfamiliesRepository10.1101/2025.08.12.670010SynergyFinder Plus (SynergyFinder+)Efficient implementations for all the popular synergy scoring models for drug combinations, including HSA, Loewe, Bliss and ZIP and visualization of the synergy scores as either a two-dimensional or a three-dimensional interaction surface over the dose matrix. R package available at https://bioconductor.org/packages/release/bioc/html/synergyfinder.html. The web server is available at https://www.synergyfinder.org or https://tangsoftwarelab.shinyapps.io/synergyfinder/https://www.synergyfinder.orgsynergyfinderbiotools:synergyfinder1.0.0RRID:SCR_019318rridBioinformatics portalWeb applicationhttp://edamontology.org/topic_3307Computational biologyMacLinuxWindowsRArtistic-2.0BioConductorhttp://edamontology.org/operation_2238Statistical calculationhttps://www.helsinki.fi/en/researchgroups/network-pharmacology-for-precision-medicineHelpdeskNETWORK PHARMACOLOGY FOR PRECISION MEDICINE, FACULTY OF MEDICINE, UNIVERSITY OF HELSINKIhttps://twitter.com/SynergyFinderSocial mediaTwitter sitehttps://tangsoftwarelab.shinyapps.io/synergyfinder/Mirrorhttp://bioconductor/packages/release/bioc/src/contrib/synergyfinder_1.0.0.tar.gzSource codehttps://sourceforge.net/projects/synergyfinder/Container filehttp://bioconductor.org/packages/release/bioc/html/synergyfinder.htmlUser manualdrugcombusedBy10.1093/bioinformatics/btx16228379339PMC5554616Primary10.1007/978-1-4939-7493-1_1729344898PMC638374710.1016/j.gpb.2022.01.00435085776PMC9801064Jing Tangjing.tang@helsinki.fihttps://scholar.google.com/citations?user=6sNdZq8AAAAJ&hl=enhttps://orcid.org/0000-0001-7480-7710PersonPrimary contactAssistant professor in statistics, Faculty of Medicine, University of HelsinkiSpatial ProteomicsEnd-to-end spatial proteomics analysis workflow with QuPath integration. Our workflow consists of cell segmentation, batch correction, unsupervised clustering, validation of clusters on the image, and cell type clustering results visualization.https://github.com/BioDepot/SpatialProteomicsspatial_proteomicsbiotools:spatial_proteomicsRRID:SCR_027835rridWorkflowPythonRMITFree of chargehttps://youtu.be/vHjdCAZQhfEOtherDemo videohttps://github.com/BioDepot/SpatialProteomicsSource code10.1101/2025.05.23.655879Other1Ling-Hong Hunglhhung@uw.eduhttps://orcid.org/0000-0002-5209-2248DeveloperKa Yee Yeungkayee@uw.eduhttps://orcid.org/0000-0002-1754-7577Primary contactBryce Fukudafukudab@uw.eduhttps://orcid.org/0009-0003-7203-5261DeveloperMassBankMassBank is a public repository of mass spectra of small chemical compounds for life sciences (<3000 Da). The database contains spectra from EI‐MS, fast atom bombardment MS, electrospray ionization (ESI)‐MSn data of thousands of authentic standards, EI‐MS and other‐MS data of thousands of volatile natural and synthetic compounds, and ESI‐MS2 data of synthetic drugs contributed by research groups worldwide. ESI‐MS2 data were analyzed under nonstandardized, independent experimental conditions. MassBank users can access either all of the MassBank data or a subset of the data by specifying one or more experimental conditions. In a spectral search to retrieve mass spectra similar to a query mass spectrum, the similarity score is calculated by a weighted cosine correlation in which weighting exponents on peak intensity and the mass‐to‐charge ratio are optimized to the ESI‐MS2 data. MassBank is useful for the identification of chemical compounds and the publication of experimental data.https://massbank.eu/massbankbiotools:massbankdoi:10.25504/FAIRsharing.dk451adoirrid:SCR_015535rridDatabase portalhttp://edamontology.org/topic_3172MetabolomicsMatureFree of chargeMetabolomicsGermanyhttps://massbank.eu/ServiceEuropean MassBank sitehttps://github.com/MassBank/Otherhttps://github.com/MassBank/MassBank-web/Source code10.1002/jms.177720623627PrimaryThe MassBank ProjectProjectDeveloperFunded by JST-BIRD 2006-2010de.NBI MASH10.13039/501100002347ProjectFunding under FKZ 031L0107NORMAN AssociationProteinProspectorA suite of protein identification tools.http://prospector.ucsf.eduproteinprospectorbiotools:proteinprospectorRRID:SCR_014558rridWeb applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_3489Database managementLinuxWindowsMacms-utilsProteomicshttp://edamontology.org/operation_2929Protein fragment weight comparisonhttp://edamontology.org/operation_3647Blind peptide database searchhttp://ms-utils.orgSoftware cataloguehttp://prospector.ucsf.edu/prospector/html/instruct/allman.htmUser manual10.1074/mcp.d500002-mcp20015937296PrimaryAdminppadmin@cgl.ucsf.eduPersonMaintainerwebmaster@ms-utils.orghttp://ms-utils.orgPersonDocumentorSILVA rRNA databaseSILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukaryota).https://www.arb-silva.desilvabiotools:silvaRRID:SCR_006423rridWeb applicationDatabase portalhttp://edamontology.org/topic_0659Functional, regulatory and non-coding RNAhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_0637Taxonomyhttp://edamontology.org/topic_3050Biodiversityhttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_0632Probes and primersCC-BY-4.0de.NBIde.NBI-biodataDSMZ Digital DiversityMatureFree of chargeOpen accessDataGermanyhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1097Sequence accession (nucleic acid)http://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/data_1868Taxonhttp://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/data_1046Strain namehttp://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/data_1088Article IDhttp://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/data_2909Organism namehttp://edamontology.org/format_1964plain text format (unformatted)The search and retrieval functions of the SILVA website can be used to build custom subsets of sequences. In addition to simple searches e.g. for accession numbers, organism names, taxonomic entities, or publication DOI/PubMed IDs, complex queries over several database fields using constraints such as sequence length or quality values are possible. The results can be sorted according to accession numbers, organism names, sequence length, sequence and alignment quality and Pintail values. The search results show accession number, organism name, sequence length, sequence quality values, taxonomic classifications, and links to view the full sequence record on SILVA and on ENA. Sequences found via search and added to download cart can be downloaded as FASTA and ARB files.http://edamontology.org/operation_2419Primer and probe designhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1207nucleotidehttp://edamontology.org/data_1240PCR primershttp://edamontology.org/format_1207nucleotideThe SILVA Probe Match and Evaluation Tool detects and displays all occurrences of a given probe or primer sequence in the SILVA datasets.
TestPrime allows you to evaluate the performance of primer pairs by running an in silico PCR on the SILVA databases. From the results of the PCR, TestPrime computes coverages for each taxonomic group in all of the taxonomies offered by SILVA.http://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_0496Global alignmenthttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/operation_0547Phylogenetic inference (maximum likelihood and Bayesian methods)http://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1984FASTA-alnThe Alignment, Classification and Tree Service (ACT) of SILVA allows to align and optionally classify sequences using the SILVA Incremental Aligner (SINA). From aligned sequences, (optionally) phylogenetic trees can be inferred using FastTree or RAxML.https://www.arb-silva.de/browser/ServiceSILVA Taxonomy Browserhttps://www.arb-silva.de/search/ServiceSILVA metadata searchhttps://www.arb-silva.de/aligner/ServiceACT: Alignment, Classification and Tree Servicehttps://www.arb-silva.de/search/testprobe/ServiceSILVA Probe Match and Evaluation Toolhttps://www.arb-silva.de/search/testprime/ServiceSILVA Primer Evaluation Toolhttps://treeviewer.arb-silva.de/ServiceWeb-based viewer for the SILVA guide treeshttps://www.arb-silva.de/download/archive/Downloads pageSILVA dataset archivehttps://www.arb-silva.de/silva-license-information/Terms of usehttps://www.arb-silva.de/contact/Citation instructionshttps://www.arb-silva.de/documentation/Generalhttps://www.arb-silva.de/documentation/faqs/FAQsilvangsusedByd3hubincludedIn10.1093/nar/gks121923193283PMC3531112Primary10.1093/nar/gkt120924293649PMC3965112Other10.1093/nar/gkm86417947321PMC2175337Other10.1093/bioinformatics/bts25222556368PMC3389763Other10.1016/j.jbiotec.2017.06.119828648396Review10.1186/s12859-017-1841-3OtherLeibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultureshub@dsmz.dehttps://www.dsmz.degrid.420081.f02tyer376InstituteProviderSILVA Teamcontact@arb-silva.dehttps://www.arb-silva.de/contact/team/grid.507782.f027z9pz32DivisionPrimary contactAutoDock VinaAutoDock Vina is a new open-source program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use.http://vina.scripps.edu/autodock_vinabiotools:autodock_vina1.1.2RRID:SCR_011958rridDesktop applicationhttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_2275Molecular dockingLinuxWindowsMacC++http://edamontology.org/operation_0478Molecular dockinghttp://www.mybiosoftware.com/autodock-vina-1-1-2-molecular-docking-virtual-screening-program.htmlSoftware cataloguehttp://vina.scripps.edu/manual.htmlUser manual10.1002/jcc.2133419499576PMC3041641Primaryhttp://olegtrott.com/PersonPrimary contactBioSimulationsBioSimulations is a web application for sharing and re-using biomodels, simulations, and visualizations of simulations results. BioSimulations supports a wide range of modeling frameworks (e.g., kinetic, constraint-based, and logical modeling), model formats (e.g., BNGL, CellML, SBML), and simulation tools (e.g., COPASI, libRoadRunner/tellurium, NFSim, VCell). BioSimulations aims to help researchers discover published models that might be useful for their research and quickly try them via a simple web-based interface.https://www.biosimulations.org/biosimulationsbiotools:biosimulationsRRID:SCR_018733rridCommand-line toolWeb APIWeb applicationWeb servicehttp://edamontology.org/topic_2259Systems biologyhttp://edamontology.org/topic_0602Molecular interactions, pathways and networksJavaScriptPythonMITEmergingFree of chargeOpen accesshttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/data_0950Mathematical modelhttp://edamontology.org/format_2585SBMLhttp://edamontology.org/format_3240CellMLhttps://github.com/reproducible-biomedical-modeling/Biosimulations/issuesIssue trackerhttps://github.com/reproducible-biomedical-modeling/BiosimulationsRepositoryhttps://api.biosimulations.org/Servicehttps://docs.biosimulations.orgGeneralhttps://api.biosimulations.org/API documentationhttps://docs.biosimulations.org/developers/conduct/Code of conducthttps://docs.biosimulations.org/about/terms/Terms of userunbiosimulationsusesbiosimulatorsusesbiomodelsusessbmlusesbionetgenusescobrapyusescopasiuseslibroadrunnerusesJonathan Karrkarr@mssm.eduhttps://www.karrlab.orghttps://orcid.org/0000-0002-2605-5080PersonDeveloperBilal Shaikhhttps://orcid.org/0000-0001-5801-5510PersonDeveloperHuman Microbiome CompendiumCollection of human microbiome sequencing data that pairs subject metadata with relative abundance data derived from amplicon and shotgun metagenomic sequencing processed via uniform pipelines.https://microbiomap.orghuman_microbiome_compendiumbiotools:human_microbiome_compendiumRRID:SCR_026991rridBioinformatics portalhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_3697Microbial ecologyhttp://edamontology.org/topic_4012FAIR datahttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_3293PhylogeneticsRPythonCC-BY-2.0microbiomeEmergingFree of chargeOpen accessDatahttps://microbiomap.orgOtherHomepage of the project with links to multiple tools and datasetshttps://doi.org/10.5281/zenodo.8186993RepositoryLink to the most recent release of the compendium datasethttps://doi.org/10.5281/zenodo.8186993Biological dataDOI links to the most recent releasehttps://zenodo.org/records/15122187/files/README.mdUser manual10.1016/j.cell.2024.12.01739848248PMC11848717Primary1.1.0Richard Abdillrabdill@uchicago.eduhttps://blekhmanlab.orghttps://orcid.org/0000-0001-9565-5832PersonPrimary contactISfinderIt is a dedicated insertion sequence (IS) database which assigns names to individual ISs to maintain a coherent nomenclature, an IS repositaory including >3000 individual ISs from both bacteria and archaea and provides a basis for IS classification. Each IS is indexed in ISfinder with various associated pieces of information and classified into a group or family to provide some insight into its phylogeny.http://www-is.biotoul.frisfinderbiotools:isfinderRRID:SCR_003020rridDatabase portalhttp://edamontology.org/topic_3068Literature and languagehttp://edamontology.org/topic_0084Phylogenyhttp://edamontology.org/topic_0798Mobile genetic elementshttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_3168SequencingLinuxWindowsMacSQLToolsFrancehttp://edamontology.org/operation_3211Genome indexinghttp://edamontology.org/operation_3349Bibliography generationhttp://edamontology.org/operation_2436Gene-set enrichment analysishttps://www-is.biotoul.fr/general_information.phpGeneral10.1093/nar/gkp94719906702PMC2808865Patricia SiguierPatricia.Siguier@ibcg.biotoul.frPersonPrimary contactPharosPharos is the web interface for data collected by the Illuminating the Druggable Genome initiative. Target, disease and ligand information are collected and displayed.
You are using an outdated browser. Please upgrade your browser to improve your experience.https://pharos.nih.gov/pharosbiotools:pharosRRID: SCR_016924rridhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/operation_3436Aggregationhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_2422Data retrievalhttps://pharos.nih.gov/apiAPI documentation10.1093/nar/gkaa99333156327PMC7778974Tudor I Opreatoprea@salud.unm.eduPersonPhenoManFreeware that provides approaches for efficient exploration and management of phenotype data.https://code.google.com/p/phenoman/phenomanbiotools:phenomanRRID: SCR_005249rridCommand-line toolhttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_0625Genotype and phenotypeLinuxMacRPythonGPL-3.0http://edamontology.org/operation_2428Validationhttp://edamontology.org/operation_2238Statistical calculationhttp://www.mybiosoftware.com/phenoman-1-0rc-exploration-and-management-of-phenotype-data.htmlSoftware cataloguehttps://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/phenoman/doc_phenoman.pdfGeneral10.1093/bioinformatics/btt68224336645PMC3904519sleal@bcm.eduPersonPrimary contactPhiliusPhilius predicts protein transmembrane topology and signal peptides.http://noble.gs.washington.edu/proj/philius/philiusbiotools:philiusRRID: SCR_004625rridCommand-line toolhttp://edamontology.org/topic_0154PeptidesLinuxPythonhttp://edamontology.org/operation_2479Protein sequence analysishttp://www.mybiosoftware.com/philius-predict-protein-transmembrane-topology-signal-peptides.htmlSoftware cataloguehttps://noble.gs.washington.edu/proj/philius/READMEGeneral10.1371/journal.pcbi.100021318989393PMC2570248Primaryhttp://noble.gs.washington.edu/PersonPrimary contactABNERABNER (A Biomedical Named Entity Recognizer) is a software tool for molecular biology text analysis.http://pages.cs.wisc.edu/~bsettles/abner/abnerbiotools:abner1.5RRID:SCR_011868rridDesktop applicationhttp://edamontology.org/topic_3070Biologyhttp://edamontology.org/topic_3047Molecular biologyLinuxWindowsMacJavahttp://edamontology.org/operation_0306Text mininghttp://www.mybiosoftware.com/abner-1-5-molecular-biology-text-analysis.htmlSoftware cataloguehttp://pages.cs.wisc.edu/~bsettles/abner/javadoc/API documentation10.1093/bioinformatics/bti47515860559Primaryhttp://www.cs.cmu.edu/~bsettles/index.htmlPersonPrimary contactACLAMEThis database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids). In addition to providing information on the MGEs content, classifications are available at various levels of organization.http://aclame.ulb.ac.be/aclamebiotools:aclameRRID:SCR_001694rridDatabase portalhttp://edamontology.org/topic_0798Mobile genetic elementshttp://edamontology.org/topic_0623Gene and protein familieshttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_3957Protein interaction experimentLinuxWindowsMacSQLhttp://edamontology.org/operation_2995Sequence classificationhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_3197Genetic variation analysishttp://aclame.ulb.ac.be/Classification/description.htmlGeneral10.1093/nar/gkp93819933762PMC2808911The ACLAME teamaclame@bigre.ulb.ac.bePersonPrimary contactAdmixToolsImplements five methods to analyze admixture: the three-population test, D-statistics, F4-ratio estimation, admixture graph fitting, and rolloff. In addition, it computes lower and upper bounds on admixture proportions based on f3-statistics. Contains 6 programs: convertf, qp3Pop, qpBound, qpDstat, qpF4Ratio, and rolloff.https://github.com/DReichLab/AdmixToolsadmixtoolsbiotools:admixtoolsRRID:SCR_018495rridCommand-line toolhttp://edamontology.org/topic_3056Population geneticsLinuxMacRC++PerlCUnlicenseAnimal and Crop Genomicshttp://edamontology.org/operation_3197Genetic variation analysishttps://github.com/DReichLab/AdmixToolsGeneral10.1534/genetics.112.14503722960212PMC3522152Primarynickp@broadinstitute.orgPersonPrimary contactALCHEMYALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods.http://alchemy.sourceforge.net/alchemybiotools:alchemy1.07RRID:SCR_005761rridCommand-line toolhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_3053GeneticsLinuxMacChttp://edamontology.org/operation_3196Genotypinghttp://www.mybiosoftware.com/alchemy-1-07-an-automated-population-genetic-model-driven-snp-genotype-calling-method.htmlSoftware cataloguehttp://alchemy.sourceforge.net/General10.1093/bioinformatics/btq53320926420PMC2982150Primaryhttp://alchemy.sourceforge.net/PersonPrimary contactAllele frequency netThe allele frequency net database is an online repository that contains information on the frequencies of immune genes and their corresponding alleles in different populations. At present, the system contains data on the frequency of genes from different polymorphic regions such as human leukocyte antigens, killer-cell immunoglobulin-like receptors, major histocompatibility complex Class I chain-related genes and a number of cytokine gene polymorphisms.http://www.allelefrequencies.netallele_frequency_netbiotools:allele_frequency_netRRID:SCR_007259rridDatabase portalhttp://edamontology.org/topic_2830Immunoproteins and antigenshttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3056Population geneticshttp://edamontology.org/topic_3305Public health and epidemiologyhttp://edamontology.org/topic_0208PharmacogenomicsLinuxWindowsMacJavaScripthttp://edamontology.org/operation_3221Species frequency estimationhttp://edamontology.org/operation_0487Haplotype mappinghttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_0542Phylogenetic tree generation (from gene frequencies)http://edamontology.org/operation_3227Variant calling10.1093/nar/gkq112821062830PMC3013710Supportsupport@allelefrequencies.netPersonPrimary contactAlohomoraAlohomora was designed to facilitate genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels such as the Affymetrix GeneChip(R) Human Mapping 10K Arrayhttp://gmc.mdc-berlin.de/alohomora/alohomorabiotools:alohomora0.33RRID:SCR_009117rridDesktop applicationhttp://edamontology.org/topic_2885Single nucleotide polymorphismhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_3678Studieshttp://edamontology.org/topic_2885SNPhttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_0102Linkagehttp://edamontology.org/topic_0199PolymorphismLinuxWindowsMacPerlhttp://edamontology.org/operation_2429Mappinghttp://edamontology.org/operation_0283Linkage analysishttp://www.mybiosoftware.com/alohomora-0-33-linkage-analysis-tools-affymetrix-mapping.htmlSoftware cataloguehttps://gmc.mdc-berlin.de/alohomora/General10.1093/bioinformatics/bti26415647291Primaryhttp://gmc.mdc-berlin.de/PersonPrimary contactAlta-CyclicAlta-Cyclic is a Illumina Genome-Analyzer (Solexa) base caller.http://hannonlab.cshl.edu/Alta-Cyclic/main.htmlalta-cyclicbiotools:alta-cyclicRRID:SCR_013373rridScripthttp://edamontology.org/topic_0080Sequence analysisLinuxPerlLegacyhttp://edamontology.org/operation_3185Base-callinghttp://hannonlab.cshl.edu/Alta-Cyclic/usage.htmlGeneral10.1038/nmeth.123018604217PMC2978646Yaniv Erlicherlich@cshl.eduPersonPrimary contactAlternative Splicing GalleryThe Alternative Splicing Gallery (ASG) takes an identifier such as an EnsEMBL gene ID or a RefSeq ID as input, and provides a graph mapping splice events to transcript information. The user can also view GO information for the record, and select one or more exons and download the resulting sequence. ASG also links out to other alternative splicing databases like ProSplicer.http://statgen.ncsu.edu/asg/alternative_splicing_gallerybiotools:alternative_splicing_galleryRRID:SCR_008129rridDatabase portalhttp://edamontology.org/topic_3320RNA splicinghttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_3120Protein variantsLinuxWindowsMachttp://edamontology.org/operation_0264Splice transcript predictionhttp://edamontology.org/operation_0433Splice site predictionhttp://edamontology.org/operation_2499Splicing model analysishttp://edamontology.org/operation_0232Sequence merginghttp://edamontology.org/operation_0526EST assembly10.1093/nar/gkh73115292448PMC506815Steffen Hebersheber@ncsu.eduPersonPrimary contactJeremy Leipzigleipzig@med.upenn.eduPersonPrimary contactANDESThe fundamental data structure underlying, is the position profile, which contains the nucleotide distributions for each genomic position resultant from a multiple sequence alignment. They include the root mean square deviation plot and the computation of base conversion frequencies, variation, inter-sample clustering and visualization, threshold-driven consensus sequence generation and polymorphism detection, and the estimation of empirically determined sequencing quality values.http://andestools.sourceforge.net/andesbiotools:andes20120225RRID:SCR_002791rridCommand-line toolhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_3277Sample collectionsLinuxRPerlhttp://edamontology.org/operation_3202Polymorphism detectionhttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_2424Comparisonhttp://edamontology.org/operation_0230Sequence generationhttp://edamontology.org/operation_3429Generationhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/operation_3432Clusteringhttp://www.mybiosoftware.com/andes-20100709-analysis-deep-sequencing.htmlSoftware cataloguehttp://andestools.sourceforge.net/OnlineManual.htmUser manual10.1186/1756-0500-3-19920633290PMC2921379Primaryhttp://www.jcvi.org/PersonPrimary contactaroma.affymetrixR package for analyzing large Affymetrix data sets which allows to analyze 100-1,000s of arrays of various chip types, e.g. expression arrays, SNP chips, exon arrays and so on.http://aroma-project.org/aroma.affymetrixbiotools:aroma.affymetrixRRID:SCR_010919rridScripthttp://edamontology.org/topic_3169ChIP-seqhttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_3056Population geneticsLinuxWindowsMacRhttp://edamontology.org/operation_0571Expression data renderinghttp://edamontology.org/operation_2495Gene expression analysishttp://www.mybiosoftware.com/aroma-affymetrix-v2-10-0-open-source-framework-microarray-analysis.htmlSoftware cataloguehttp://aroma-project.org/docs/General10.1093/bioinformatics/btq30020529889PMC2913655http://aroma-project.org/aboutPersonPrimary contactArrayPipeArrayPipe allows users to customize a processing pipeline for the analysis of microarray data. Includes methods for quality assessment of slides, data visualization, normalization, and detection of differentially expressed genes. Output consists of reports formatted as standard web pages and tab-delimited lists of calculated values.http://koch.pathogenomics.ca/cgi-bin/pub/arraypipe.plarraypipebiotools:arraypipeRRID:SCR_010934rridWeb applicationhttp://edamontology.org/topic_3518Microarray experimenthttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_3365Data architecture, analysis and designhttp://edamontology.org/topic_3179ChIP-on-chipLinuxWindowsMachttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_3223Differential gene expression analysishttp://edamontology.org/operation_0314Gene expression profilinghttp://edamontology.org/operation_2495Gene expression analysishttp://www.pathogenomics.ca/arraypipe/info/General10.1093/nar/gkh44615215429PMC441584Karsten Hokampkarsten.hokamp@tcd.iePersonPrimary contactASPEXASPEX is a set of programs for performing multipoint exclusion mapping of affected sibling pair data for discrete traits.There are five main analysis programs: sib_ibd, sib_phase, sib_map, sib_tdt, and sib_kin.http://aspex.sourceforge.net/aspexbiotools:aspexRRID:SCR_008414rridCommand-line toolhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_3053GeneticsLinuxPerlhttp://edamontology.org/operation_2429Mappinghttp://www.mybiosoftware.com/aspex-2-5-affected-sib-pair-exclusion-mapping.htmlSoftware cataloguehttp://aspex.sourceforge.net/usage.pdfUser manual10.1002/gepi.137017073210597434David Hindsdahinds@users.sourceforge.netPersonPrimary contactAssociation ViewerAssociationViewer is a Java application used to display SNPs in a genetic context. Supplementary data (such as genes or LD plots) is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks.http://associationviewer.vital-it.ch/association_viewerbiotools:association_viewerRRID:SCR_009063rridWeb applicationhttp://edamontology.org/topic_0622GenomicsLinuxWindowsMacJavahttp://edamontology.org/operation_0226Annotationhttp://associationviewer.vital-it.ch/usage.phpGeneral10.1093/bioinformatics/btp01719168913PMC2647839PrimaryOlivier Martinhttps://sourceforge.net/u/voltigeur/profile/PersonPrimary contactASTDAltSplice and AltExtron provide information on alternative intron/exons, alternative splice events, and isoform splice patterns. AEdb contains: AEdb-Sequence (sequence and properties of alternatively splice exons), AEdb-Function (data on functional aspects of alternative splicing), AEdb-motif (data and sequence of known splice regulatory motifs), and AEdb-minigene (a collection of known minigene constructs for alternative splice events).http://www.ebi.ac.uk/astd/astdbiotools:astdRRID:SCR_001883rridDatabase portalhttp://edamontology.org/topic_0114Gene structureLinuxWindowsMacDRCAThttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1033Ensembl gene IDhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1033Ensembl gene IDhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1033Ensembl gene IDhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1033Ensembl gene IDhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1033Ensembl gene IDhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_2367ASTD IDhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_2367ASTD IDhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_2367ASTD IDhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_2367ASTD IDhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_2398Ensembl protein IDhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_2398Ensembl protein IDhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_2368ASTD ID (exon)http://edamontology.org/data_2367ASTD IDhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_2369ASTD ID (intron)http://edamontology.org/data_2367ASTD IDhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_2371ASTD ID (tss)http://edamontology.org/data_2367ASTD IDhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_2370ASTD ID (polya)https://www.ebi.ac.uk/asdGeneral10.1093/nar/gkv135226673705PMC4702932OtherDRCATProjectDocumentorContact Listhttp://www.ensembl.org/info/about/contact/index.htmlPersonPrimary contactAthaMapAthaMap is a genome-wide map of putative transcription factor binding sites in Arabidopsis thalianahttp://www.athamap.de/athamapbiotools:athamapRRID:SCR_006717rridWeb applicationhttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_3125DNA binding sitesLinuxhttp://edamontology.org/operation_0445Transcription factor binding site predictionhttp://edamontology.org/operation_2436Gene-set enrichment analysishttp://edamontology.org/operation_0438Transcriptional regulatory element predictionhttp://www.athamap.de/documentation.phpGeneral10.1093/nar/gkh01714681436PMC30875210.1093/nar/gki39515980498PMC116015610.1093/nar/gkl100617148485PMC176142210.1093/nar/gkn70918842622PMC268647410.1093/database/baq03421177332PMC3011983Artyom Romanov (Webmaster)k.romanov@tu-braunschweig.dePersonPrimary contactAutoAssemblyDA software which performed the local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers.http://sourceforge.net/projects/autoassemblyd/autoassemblydbiotools:autoassemblydRRID:SCR_001087rridDesktop applicationhttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0622GenomicsLinuxWindowsMachttp://edamontology.org/operation_0525Genome assemblyhttp://edamontology.org/operation_0525Genome assemblyhttp://www.mybiosoftware.com/autoassemblyd-0-1-graphical-user-interface-system-for-several-genome-assembler.htmlSoftware cataloguehttps://sourceforge.net/projects/autoassemblyd/files/release/version_0.1/AutoAssemblyD_USER%20GUIDE.pdf/downloadUser manual10.6026/9732063000984024143057PMC3796888http://sourceforge.net/projects/autoassemblyd/PersonPrimary contactAvogadroAvogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.http://avogadro.cc/avogadrobiotools:avogadro2.0.8.0RRID:SCR_015983rridDesktop applicationhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_3332Computational chemistryhttp://edamontology.org/topic_3314ChemistryLinuxWindowsMacPythonhttp://edamontology.org/operation_0337Visualisationhttp://www.mybiosoftware.com/avogadro-1-0-3-molecule-editor-visualizer.htmlSoftware cataloguehttps://avogadro.cc/docs/User manual10.1186/1758-2946-4-1722889332PMC3542060Primaryhttp://blog.cryos.net/PersonPrimary contactBamViewInteractive Java application for visualising the large amounts of data stored for sequence reads which are aligned against a reference genome sequencehttp://bamview.sourceforge.net/bamviewbiotools:bamviewRRID:SCR_004207rridDesktop applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacJavaGPL-3.0http://edamontology.org/operation_0564Sequence visualisationhttp://bamview.sourceforge.netGeneral10.1093/bib/bbr07322253280PMC3603209PrimaryBamView development teamartemis@sanger.ac.ukPersonPrimary contactBarraCUDABarracuda is a high-speed sequence aligner based on BWA and uses the latest Nvidia CUDA architecture for accelerating alignments of sequence reads generated by the next-generation sequencers.http://seqbarracuda.sourceforge.net/barracudabiotools:barracudaRRID:SCR_006881rridCommand-line toolhttp://edamontology.org/topic_0080Sequence analysisLinuxC++CMITMaturehttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/operation_0292Sequence alignment10.1186/1756-0500-5-2722244497PMC3278344Klus P.yhbl2@cam.ac.ukPersonPrimary contactBARSBARS 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.http://wpicr.wpic.pitt.edu/WPICCompGen/bars.htmbarsbiotools:barsRRID:SCR_009123rridCommand-line toolhttp://edamontology.org/topic_3053GeneticsLinuxRhttp://edamontology.org/operation_3659Regressionhttp://www.mybiosoftware.com/bars-bayesian-adaptive-regression-splines.htmlSoftware cataloguehttp://wpicr.wpic.pitt.edu/WPICCompGen/BARS/BARS_R_INSTRUCTIONS.htmGeneral10.1186/1479-7364-1-1-2015601530PMC3525002Primaryhttp://wpicr.wpic.pitt.edu/WPICCompGen/PersonPrimary contactBayesCallBayesian basecallerhttp://bayescall.sourceforge.net/bayescallbiotools:bayescallRRID:SCR_011866rridCommand-line toolhttp://edamontology.org/topic_3168SequencingLinuxWindowsMacC++PythonGPL-3.0Legacyhttp://edamontology.org/operation_3185Base-callinghttp://bayescall.sourceforge.net/README.txtGeneral10.1101/gr.095299.10919661376PMC2765266Wei-Chun Kaowckao@eecs.berkeley.eduPersonPrimary contactYun S. Songyss@eecs.berkeley.eduPersonPrimary contactBAYESFSTBayesian estimation of the coancestry coefficient FSThttp://www.reading.ac.uk/Statistics/genetics/software.htmlbayesfstbiotools:bayesfstRRID:SCR_013479rridCommand-line toolhttp://edamontology.org/topic_3053Geneticshttp://edamontology.org/topic_3056Population geneticshttp://edamontology.org/topic_2269Statistics and probabilityLinuxWindowshttp://edamontology.org/operation_3658Statistical inferencehttp://www.mybiosoftware.com/bayesfst-bayesian-estimation-coancestry-coefficient-fst.htmlSoftware cataloguehttp://www.reading.ac.uk/Statistics/genetics/software.htmlGeneral10.1111/j.1365-294x.2004.02125.x15012769D.J. Baldingd.balding@ic.ac.ukhttp://www.reading.ac.uk/maths-and-stats/PersonPrimary contactBBSeqAn R package for analyzing RNA-Seq transcriptional count data.http://www.bios.unc.edu/research/genomic_software/BBSeq/bbseqbiotools:bbseqRRID:SCR_011877rridLibraryhttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_0203Gene expressionLinuxWindowsMacRhttp://edamontology.org/operation_3800RNA-Seq quantificationhttp://edamontology.org/operation_3563RNA-seq read count analysishttp://edamontology.org/operation_2495Gene expression analysishttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/data_3495RNA sequencehttp://edamontology.org/format_1213rnahttp://www.bios.unc.edu/research/genomic_software/BBSeq/index_files/manual.pdfUser manual10.1093/bioinformatics/btr44921810900PMC3179656Yi-Hui Zhouyzhou@bios.unc.eduhttp://www.bios.unc.edu/~yihuizPersonPrimary contactBCBtoolkitAims to provide the scientific community with the several tools to indirectly assess brain disconnections.http://toolkit.bcblab.com/bcbtoolkitbiotools:bcbtoolkitRRID:SCR_015519rridCommand-line toolhttp://edamontology.org/topic_3334Neurologyhttp://edamontology.org/topic_3304Neurobiologyhttp://edamontology.org/topic_0602Molecular interactions, pathways and networksLinuxMacRJavaBSD-3-Clausehttp://edamontology.org/operation_2497Pathway or network analysishttp://toolkit.bcblab.com/General10.1093/gigascience/giy00429432527PMC5863218Michel Thiebaut de Schottenmichel.thiebaut@gmail.comPersonPrimary contactBeetleBaseThe database contains genomic sequence scaffolds mapped to 10 linkage groups, genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The database was reconstructed using the upgraded Generic Model Organism Database (GMOD) modules, it has been updated to provide more comprehensive genomic information for the red flour beetle Tribolium castaneum.http://beetlebase.org/beetlebasebiotools:beetlebaseRRID:SCR_001955rridDatabase portalhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_3053GeneticsLinuxWindowsMachttp://edamontology.org/operation_0525Genome assemblyhttp://edamontology.org/operation_2871Sequence tagged site (STS) mappinghttp://edamontology.org/operation_0282Genetic mappinghttp://edamontology.org/operation_3216Scaffoldinghttp://edamontology.org/operation_2429Mappinghttp://beetlebase.org/?q=homeGeneral10.1093/nar/gkp80719820115PMC2808946Supportbioinfo@ksu.eduPersonPrimary contactBiNGOA tool to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network.http://www.psb.ugent.be/cbd/papers/BiNGO/Home.htmlbingobiotools:bingo3.0.2RRID:SCR_005736rridDesktop applicationhttp://edamontology.org/topic_0085Functional genomicsLinuxWindowsMacVIBPlant Systems BiologyUGenthttp://edamontology.org/operation_3501Enrichment analysishttp://edamontology.org/data_1025Gene identifierhttp://edamontology.org/data_2338Ontology identifierGO enrichment analysishttps://www.psb.ugent.be/cbd/papers/BiNGO/Tutorial.htmlGeneral10.1093/bioinformatics/bti55115972284PrimaryPSBInstituteProviderSteven Maeresteven.maere@psb.vib-ugent.behttp://www.psb.ugent.be/esb/ESB/Home.htmlPersonPrimary contactBio-Analytic Resource (BAR)User-friendly web-based tools for working with functional genomics and other data. Most are designed with the plant (mainly Arabidopsis) reseacher in mind, but a couple of them can be useful to the wider research community.http://bar.utoronto.ca/welcome.htmbioanalres_barbiotools:bioanalres_barRRID:SCR_006748rridWeb applicationhttp://edamontology.org/topic_3173Epigenomicshttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0203Gene expressionLinuxWindowsMachttp://edamontology.org/operation_3501Over-representation analysishttp://edamontology.org/operation_0314Gene expression profilinghttp://edamontology.org/operation_3463Gene expression correlation analysishttp://edamontology.org/operation_2464Protein-protein binding site prediction10.1007/978-1-4939-6658-5_62798716710.1111/tpj.1326127401965Nicholas J. Provartnicholas.provart@utoronto.caPersonPrimary contactGenMAPPMicroarray expression data visualization tool, allowing data to be viewed on maps representing gene groupings and biological pathways.http://www.genmapp.org/genmappbiotools:genmappRRID:SCR_005094rridWeb applicationhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_3518Microarray experimenthttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_0102MappingLinuxWindowsMachttp://edamontology.org/operation_0313Gene expression clusteringhttp://edamontology.org/operation_0315Gene expression comparisonhttp://edamontology.org/operation_0314Gene expression profilinghttp://edamontology.org/operation_2495Gene expression analysis10.1038/ng0502-1911984561Bruce R. Conklinbconklin@gladstone.ucsf.eduPersonPrimary contactGenome ProjectorSearchable database browser with zoomable user interface using Google Map API. Genome Projector currently contains 4 views: Genome map, Plasmid map, Pathway map, and DNA walk.http://www.g-language.org/GenomeProjector/genome_projectorbiotools:genome_projectorRRID:SCR_011790rridWeb applicationhttp://edamontology.org/topic_3070Biologyhttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0092Data visualisationLinuxWindowsMacJavaScriptPerlhttp://edamontology.org/operation_3208Genome visualisationhttp://www.mybiosoftware.com/genome-projector-zoomable-user-interface-molecular-biology.htmlSoftware cataloguehttp://www.g-language.org/GenomeProjector/wiki/General10.1186/1471-2105-10-3119166610PMC2636772http://www.g-language.org/GenomeProjector/members.htmlPersonPrimary contactGenomedataGenomedata is a format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint.http://noble.gs.washington.edu/proj/genomedata/genomedatabiotools:genomedataRRID:SCR_004544rridLibraryhttp://edamontology.org/topic_3071Data managementhttp://edamontology.org/topic_0080Sequence analysisLinuxMacPythonCGPL-3.0Maturehttp://edamontology.org/operation_2478Nucleic acid sequence analysishttps://hoffmanlab.org/proj/genomedata/doc/1.4.0/genomedata.pdfGeneral10.1093/bioinformatics/btq16420435580PMC2872006PrimaryJay Hesselberthjay.hesselberth@ucdenver.eduPersonPrimary contactGenometaJava based local bioinformatics program which allows rapid analysis of metagenomic short read datasets. Millions of short reads can be accurately analysed within minutes and visualised in the browser component. A large database of diverse bacteria and archaea has been constructed as a reference sequence.http://genomics1.mh-hannover.de/genometa/index.php?Site=Homegenometabiotools:genometaRRID:SCR_001181rridDesktop applicationhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_0622GenomicsLinuxWindowsMacJavaMaturehttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3198Read mappinghttp://genomics1.mh-hannover.de/genometa/index.php?Site=Tutorial%201User manualhttp://genomics1.mh-hannover.de/genometa/index.php?Site=Tutorial%202User manual10.1371/journal.pone.004122422927906PMC3424124PrimaryDr. Colin Davenportdavenport.colin@mh-hannover.dePersonPrimary contactGenomeToolsFree collection of bioinformatics tools for genome informatics.http://genometools.org/genometoolsbiotools:genometoolsRRID:SCR_018970rridSuitehttp://edamontology.org/topic_3511Nucleic acid sites, features and motifshttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacCBSD-3-ClauseAnimal and Crop GenomicsMaturehttp://edamontology.org/operation_2403Sequence analysishttp://genometools.org/documentation.htmlGeneral10.1109/tcbb.2013.6824091398PrimaryGenomeTools Supportgordon@gremme.orgPersonPrimary contact