WEBnmaWEBnm@ provides quick, automated computation and analysis of low-frequency normal modes for protein structures.http://apps.cbu.uib.no/webnmawebnmabiotools:webnma3.5Web APISuitehttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0736Protein folds and structural domainsLinuxWindowsMacPythonGPL-3.0BiB toolsCBU toolsUiB toolsELIXIR-NOELIXIR-NorwayMatureFree of chargeOpen access3D-BioInfoNorwayhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0244Protein flexibility and motion analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBConstructs elastic network model from alpha carbon coordinates of the protein, and computes properties to describe large scale conformations. Computes normal modes, fluctuation profiles, inter-residue correlations, conformational overlap analysis and vector field representations. Structural amino acid profiles, and normal mode characteristics describing protein motion, visualized in plots and decorated structure visualizations. White space delimited tabular data for normal modes and the provided plotshttp://edamontology.org/operation_2487Protein structure comparisonhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/data_0886Structure alignmenthttp://edamontology.org/format_2200FASTA-like (text)http://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBPerforms comparative analysis of the normal modes of protein structures. Computes the Bhattacharyya Coefficient (BC) and the Root Mean Squared Inner Product (RMSIP) of aligned parts of the proteins. Alignment of sets of proteins to be compared. Multiple protein structures Heatmaps, dendrograms and structural amino acid profiles for visual comparison of structural similarity. White space delimited tabular data for the provided plotshttps://github.com/reuter-group/webnma3RepositoryIssue trackerhttps://elixir.no/helpdeskHelpdeskHelpdesk and support for ELIXIR Norway services.http://apps.cbu.uib.no/webnma3/howto/singleQuick start guidehttp://apps.cbu.uib.no/webnma3/qandaFAQhttp://apps.cbu.uib.no/webnma3/aboutGeneralCitation instructionsnumpyusesbiopythonusesmatplotlibusesmustangusesdsspuses10.1186/s12859-014-0427-625547242PMC4339738Primary2.010.1186/1471-2105-6-5215762993PMC1274249Primary1.0Nathalie ReuterNathalie.Reuter@uib.nohttp://www.cbu.uib.no/reuter/https://orcid.org/0000-0002-3649-7675PersonPrimary contactDeveloperSandhya P Tiwarihttps://orcid.org/0000-0002-0747-3826PersonDeveloperKidane M TeklePersonDeveloperTristan CragnoliniPersonDeveloperSvenn H GrindhaugPersonDeveloperLars SkjærvenPersonDeveloperGisle SalensmindePersonDeveloperEdvin FuglebakkPersonDeveloperSiv M HollupPersonDeveloperDepartment of Molecular Biology, University of Bergen, NorwayInstituteProviderComputational Biology Unit, Department of Informatics, University of Bergen, NorwayInstituteProviderUiBInstituteProviderProfilerProfiler is a peer-reviewed, open-source web platform and desktop version for end-to-end multi-omics data analysis, integrating statistical methods, machine learning, and artificial intelligence into a unified workflow.
The platform supports proteomics, metabolomics, lipidomics, transcriptomics, genomics, and other omics datasets from raw or tabular inputs. Profiler provides automated preprocessing, data exploration, biomarker discovery, AI-driven modeling, survival analysis, and biological interpretation using enrichment analysis.
Designed for both bioinformaticians and experimental scientists, Profiler enables reproducible, explainable, and high-performance omics analysis through an intuitive web interface.
Profiler is developed by the PRISM U1192 laboratory and protected by INSERM Transfer.https://prism-profiler.univ-lille.fr/profilerbiotools:profiler1.0doi:10.1093/bioinformatics/btaf644doi1.0Desktop applicationWeb applicationWorkflowhttp://edamontology.org/topic_3316Computer scienceMacLinuxWindowsOtherMatureFree of chargeOpen accessToolsTrainingInteroperabilityMetabolomicsProteomicsRare DiseasesFrancehttps://prism-profiler.univ-lille.fr/Othersofteware linkhttps://github.com/yanisZirem/Profiler_v1_requests_datatestsRepositorydataset exampleshttps://github.com/yanisZirem/prism-profilerRepositoryDesktop versionhttps://doi.org/10.5281/zenodo.17478158Source codehttps://github.com/yanisZirem/Profiler_v1_requests_datatestsTest data1.0https://prism-profiler.univ-lille.fr/app/Software packagehttps://prism-profiler.univ-lille.fr/citation/Citation instructions10.1093/bioinformatics/btaf64441324558Primary1.0Michel Salzetmichel.salzet@univ-lille.frhttps://www.laboratoire-prism.fr/member/michel-salzet/https://orcid.org/0000-0003-4318-0817PersonProfessor Michel Salzet known for his work in immunology, oncology and proteomicASAFindASAFind is a software that predicts the intracellular location of proteins in cells with four membrane-bound complex plastids of red algal origin.
These plastids evolved via eukaryote-eukaryote endosymbiosis and for example can be found in diatoms and cryptophytes. ASAFind uses protein sequence data and external predictions of signal peptides (by the tools SignalP and TargetP), and predicts plastid proteins, and proteins that are targeted to the periplastidic compartment from these data; optionally, a graphical output can generated.https://asafind.jcu.cz/asafindbiotools:asafind2.0ScriptCommand-line toolWeb servicehttp://edamontology.org/topic_2229Cell biologyhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0780Plant biologyhttp://edamontology.org/topic_0622GenomicsMacLinuxPythonCC-BY-SA-4.0ELIXIR-CZCzech RepublicMatureFree of chargeOpen accessToolsPlant SciencesMarine MetagenomicsMicrobial BiotechnologyCzech Republichttp://edamontology.org/operation_2489Subcellular localisation predictionhttp://edamontology.org/operation_0239Sequence motif recognitionhttp://edamontology.org/operation_0422Protein cleavage site predictionhttp://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1270Feature tablehttps://asafind.jcu.czServiceWeb Servicehttps://github.com/ASAFind/ASAFind-2RepositoryInformation and source code, for local installation or developmenthttps://asafind.jcu.cz/download-page/Downloads pageDownload page on web-service, links to repository2.0https://asafind.jcu.cz/download-page/Installation instructionssignalpusestargetpuses10.1111/tpj.7013840464854PMC12136025Primary2.0Publication of the current version of ASAFind (2.0)10.1111/tpj.1273425438865PMC4329603Other1.0Publication of the first version of ASAFind10.48550/arXiv.2303.02509Benchmarking study1.0Benchmarking of the performance of the first version of ASAFindMarta Vohnoutovámvohnoutova@jcu.czhttps://www.jcu.cz/cz/univerzita/lide/clovek?identita=Vohnoutova_Marta_61699https://orcid.org/0000-0002-8915-8626PersonContributorDeveloperMaintainerAnsgar Gruberagruber@prf.jcu.czhttps://www.jcu.cz/cz/univerzita/lide/clovek?identita=Gruber_Ansgar_118401https://orcid.org/0000-0002-5876-4391PersonPrimary contactDeveloperDocumentorseqfuA collection of utilities to manipulate FASTA and FASTQ files, supporting Gzipped input.https://telatin.github.io/seqfu2/seqfubiotools:seqfu1.10.01.11.01.12.01.13.01.14.01.15.01.16.01.17.01.19.01.20.01.21.01.22.01.22.3Command-line toolhttp://edamontology.org/topic_0077Nucleic acidshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/data_2044Sequenceseqfu [subcommand] FASTX > FASTXhttps://telatin.github.io/seqfu2OtherDocumentationhttps://github.com/telatin/seqfu2/Repositoryhttps://github.com/telatin/seqfu2Software packagehttps://github.com/telatin/seqfu2/releasesDownloads pagehttps://bioconda.github.io/recipes/seqfu/README.htmlSoftware package1.0.0-1.22.3https://telatin.github.io/seqfu2/User manual10.3390/bioengineering805005934066939PMC8148589Primary1.0MS AnnikaMS Annika is a crosslink search engine based on MS Amanda, aimed at identifying crosslinks of cleavable and non-cleavable crosslinkers from MS2 and MS3 spectra. It can deal with a wide variety of cross-linkers and provides robust and transparent FDR control based on a target-decoy approach. MS Annika is available free of charge as a plug-in for Proteome Discoverer.https://github.com/hgb-bin-proteomics/MSAnnikams_annikabiotools:ms_annikaProteome Discoverer 3.2: MS Annika 3.0 v3.0.7Proteome Discoverer 3.1: MS Annika 3.0 v3.0.7Proteome Discoverer 3.0: MS Annika 2.0 v1.1.4fixProteome Discoverer 2.5: MS Annika 2.0 v1.1.3Proteome Discoverer 2.4: MS Annika v1.0.0Proteome Discoverer 2.3: MS Annika v1.0.0Plug-inhttp://edamontology.org/topic_0130Protein folding, stability and designhttp://edamontology.org/topic_0736Protein folds and structural domainshttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0091BioinformaticsWindowsC#FreewareMatureFree of chargeOpen accesshttp://edamontology.org/operation_3631Peptide identificationhttp://edamontology.org/operation_3646Peptide database searchhttp://edamontology.org/operation_3755PTM localisationhttp://edamontology.org/operation_3645PTM identificationhttp://edamontology.org/operation_3649Target-Decoyhttp://edamontology.org/data_0943Mass spectrumhttp://edamontology.org/format_3651MGFhttp://edamontology.org/format_3712Thermo RAWhttp://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_1929FASTAhttps://github.com/hgb-bin-proteomics/MSAnnikaRepositoryMS Annika version archivehttps://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.2/latest.zipSoftware packageLatest MS Annika version for Proteome Disoverer 3.2PD3.2:latesthttps://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.1/latest.zipSoftware packageLatest MS Annika version for Proteome Disoverer 3.1PD3.1:latesthttps://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.0/latest.zipSoftware packageLatest MS Annika version for Proteome Disoverer 3.0PD3.0:latesthttps://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD2.5/latest.zipSoftware packageLatest MS Annika version for Proteome Disoverer 2.5PD2.5:latesthttps://hgb-bin-proteomics.github.io/MSAnnika/Generalhttps://github.com/hgb-bin-proteomics/MSAnnika/raw/master/MS_Annika_3.0_UserManual.pdfUser manualhttps://github.com/hgb-bin-proteomics/MSAnnika/raw/master/tutorial/MS_Annika_3.0_Tutorial.pdfTraining materialDetailed tutorial how to use MS Annikahttps://www.youtube.com/watch?v=L1lVt35PYv4Training materialDetailed tutorial how to use MS Annikams_amandauses10.1021/acs.jproteome.0c0100033852321PMC8155564Primary1.0MS Annika for cleavable crosslink identification from MS2 spectra10.1021/acs.jproteome.3c0032537566781PMC10476269Primary2.0MS Annika 2.0 for cleavable crosslink identification from MS3 spectra10.1038/s42004-024-01386-x39702463PMC11659399Primary3.0MS Annika 3.0 for non-cleavable crosslink identificationViktoria Dorferviktoria.dorfer@fh-hagenberg.athttp://bioinformatics.fh-hagenberg.at/https://orcid.org/0000-0002-5332-5701PersonPrimary contactMicha Birklbauermicha.birklbauer@fh-hagenberg.athttp://bioinformatics.fh-hagenberg.at/https://orcid.org/0009-0005-1051-179XPersonDeveloperViVo PlatformViVo Platform is a free, open-access web application for the analysis of in vivo tumor growth data in mouse models.
Designed to standardize in vivo efficacy analysis, improve research reproducibility, and reduce animal usage, it provides tools to upload tumor volume or bioluminescence imaging (BLI) datasets, configure analysis parameters, detect outliers, and automatically compute tumor growth rates (TGR), group comparisons, and reports.
By standardizing data processing and incorporating advanced temporal modeling, ViVo Platform enhances statistical power and contributes to the 3Rs principle by reducing the number of animals needed in preclinical efficacy studies.https://gcanudo-barreras.github.io/ViVo-Platform/vivo_platformbiotools:vivo_platformResearch Beta 1.0Web applicationhttp://edamontology.org/topic_3379Preclinical and clinical studieshttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_3386Laboratory animal sciencehttp://edamontology.org/topic_0091BioinformaticsJavaScriptMITEmergingFree of chargeOpen accesshttp://edamontology.org/operation_2945Data analysishttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/data_3722Physiology parameterhttp://edamontology.org/format_3752CSVhttp://edamontology.org/data_3723Morphology parameterhttp://edamontology.org/format_3752CSVhttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_0337Visualisationhttps://gcanudo-barreras.github.io/ViVo-Platform/Servicehttps://www.biorxiv.org/content/10.1101/2025.10.14.682266v1OtherbioRxiv preprinthttps://github.com/gcanudo-barreras/ViVo-PlatformRepositoryhttps://github.com/gcanudo-barreras/ViVo-Platform/blob/main/README.mdGeneralhttps://github.com/gcanudo-barreras/ViVo-Platform/blob/main/ViVo_USER_MANUAL.mdUser manualhttps://www.biorxiv.org/content/10.1101/2025.10.14.682266v1OtherFull methodologyhttps://github.com/gcanudo-barreras/ViVo-Platform/releases/tag/v1.0-betaRelease notes10.1101/2025.10.14.682266MethodResearch Beta 1.0Guillermo Canudo-Barrerascanudobarreras@unizar.eshttps://orcid.org/0000-0002-1949-9185PersonDeveloperPrimary contactMaintainerSupportResearcher at Spanish National Research Council (CSIC). Developer.Eduardo Romanoseromanos.iacs@aragon.eshttps://orcid.org/0000-0002-9918-3374PersonContributorResearcher at Biomedical Research Center of Aragon (CIBA).Raquel P. Herreraraquelph@unizar.eshttps://orcid.org/0000-0002-5244-9569PersonContributorSenior scientist at Spanish National Research Council (CSIC).M. Concepción Gimenogimeno@unizar.eshttps://orcid.org/0000-0003-0553-0695PersonContributorFull professor at Spanish National Research Council (CSIC).MaCPepDB - Mass Centric Peptide DatabaseA Database to Quickly Access All Tryptic Peptides of the UniProtKBhttps://macpepdb.cubimed.rub.de/macpepdb_-_mass_centric_peptide_databasebiotools:macpepdb_-_mass_centric_peptide_database3.0.0Database portalhttp://edamontology.org/topic_0121ProteomicsRustJavaScriptOtherCUBiMed.RUBBioInfra.ProtMatureFree of chargeOpen accessGermanyhttps://github.com/medbioinf/macpepdbRepositoryBackend implementation written in Rust / Axumhttps://github.com/medbioinf/macpepdb-frontendRepositoryFrontend implementation written in Rust / Dioxushttps://docs.rs/macpepdb/latest/macpepdb/web/index.htmlAPI documentation10.1021/acs.jproteome.0c0096733724838Primary1.0Julian Uszkoreithttp://orcid.org/0000-0001-7522-4007Dirk Winkelhardtdirk.winkelhardt@rub.dehttps://orcid.org/0000-0001-8770-2221PD Dr. Martin Eisenacherhttps://orcid.org/0000-0003-2687-7444MirGeneDBMirGeneDB is a database of manually curated microRNA genes that have been validated and annotated as initially described in Fromm et al. 2015 , Fromm et al. 2020 and Fromm et al 2022. MirGeneDB 3.0 (Clarke and Hoye et al. 2024 ) includes more than 21,000 microRNA gene entries representing more than 1,700 microRNA families from 114 metazoan species. All microRNAs can be browsed, searched and downloaded.http://mirgenedb.org/mirgenbiotools:mirgen3.0doi:10.25504/FAIRsharing.QXSgvFdoi2.0Database portalhttp://edamontology.org/topic_0659Functional, regulatory and non-coding RNAhttp://edamontology.org/topic_0204Gene regulationhttp://edamontology.org/topic_3299Evolutionary biologyhttp://edamontology.org/topic_3500Zoologyhttp://edamontology.org/topic_2815Human biologyLinuxWindowsMacCC0-1.0UiO toolsELIXIR-NOELIXIR-NorwayMatureFree of chargeOpen accessNorwayhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/data_1097Sequence accession (nucleic acid)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1869Organism identifierData retrieval: curated miRNA. Organism identifier: a specific miRNA identifier or a species for all miRNAs for that species. Gene transcript report: with metadata and visualization. RNA secondary structure: the hairpin loop of the miRNA with bases.http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1097Sequence accession (nucleic acid)https://elixir.no/helpdeskHelpdeskhttps://www.mirgenedb.org/downloadBiological dataSequence downloads for 75 species3.0https://www.mirgenedb.org/informationGeneral10.1093/nar/gkab110134850127PMC8728216Primary2.110.1093/nar/gkz88531598695PMC6943042Primary2.010.1146/annurev-genet-120213-09202326473382PMC4743252Primary1.010.1093/nar/gkae109439673268PMC11701709Primary3.0Bastian FrommBastianFromm@gmail.comhttps://orcid.org/0000-0003-0352-3037PersonPrimary contactDeveloperMaintainerSupportKevin J. Petersonkevin.j.peterson@dartmouth.eduPersonDeveloperMaintainerThe Norwegian Bioinformatics Platform (ELIXIR-Norway) Helpdesksupport@elixir.nohttps://elixir.no/helpdeskConsortiumSupportUniversity of Oslohttps://www.uio.no/english/index.htmlgrid.5510.101xtthb5610.13039/501100005366InstituteProviderDeepSigPrediction of secretory signal peptides in protein sequenceshttps://busca.biocomp.unibo.it/deepsig/deepsigbiotools:deepsig1.2.5Web applicationCommand-line toolhttp://edamontology.org/topic_3307Computational biologyhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0123Protein propertiesLinuxWindowsMacPythonC++GPL-3.0Bologna Biocomputing GroupMatureFree of chargeOpen accessItalyhttp://edamontology.org/operation_0418Protein signal peptide detectionhttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3028Taxonomyhttp://edamontology.org/format_2330Textual formathttps://github.com/BolognaBiocomp/deepsigSource code1.2.5https://hub.docker.com/r/bolognabiocomp/deepsigContainer file1.2.5https://github.com/BolognaBiocomp/deepsigCommand-line options10.1093/bioinformatics/btx81829280997PMC5946842Primary1.0ELIXIR-ITA-BOLOGNAhttp://biocomp.unibo.itInstituteProviderCastrense Savojardocastrense.savojardo2@unibo.ithttps://orcid.org/0000-0002-7359-0633PersonDeveloperPrimary contactPier Luigi Martellipierluigi.martelli@unibo.ithttp://biocomp.unibo.ithttps://orcid.org/0000-0002-0274-5669PersonPrimary contactMuGVREThe MuG Virtual Research Environment is an analysis platform for 3D/4D genomics analyses. It integrates genomics tools for chromatin dynamics data.https://www.multiscalegenomics.eu/mugvrebiotools:mugvre1.0Web applicationWorkbenchhttp://edamontology.org/topic_3176DNA packaginghttp://edamontology.org/topic_3169ChIP-seqhttp://edamontology.org/topic_0097Nucleic acid structure analysishttp://edamontology.org/topic_2275Molecular modellingPHPPythonApache-2.0RIS3CAT VEISFree of chargeOpen accesshttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3210Genome indexhttp://edamontology.org/operation_0475Nucleic acid structure predictionhttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/operation_0279Nucleic acid folding analysishttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_2200FASTA-like (text)http://edamontology.org/data_1255Sequence featureshttp://edamontology.org/format_2305GFFhttp://edamontology.org/operation_0478Molecular dockinghttp://edamontology.org/operation_3900DNA-binding protein predictionhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/operation_3222Peak callinghttp://edamontology.org/operation_1781Gene regulatory network analysishttp://edamontology.org/data_0905Protein interaction raw datahttp://edamontology.org/format_2572BAMhttp://edamontology.org/operation_3927Network analysishttp://edamontology.org/operation_0279Nucleic acid folding analysishttp://edamontology.org/data_0905Protein interaction raw datahttp://edamontology.org/format_1930FASTQhttp://edamontology.org/operation_2478Nucleic acid sequence analysishttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDBhttp://edamontology.org/operation_2476Molecular dynamicshttp://edamontology.org/operation_2481Nucleic acid structure analysishttp://edamontology.org/data_0883Structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/operation_0432Nucleosome position predictionhttp://edamontology.org/operation_3454Phasinghttp://edamontology.org/data_0905Protein interaction raw datahttp://edamontology.org/format_2572BAMhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/data_2012Sequence coordinateshttp://edamontology.org/data_3002Annotation trackhttp://edamontology.org/data_3869Simulationhttp://edamontology.org/data_0883Structurehttp://vre.multiscalegenomics.euServicehttps://github.com/Multiscale-Genomics/VRERepositoryhttps://www.multiscalegenomics.eu/MuGVRE/terms-of-use/Terms of usehttp://vre.multiscalegenomics.eu/help/starting.phpQuick start guidehttps://www.multiscalegenomics.eu/MuGVRE/training/Training materialnucleosome_dynamicsincludestadbitincludesjbrowseincludesnglincludes10.1101/602474Primary1.0Laia Codólaia.codo@bsc.eshttps://orcid.org/0000-0002-6797-8746PersonPrimary contactJosep Lluís Gelpíhttp://orcid.org/0000-0002-0566-7723PersonContributorMultiscale Complex Genomics Communityvre@multiscalegenomics.euhttps://www.multiscalegenomics.eu/ConsortiumDevelopercompareMS2compareMS2 is a tool for comparing sets of (tandem) mass spectra for clustering samples, molecular phylogenetics, identification of biological species or tissues, and quality control. compareMS2 currently consumes Mascot Generic Format, or MGF, and produces output in a variety of common image and distance matrix formats.https://github.com/524D/compareMS2comparems2biotools:comparems21.02.0Command-line toolDesktop applicationhttp://edamontology.org/topic_0084Phylogenyhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_3520Proteomics experimentLinuxWindowsMacCJavaScriptMITms-utilsProteomicsMatureFree of chargeProteomicsNetherlandshttp://edamontology.org/operation_2424Comparisonhttp://edamontology.org/operation_0567Phylogenetic tree visualisationhttp://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3651MGFhttps://github.com/524D/compareMS2Repositoryhttps://www.ms-utils.org/compareMS2.htmlSoftware cataloguehttps://research-software-directory.org/software/comparems2Software cataloguehttp://www.ms-utils.org/compareMS2.cSource code1.0http://www.ms-utils.org/compareMS2.htmlBinaries1.0http://www.ms-utils.org/compareMS2.cSource code1.0https://github.com/524D/compareMS2/tree/main/srcSource code2.0https://github.com/524D/compareMS2/tree/mainBinaries2.0http://www.ms-utils.org/compareMS2.htmlGeneralCommand-line optionshttps://github.com/524D/compareMS2GeneralUser manualCommand-line optionsInstallation instructions10.1002/rcm.616222368051Primary1.010.1021/acs.jproteome.2c0045736173614PMC9903320Primary2.010.1021/acs.jproteome.1c0052834523928PMC8491155Review2.0lumc.nlhttps://www.lumc.nlInstituteSupportMagnus Palmbladmagnus.palmblad@gmail.comhttps://github.com/magnuspalmbladhttp://orcid.org/0000-0002-5865-8994PersonDeveloperPrimary contactDocumentorRob Marissenhttps://github.com/524Dhttps://orcid.org/0000-0002-1220-9173PersonDeveloperARTEMISa method for topology-independent superposition of RNA 3D structures and structure-based sequence alignmenthttps://github.com/david-bogdan-r/ARTEMISartemis3Dbiotools:artemis3Dversion 1.51Command-line toolScripthttp://edamontology.org/topic_3307Computational biologyhttp://edamontology.org/topic_0077Nucleic acidshttp://edamontology.org/topic_0097Nucleic acid structure analysishttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_3511Nucleic acid sites, features and motifshttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_0099RNAMacLinuxWindowsPythonApache-2.03D-BioInfo-Structure-FunctionMatureFree of chargeOpen accesshttp://edamontology.org/operation_0503Pairwise structure alignmenthttp://edamontology.org/operation_2518Nucleic acid structure comparisonhttp://edamontology.org/data_1459Nucleic acid structurehttp://edamontology.org/format_1477mmCIFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1459Nucleic acid structurehttp://edamontology.org/format_1477mmCIFhttp://edamontology.org/format_1476PDBpython3 artemis.py r=FILENAME q=FILENAME [OPTIONS]https://github.com/david-bogdan-r/ARTEMISRepositoryhttps://github.com/david-bogdan-r/ARTEMISSource codeversion 1.5https://github.com/david-bogdan-r/ARTEMIS/blob/main/README.mdQuick start guideREADME filehttps://github.com/david-bogdan-r/ARTEMIS/blob/main/ARTEMIS_TUTORIAL_v1.51.pdfUser manualTutorial in pdfartemuses10.1093/nar/gkae75839258540PMC11472068Primaryversion 1.510.1101/2024.04.06.588371version 1.0Davyd Bohdanhttps://orcid.org/0000-0002-6456-6658Janusz Bujnickihttps://orcid.org/0000-0002-6633-165XEugene Baulinhttps://orcid.org/0000-0003-4694-9783ChannelsDB 2.0A comprehensive resource of channels, pores and tunnels found in biomacromolecular structures deposited in the Protein Data Bank.https://channelsdb2.biodata.ceitec.cz/channelsdbbiotools:channelsdb2.0Database portalhttp://edamontology.org/topic_1317Structural biologyhttp://edamontology.org/topic_3306Biophysicshttp://edamontology.org/topic_0123Protein propertieshttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0821Enzymeshttp://edamontology.org/topic_0820Membrane and lipoproteinshttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_3068Literature and languageLinuxWindowsMacJavaScriptC#FreewareLCC NCBRELIXIR-CZMatureFree of chargeOpen accessData3D-BioInfoCzech Republichttp://edamontology.org/operation_3431Data depositionhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0250Protein property calculationhttp://edamontology.org/operation_0245Protein structural motif recognitionhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_1127PDB IDhttp://edamontology.org/format_1477mmCIFhttp://edamontology.org/format_1476PDBhttps://channelsdb2.biodata.ceitec.czServicehttps://channelsdb2.biodata.ceitec.cz/documentation.htmlUser manualQuick start guideDatabase content
Channels nomenclature
MOLE settings
List of cofactors used for channel determination.
Description how to read the resuls page.
How to access content of the database programatically.https://channelsdb2.biodata.ceitec.cz/methods.htmlGeneralFAQInfo about methodologyhttps://channelsdb2.biodata.ceitec.cz/about.htmlCitation instructionsContributions policyhttps://channelsdb2.biodata.ceitec.cz/apiAPI documentationmoleusescaverusesmoleonline_2.0usescaver_webuses10.1093/nar/gkx868Method1.010.1093/nar/gkad1012Primary2.0Lukáš Pravdaxpravda@ncbr.muni.czhttps://orcid.org/0000-0002-6435-4719PersonDeveloperDavid Sehnaldavid.sehnal@mail.muni.czhttps://orcid.org/0000-0002-0682-3089PersonDeveloperKarel Berkakarel.berka@upol.czhttps://orcid.org/0000-0001-9472-2589PersonPrimary contactContributorRadka Svobodováradka.svobodova@ceitec.muni.czhttps://orcid.org/0000-0002-3840-8760PersonContributorProviderDavid Bednář222755@mail.muni.czhttps://orcid.org/0000-0002-6803-0340PersonContributorPalacky University Olomouchttps://www.upol.cz/en/InstituteMasaryk University Brnohttps://www.muni.cz/enInstituteVáclav Bazgiervaclav.bazgier@upol.czhttps://orcid.org/0000-0003-3393-3010PersonDocumentorContributorAnna Špačkováanna.spackova@upol.czhttps://orcid.org/0000-0001-7142-3092PersonContributorDocumentorOndřej Vávravavra@enantis.comhttps://orcid.org/0000-0003-1396-2543PersonContributorTomáš Raček324965@mail.muni.czhttps://orcid.org/0000-0002-0296-2452PersonDeveloperMaintainerJiří Damborskýjiri@chemi.muni.czhttps://orcid.org/0000-0002-7848-8216PersonContributorPROTEOFORMERProteogenomic pipeline integrating ribosome profiling (RIBO-seq) data in the search for new proteoforms in proteomic validation data. The pipeline does a genome-wide construction of candidate translation products based on ribosome occupancy.https://github.com/Biobix/proteoformerproteoformerbiotools:proteoformer1.02.0Command-line toolhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3120Protein variantshttp://edamontology.org/topic_3308TranscriptomicsLinuxMacRPerlSQLPythonGPL-3.0BIG N2NProteomicsBioBixUGentMatureFree of chargeOpen accesshttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/operation_3563RNA-seq read count analysishttp://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/operation_2284Nucleic acid density plottinghttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/operation_3182Genome alignmenthttp://edamontology.org/operation_3800RNA-Seq quantificationhttp://edamontology.org/operation_3661SNP annotationhttp://edamontology.org/data_3496RNA sequence (raw)http://edamontology.org/format_1930FASTQperl mapping.pl --helphttps://github.com/Biobix/proteoformerRepositoryGitHub tool repo (PROTEOFORMER version 2.0)http://galaxy.ugent.be/Galaxy serviceGalaxy service of PROTEOFORMER version 1.0 (the Galaxy service of PROTEOFORMER version 2.0 is under way)http://www.biobix.be/research/downloads/proteoformer/OtherExplanation of the tool on the lab's websitehttps://github.com/Biobix/proteoformerSource codeGitHub repo2.0https://github.com/Biobix/proteoformer/tree/master/Galaxy%20filesTool wrapper (Galaxy)Galaxy wrapper files1.0https://github.com/Biobix/proteoformer/blob/master/README.mdUser manualFull elaborate documentation on usage and installation with lots of examples. Main documentation source.https://github.com/Biobix/proteoformer/blob/master/LICENSETerms of useGPU 3.0 license10.1093/nar/gku128325510491PMC4357689Primary1.010.1074/mcp.ra118.00121831040227PMC6692777Primary2.0Steven VerbruggenSteven.Verbruggen@UGent.behttps://orcid.org/0000-0001-9441-9539PersonPrimary contactDeveloperDocumentorMaintainerMain developer of the 2.0 versionGerben MenschaertGerben.Menschaert@ugent.behttps://orcid.org/0000-0002-7575-2085PersonPrimary contactContributorPI of this projectJeroen Crappéhttps://orcid.org/0000-0003-1677-9533PersonDeveloperMain developer of the 1.0 versionElvis NdahPersonDeveloperMain developer of the 1.0 versionSandra SteyaertPersonContributorContributor to the 1.0 versionAlexander KochPersonContributorContributor to the 1.0 versionGhent Universityhttps://www.ugent.be/enInstituteBioBixhttp://www.biobix.be/DivisionEBprotPerseus plugin for differential protein abundance analysis of labeling-based and label-free quantitative proteomics datahttps://github.com/cssblab/EBprotebprotbiotools:ebprot2.0Plug-inhttp://edamontology.org/topic_0121ProteomicsWindowsC++Apache-2.0ProteomicsMatureFree of chargeOpen accesshttp://edamontology.org/operation_3634Label-free quantificationhttp://edamontology.org/operation_3635Labeled quantificationhttp://edamontology.org/data_0945Peptide identificationhttps://github.com/cssblab/EBprotRepositoryhttps://github.com/cssblab/EBprot/issuesIssue trackerhttps://github.com/cssblab/EBprot/releasesSoftware packagehttps://github.com/cssblab/EBprot/wikiUser manual10.1021/acs.jproteome.8b0048330411623PMC6433620Primary2.010.1002/pmic.20140062025913743Primary1.0Hiromi W.L. Kohhiromi_koh@nuhs.edu.sgPersonPrimary contactYunbin Zhangyz2236@nyu.eduPersonPrimary contactChristine Vogelcvogel@nyu.eduPersonPrimary contactHyungwon Choihwchoi@nus.edu.sgPersonPrimary contactInterEvDockAb initio protein docking based on rigid-body sampling followed by consensus scoring using physics-based and statistical potentials, including the InterEvScore function specifically developed to incorporate co-evolutionary information in docking.https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::InterEvDock2interevdock2biotools:interevdock22.0Web applicationhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0080Sequence analysisFreewareMatureFree of chargeOpen accesshttp://edamontology.org/operation_3899Protein-protein dockinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_3899Protein-protein dockinghttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttp://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock2/General10.1093/nar/gky37729741647PMC6030979Primary2.010.1093/nar/gkw34027131368PMC4987904Primary1.010.1093/bioinformatics/btt26023652426MethodRaphael Gueroisraphael.guerois@cea.frhttps://orcid.org/0000-0001-5294-2858PersonPrimary contactJessica Andreanijessica.andreani@cea.frPersonPrimary contactHousekeeping and Reference Transcript AtlasRedefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets.
Web-based tools to search tissue specific housekeeping genes.http://www.housekeeping.unicamp.brHousekeepingbiotools:Housekeeping1.0Web applicationhttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_0632Probes and primershttp://edamontology.org/topic_3518Microarray experimenthttp://edamontology.org/topic_3307Computational biologyhttp://edamontology.org/topic_3361Laboratory techniqueshttp://edamontology.org/topic_3678Experimental design and studiesRFree of chargeOpen accesshttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_3840Multilocus sequence typinghttp://edamontology.org/operation_2424Comparisonhttp://www.housekeeping.unicamp.brServiceRepositoryDatabase home pagehttps://github.com/Bidossessih/HRT_AtlasRepositoryHrt Atlas Githubhttp://housekeeping.unicamp.br/?aboutGeneral10.1093/nar/gkaa60932663312PMC7778946Primary1.0Bidossessi Wilfried Hounkpebidossessi1@live.frhttp://orcid.org/0000-0002-9992-1939PersonMaintainerFast-GBSFast-GBS is an analysis toolkit for genotyping-by-sequencing data. Genotyping-by-sequencing (GBS) is a rapid, flexible, low-cost, and robust genotyping method that simultaneously discovers variants and calls genotypes within a broad range of samples. These characteristics make GBS an excellent tool for many applications and research questions from conservation biology to functional genomics in both model and non-model species. Continued improvement of GBS relies on a more comprehensive understanding of data analysis, development of fast and efficient bioinformatics pipelines, accurate missing data imputation, and active post-release support.https://bitbucket.org/jerlar73/fast-gbs_v2/src/master/fast-gbsbiotools:fast-gbs2.0http://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/operation_3557Imputationhttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_3227Variant callinghttps://hub.docker.com/repository/docker/jelar5/fast-gbs_v2Container file10.1139/gen-2020-007733006480Primary1.010.1186/s12859-016-1431-928049422PMC5210301Primary1.0PredictSNP2A consensus classifier that combines five of the top performing tools (CADD, DANN, FATHMM, FunSeq2 and GWAVA) for the evaluation of pathogenic effect of SNPs within the human genome. The obtained results are provided together with annotations extracted from dbSNP, GenBank, Clinvar, OMIM, RegulomeDB, HaploReg, UCSC and Ensembl databases.https://loschmidt.chemi.muni.cz/predictsnp2predictsnp2biotools:predictsnp21.0Web applicationhttp://edamontology.org/topic_3063Medical informaticshttp://edamontology.org/topic_2533DNA mutationhttp://edamontology.org/topic_3325Rare diseaseshttp://edamontology.org/topic_0622GenomicsLinuxWindowsMacJavaScriptJavaProprietaryCzech RepublicRare DiseaseELIXIR-CZMatureFree of charge (with restrictions)Open accessToolsCzech Republichttp://edamontology.org/operation_3672Gene functional annotationhttp://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/data_3498Sequence variationshttp://edamontology.org/format_3019GVFhttp://edamontology.org/format_3016VCFVCF file containing scores and PDF file containing scores and database linkshttps://loschmidt.chemi.muni.cz/peg/software/predictsnp2-standalone/Downloads page1.0https://loschmidt.chemi.muni.cz/predictsnp2/docs/userguide.pdfUser manual10.1371/journal.pcbi.100496227224906PMC4880439Primary1.0Jaroslav Bendljaroslav.bendl@gmail.comhttps://orcid.org/0000-0001-9989-2720PersonDeveloperJan Stouracstourac.jan@gmail.comhttps://orcid.org/0000-0003-3139-3700PersonDeveloperSupportMilos Musilxmusil46@stud.fit.vutbr.czhttps://orcid.org/0000-0001-9373-7930PersonDeveloperJan Brezovskybrezovsky@mail.muni.czhttps://orcid.org/0000-0001-9677-5078PersonContributorJiri Damborsky1441@mail.muni.czhttps://orcid.org/0000-0002-7848-8216PersonContributorEric D. WiebenPersonContributorJaroslav Zendulkazendulka@fit.vut.czhttps://orcid.org/0000-0001-8718-7493PersonContributorAntonin Pavelka99207@mail.muni.czPersonDeveloperLoschmidt Laboratorieshttps://loschmidt.chemi.muni.cz/peg/InstituteProviderMasaryk University, Brno, Czech Republichttps://www.muni.cz/InstituteProviderInternational Centre for Clinical Research, Brno, Czech Republichttps://www.fnusa-icrc.org/en/InstituteProviderBrno University of Technology, Brno, Czech Republichttps://www.vutbr.cz/InstituteProviderELIXIR-CZhttps://www.elixir-czech.cz/ConsortiumProviderPredictSNP teampredictsnp@sci.muni.czPersonPrimary contactEuropean Regional Development FundFunding agencyContributorEuropean Social FundFunding agencyContributorGrant Agency of the Czech RepublicFunding agencyContributorMinistry of Education of the Czech RepublicFunding agencyContributorBrno University of TechnologyFunding agencyContributorCaverDockPerforms rapid analysis of transport processes in proteins. It models the transportation of a ligand from outside environment into the protein active or binding site and vice versa. It implements a novel algorithm to produce contiguous ligand trajectory and estimation of a binding energy along the pathway. The current version uses CAVER for pathway identification and heavily modified Autodock Vina as a docking engine.https://loschmidt.chemi.muni.cz/caverdock/caverdockbiotools:caverdock1.01.1Command-line toolhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_0078ProteinsLinuxWindowsMacC++PythonProprietaryCAVERELIXIR-CZMatureFree of charge (with restrictions)Tools3D-BioInfoCzech Republichttp://edamontology.org/operation_0482Protein-ligand dockinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_1476PDBtrajectory of ligand passing through protein tunnel and its energyhttps://www.fi.muni.cz/~xfilipov/caverdock/caverdock-ubuntu-14.04.tar.gzBinariesv1.0, Ubuntu 14.041.0https://www.fi.muni.cz/~xfilipov/caverdock/caverdock-ubuntu-16.04.tar.gzBinariesv1.0, Ubuntu 16.041.0https://www.fi.muni.cz/~xfilipov/caverdock/caverdock-1.1-ubuntu-16.04.tar.xzBinariesv1.1, Ubuntu 16.041.1https://www.fi.muni.cz/~xfilipov/caverdock/caverdock-1.1-ubuntu-18.04.tar.xzBinariesv1.1, Ubuntu 18.041.1https://www.fi.muni.cz/~xfilipov/caverdock/manual.pdfUser manualversion 1.0https://www.fi.muni.cz/~xfilipov/caverdock/manual-1.1.pdfUser manualversion 1.110.1093/bioinformatics/btz38631077297Primary1.010.1109/tcbb.2019.290749230932844Primary1.0Jiri Filipovicfila@mail.muni.czhttps://orcid.org/0000-0002-5703-9673PersonDeveloperOndrej Vavrao.vavra@mail.muni.czPersonContributorJan Plhak408420@mail.muni.czPersonDeveloperDavid Bednar222755@mail.muni.czhttps://orcid.org/0000-0002-6803-0340PersonContributorSergio Marquessmar96@gmail.comhttps://orcid.org/0000-0002-6281-7505PersonContributorJan Brezovskybrezovsky@mail.muni.czhttps://orcid.org/0000-0001-9677-5078PersonContributorJan Stouracstourac.jan@gmail.comhttps://orcid.org/0000-0003-3139-3700PersonDeveloperSupportLudek MatyskaLudek.Matyska@muni.czhttps://orcid.org/0000-0001-6399-5453PersonContributorJiri Damborsky1441@mail.muni.czhttps://orcid.org/0000-0002-7848-8216PersonContributorLoschmidt Laboratorieshttps://loschmidt.chemi.muni.cz/peg/InstituteProviderMasaryk University, Brno, Czech Republichttps://www.muni.cz/InstituteProviderInternational Centre for Clinical Research, Brno, Czech Republichttps://www.fnusa-icrc.org/en/InstituteProviderELIXIR-CZhttps://www.elixir-czech.cz/ConsortiumProviderCaverDock teamcaver@caver.czPersonPrimary contactEuropean CommissionFunding agencyContributorCzech Science FoundationFunding agencyContributorBrno City MunicipalityFunding agencyContributorPredictSNPA consensus classifier that combines six of the top performing tools for the prediction of the effects of mutation on protein function. The obtained results are provided together with annotations extracted from the Protein Mutant Database and the UniProt database.https://loschmidt.chemi.muni.cz/predictsnp1predictsnpbiotools:predictsnp1.0Command-line toolWeb applicationhttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_3063Medical informaticshttp://edamontology.org/topic_3325Rare diseaseshttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_3053GeneticsLinuxWindowsMacJavaScriptJavaPythonProprietaryCzech RepublicRare DiseaseELIXIR-CZMatureFree of charge (with restrictions)Open accessToolsCzech Republichttp://edamontology.org/operation_0331Variant effect predictionhttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_1929FASTAPrediction of the effect of amino acid substitution on protein functionhttps://loschmidt.chemi.muni.cz/predictsnp1/docs/predictsnp-1.0.tar.gzBinarieshttps://loschmidt.chemi.muni.cz/predictsnp1/docs/USER_GUIDE.pdfUser manualmappusesnssnpanalyzerusespantherusesphd-snpusespolyphenusespolyphen-2usessiftusessnapuses10.1371/journal.pcbi.100344024453961PMC3894168Primary1.0Jaroslav Bendljaroslav.bendl@gmail.comhttps://orcid.org/0000-0001-9989-2720PersonDeveloperJan Stouracstourac.jan@gmail.comhttps://orcid.org/0000-0003-3139-3700PersonDeveloperSupportOndrej SalandaPersonDeveloperJan Brezovskybrezovsky@mail.muni.czhttps://orcid.org/0000-0001-9677-5078PersonContributorJiri Damborsky1441@mail.muni.czhttps://orcid.org/0000-0002-7848-8216PersonContributorEric D. WiebenPersonContributorJaroslav Zendulkazendulka@fit.vut.czhttps://orcid.org/0000-0001-8718-7493PersonContributorAntonin Pavelka99207@mail.muni.czPersonDeveloperLoschmidt Laboratorieshttps://loschmidt.chemi.muni.cz/peg/InstituteProviderMasaryk University, Brno, Czech Republichttps://www.muni.cz/InstituteProviderInternational Centre for Clinical Research, Brno, Czech Republichttps://www.fnusa-icrc.org/en/InstituteProviderBrno University of Technology, Brno, Czech Republichttps://www.vutbr.cz/InstituteProviderMayo Clinic, Rochester, New York, United States of Americahttps://www.mayoclinic.org/InstituteProviderELIXIR-CZhttps://www.elixir-czech.cz/ConsortiumProviderPredictSNP teampredictsnp@sci.muni.czPersonPrimary contactEuropean Regional Development FundFunding agencyContributorEuropean Social FundFunding agencyContributorGrant Agency of the Czech RepublicFunding agencyContributorMinistry of Education of the Czech RepublicFunding agencyContributorBrno University of TechnologyFunding agencyContributorAraQTLAraQTL is the A.thaliana workbench and database for eQTL analysis.
It allows easy access to the data of all published Arabidopsis thaliana genetical genomics experiments.https://www.bioinformatics.nl/AraQTLaraqtlbiotools:araqtl1.0Web applicationhttp://edamontology.org/topic_3360Biomarkershttp://edamontology.org/topic_3517GWAS studyhttp://edamontology.org/topic_0625Genotype and phenotypeMaturehttp://edamontology.org/operation_3232Gene expression QTL analysishttp://edamontology.org/operation_0282Genetic mappinghttp://edamontology.org/operation_0224Query and retrieval10.1111/tpj.13457279956641.0Harm Nijveenharm.nijveen@wur.nlhttps://orcid.org/0000-0002-9167-4945PersonDeveloperWilco Ligterinkhttps://orcid.org/0000-0002-0228-169XPersonJoost J. B. Keurentjeshttps://orcid.org/0000-0001-8918-0711PersonOlivier Loudethttps://orcid.org/0000-0003-3717-0137PersonJiao LongPersonMark G. Sterkenhttps://orcid.org/0000-0001-7119-6213PersonPjotr PrinsPersonHenk W. Hilhorsthttps://orcid.org/0000-0002-6743-583XPersonDick de Ridderhttps://orcid.org/0000-0002-4944-4310PersonJan E. KammengaPersonBasten L. Snoekbasten.snoek@wur.nlPersonPrimary contacttriprT-cell Receptor/Immunoglobulin Profiler (TRIP)https://github.com/BiodataAnalysisGroup/TRIPTRIP_-_T-cell_Receptor_Immunoglobulin_Profilerbiotools:TRIP_-_T-cell_Receptor_Immunoglobulin_Profiler1.0Libraryhttp://edamontology.org/topic_2830Immunoproteins and antigensMacLinuxWindowsRMITEmergingFree of chargeOpen accessGreecehttp://edamontology.org/operation_2403Sequence analysishttps://www.bioconductor.org/packages/devel/bioc/html/tripr.htmlRepositoryhttps://www.bioconductor.org/packages/devel/bioc/manuals/tripr/man/tripr.pdfUser manual10.1186/s12859-020-03669-132993478PMC7525938Primary1.0Fotis E. Psomopoulosfpsom@certh.grhttps://biodataanalysisgroup.github.io/https://orcid.org/0000-0002-0222-4273PersonPrimary contactMaria Th. KotouzaKaterina GemenetziChrysi GaligalidoutriprT-cell Receptor/Immunoglobulin Profiler (TRIP)https://github.com/BiodataAnalysisGroup/TRIPtriprbiotools:tripr1.0Libraryhttp://edamontology.org/topic_2830Immunoproteins and antigensMacLinuxWindowsRMITEmergingFree of chargeOpen accessGreecehttp://edamontology.org/operation_2403Sequence analysishttps://www.bioconductor.org/packages/devel/bioc/html/tripr.htmlRepositoryhttps://www.bioconductor.org/packages/devel/bioc/manuals/tripr/man/tripr.pdfUser manual10.1186/s12859-020-03669-132993478PMC7525938Primary1.0Fotis E. Psomopoulosfpsom@certh.grhttps://biodataanalysisgroup.github.io/https://orcid.org/0000-0002-0222-4273PersonPrimary contactMaria Th. KotouzaKaterina GemenetziChrysi GaligalidoubamtocovTools to extract coverage informations from BAM (and CRAM) files, based on the covtobed algorithm that supports stranded coverage and physical coverage, input from streams and uses a memory-efficient algorithm.https://telatin.github.io/bamtocov/bamtocovbiotools:bamtocov2.5.02.7.02.8.0Command-line toolLinuxMacCMIThttp://edamontology.org/operation_0260Sequence alignment conversionhttp://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_3462CRAMhttp://edamontology.org/data_3002Annotation trackhttp://edamontology.org/format_3003BEDhttps://telatin.github.io/bamtocov/Otherhttps://github.com/telatin/bamtocovRepositoryhttps://anaconda.org/bioconda/bamtocovSoftware catalogue10.1101/2021.11.12.466787MethodPreprint hosted by biorXiv10.1093/bioinformatics/btac12535199151PMC90486501.0Bioinformatics Application note on BamToCovAndrea Telatinhttps://github.com/telatinhttps://orcid.org/0000-0001-7619-281XPersonPrimary contactGiovanni Birolohttps://orcid.org/0000-0003-0160-9312PersonDeveloperCordaxThe amyloid conformation can be adopted by a variety of sequences, but the precise boundaries of amyloid sequence space are still unclear. The currently charted amyloid sequence space is strongly biased towards hydrophobic, beta-sheet prone sequences that form the core of globular proteins and by Q/N/Y rich yeast prions. Here, we took advantage of the increasing amount of high-resolution structural information on amyloid cores currently available in the protein databank to implement a machine learning approach, named Cordax (https://cordax.switchlab.org), that explores amyloid sequence beyond its current boundaries.https://cordax.switchlab.orgcordaxbiotools:cordax1.0http://edamontology.org/topic_0621Model organismsVIBKU Leuven10.1038/s41467-020-17207-332620861PMC7335209Primary1.0Joost Schymkowitzhttps://orcid.org/0000-0003-2020-0168Primary contactPDBinderPDBinder is a bioinformatic method for the prediction of small ligand binding sites in protein structureshttp://cbm.bio.uniroma2.it/pdbinder/pdbinderbiotools:pdbinderhttp://edamontology.org/topic_3534Protein binding siteshttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/operation_3897Ligand-binding site predictionhttp://edamontology.org/operation_2464Protein-protein binding site predictionhttp://edamontology.org/operation_0420Nucleic acids-binding site predictionhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1208proteinhttp://edamontology.org/data_1277Protein features10.1186/1471-2105-13-s4-s1722536963PMC3434446Method1.0Plant PTM ViewerThe Plant PTM Viewer is an integrative PTM resource that comprises approximately 370 000 PTM sites for 19 types of protein modifications in plant proteins from five different species.http://www.psb.ugent.be/PlantPTMViewerplant_ptm_viewerbiotools:plant_ptm_viewer1.0Web applicationhttp://edamontology.org/topic_0601Protein modificationshttp://edamontology.org/topic_0780Plant biologyJavaScriptNot licensedVIBUGentBIG N2NMatureFree of chargeOpen accessBelgiumhttp://edamontology.org/operation_3645PTM identificationhttp://edamontology.org/operation_0417PTM site predictionhttps://www.psb.ugent.be/webtools/ptm-viewer/tutorial.phpUser manual10.1111/tpj.1434531004550Primary1.0Patrick WillemsProviderPrimary contactThomas Van ParysDeveloperAlison HorneDeveloperBeyondcellBeyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq data and proposing cancer-specific treatments.https://github.com/cnio-bu/beyondcellbeyondcellbiotools:beyondcell2.1Workflowhttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_0208Pharmacogenomicshttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_2229Cell biologyhttp://edamontology.org/topic_3308TranscriptomicsMacLinuxROtherIMPaCT-DataMatureFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_3223Differential gene expression profilinghttp://edamontology.org/operation_4009Small molecule designhttp://edamontology.org/operation_0313Expression profile clusteringhttp://edamontology.org/data_3112Gene expression matrixhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3475TSVhttp://edamontology.org/data_0928Gene expression profilehttp://edamontology.org/format_1915FormatBeyondcell can make use of custom gene expression profiles on top of its own catalogue of drug related signatures. Beyondcell allows the user to input a GMT file containing the functional pathways/signatures of interest as well as numeric matrices containing a ranking
criteria such as the t-statistic or logFoldChange.https://gitlab.com/bu_cnio/beyondcell/-/issues?sort=updated_desc&state=openedIssue trackerhttps://gitlab.com/bu_cnio/beyondcell/-/archive/master/beyondcell-master.zipSource codeSource code for the current software version1.3.3.https://anaconda.org/bioconda/r-beyondcellSoftware packageConda package for the current software version.1.3.3https://gitlab.com/bu_cnio/beyondcell/-/tree/master/tutorial/analysis_workflowQuick start guidehttps://gitlab.com/bu_cnio/beyondcell/-/tree/master/tutorial/analysis_workflowInstallation instructionshttps://gitlab.com/bu_cnio/beyondcell/-/tree/master/tutorial/analysis_workflowCitation instructionshttps://gitlab.com/bu_cnio/beyondcell/-/blob/master/CHANGELOG.mdRelease notes10.1101/2021.04.08.438954Primary1.0Publication about the methodology and its application in a variety of experimental models, from cancer cell lines to human data.Dr. Fátima Al-Shahrourfalshahrour@cnio.eshttps://orcid.org/0000-0003-2373-769XPersonPrimary contactCNIOInstituteProviderBU_CNIODivisionProviderkmerAnalyzerAn alignment-free method capable of processing and counting k-mers in a reasonable time, while evaluating multiple values of the k parameter concurrently.https://github.com/BiodataAnalysisGroup/kmerAnalyzerkmeranalyzerbiotools:kmeranalyzer1.0Scripthttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_0196Sequence assemblyMacLinuxWindowsPythonRMITEmergingFree of chargeOpen accessGreecehttp://edamontology.org/operation_3472k-mer countinghttp://edamontology.org/operation_3478Phylogenetic reconstructionhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_3891Essential dynamicshttp://edamontology.org/data_1667E-value10.3389/fgene.2021.61817034122498PMC81942961.0Fotis E. Psomopoulosfpsom@certh.grhttps://orcid.org/0000-0002-0222-4273PersonPrimary contactNikolaos PechlivanisAnastasios TogkousidisIlias KappasKojakA database search algorithm for solving cross-linked peptide mass spectra.https://kojak-ms.systemsbiology.net/kojakbiotools:kojak2.0.0Command-line toolhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0078ProteinsLinuxWindowsC++Apache-2.0MatureFree of chargeOpen accessProteomicshttps://kojak-ms.systemsbiology.net/download.htmlDownloads page1.0 - 2.0.0https://kojak-ms.systemsbiology.net/docs/index.htmlQuick start guideInstallation instructionsUser manualhttps://kojak-ms.systemsbiology.net/param/index.htmlCommand-line options10.1021/pr501321h25812159PMC4428575Primary1.010.1021/acs.jproteome.2c0067036629399PMC10234491Primary2.0.0Variant Combination Pathogenicity Predictor (VarCoPP) 2.0VarCoPP is a machine learning method that predicts the potential pathogenicity of variant combinations in gene pairs. It is based on digenic data present in OLIDA and it was trained against variants from the 1000 Genomes Project. VarCoPP2.0 is a Balanced Random Forest predictor consisting of 400 decision trees.
A variant combination can be either predicted as disease-causing (i.e. candidate or probably pathogenic) or neutral (i.e. probably neutral).
VarCoPP can be applied for Single Nucleotide Variants (SNVs) and small insertions/deletions from a single individual. It is highly recommended to perform beforehand an initial variant filtering procedure and generally restrict the analysis to variants from up to 150 genes.
VarCoPP was developed in the Interuniversity Institute of Bioinformatics in Brussels, under the collaboration of Université libre de Bruxelles and Vrije Universiteit Brussel.
You can use it through the online tool ORVAL: https://orval.ibsquare.be.http://varcopp.ibsquare.beVariant_Combinaton_Pathogenicity_Predictorbiotools:Variant_Combinaton_Pathogenicity_Predictor1.02.0Plug-inhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3063Medical informaticshttp://edamontology.org/topic_3325Rare diseaseshttp://edamontology.org/topic_0625Genotype and phenotypeLinuxWindowsMacGPL-3.0ELIXIR-BERD-ConnectRare DiseaseMatureFree of chargeOpen accessRare DiseasesBelgiumhttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/operation_3197Genetic variation analysishttps://github.com/oligogenic/VarCoPP2.0Repositoryhttps://github.com/sofiapapad90/VarCoPP/Repositoryhttps://orval.ibsquare.beServiceWeb app integrating VarCoPP2.0oligogenic_resource_for_variant_analysisincludedInolidauses10.1073/pnas.181560111631127050PMC65756321.010.1186/s12859-023-05291-337127601PMC101527952.0Tom Lenaertstlenaert@ulb.ac.behttp://www.ibsquare.behttps://orcid.org/0000-0003-3645-1455PersonPrimary contactSofia Papadomitriousofiapapad.bio@gmail.comPersonDeveloperInteruniversity Institute of Bioinformatics in Brusselshttps://ibsquare.beInstituteProviderPlanet MicrobeEnabling the discovery and integration of oceanographic ‘omics, environmental and physiochemical data layers.https://www.planetmicrobe.org/planet_microbebiotools:planet_microbe1.0Bioinformatics portalhttp://edamontology.org/topic_3387Marine biologyhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0089Ontology and terminologyLinuxElmMITMatureFree of chargeOpen accesshttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_0291Sequence clusteringhttp://edamontology.org/operation_3436Aggregationhttp://edamontology.org/operation_0361Sequence annotationhttps://github.com/hurwitzlab/planet-microbe-appRepositoryPlanet Microbe Applicationhttps://github.com/hurwitzlab/planet-microbe-datapackagesRepositoryPlanet Microbe frictionless data packageshttps://github.com/hurwitzlab/planet-microbe-ontologyRepositoryPlanet Microbe ontologyhttps://github.com/hurwitzlab/planet-microbe-functional-annotationRepositoryFunctional Annotation Pipelinehttps://github.com/hurwitzlab/planet-microbe-semantic-web-analysisRepositorySemantic web analysishttps://github.com/hurwitzlab/planet-microbe-appSource codeSource code for the website1.010.1093/nar/gkaa63732735679PMC7778950Primary1.0In recent years, large-scale oceanic sequencing efforts have provided a deeper understanding of marine microbial communities and their dynamics. These research endeavors require the acquisition of complex and varied datasets through large, interdisciplinary and collaborative efforts. However, no unifying framework currently exists for the marine science community to integrate sequencing data with physical, geological, and geochemical datasets. Planet Microbe is a web-based platform that enables data discovery from curated historical and on-going oceanographic sequencing efforts. In Planet Microbe, each 'omics sample is linked with other biological and physiochemical measurements collected for the same water samples or during the same sample collection event, to provide a broader environmental context. This work highlights the need for curated aggregation efforts that can enable new insights into high-quality metagenomic datasets.Bonnie Hurwitzbhurwitz@arizona.eduhttp://www.hurwitzlab.org/https://orcid.org/0000-0001-8699-957XPersonPrimary contactProfessor at the University of Arizona known for her work in cyberinfrastructure development.Alise Ponseroaponsero@arizona.eduhttps://orcid.org/0000-0002-4125-7561PersonContributorKai Blumbergkblumberg@arizona.eduhttps://orcid.org/0000-0002-3410-4655PersonContributorMatthew Millermattmiller899@arizona.eduhttps://orcid.org/0000-0002-3491-8763PersonDeveloperMatthew Bomhoffmbomhoff@arizona.eduhttps://orcid.org/0000-0002-8014-9184PersonDeveloperKen Youens-Clarkkyclark@arizona.eduhttps://orcid.org/0000-0001-9961-144XPersonDeveloperPlanet MicrobeEnabling the discovery and integration of oceanographic ‘omics, environmental and physiochemical data layers.https://www.planetmicrobe.org/planetmicrobebiotools:planetmicrobe1.0Bioinformatics portalhttp://edamontology.org/topic_3387Marine biologyhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0089Ontology and terminologyLinuxElmMITMatureFree of chargeOpen accesshttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_0291Sequence clusteringhttp://edamontology.org/operation_3436Aggregationhttp://edamontology.org/operation_0361Sequence annotationhttps://github.com/hurwitzlab/planet-microbe-appRepositoryPlanet Microbe Applicationhttps://github.com/hurwitzlab/planet-microbe-datapackagesRepositoryPlanet Microbe frictionless data packageshttps://github.com/hurwitzlab/planet-microbe-ontologyRepositoryPlanet Microbe ontologyhttps://github.com/hurwitzlab/planet-microbe-functional-annotationRepositoryFunctional Annotation Pipelinehttps://github.com/hurwitzlab/planet-microbe-semantic-web-analysisRepositorySemantic web analysishttps://github.com/hurwitzlab/planet-microbe-appSource codeSource code for the website1.0https://hurwitzlab.gitbook.io/planet-microbe-documentation/GeneralDocumentation on how to use the website10.1093/nar/gkaa63732735679PMC7778950Primary1.0In recent years, large-scale oceanic sequencing efforts have provided a deeper understanding of marine microbial communities and their dynamics. These research endeavors require the acquisition of complex and varied datasets through large, interdisciplinary and collaborative efforts. However, no unifying framework currently exists for the marine science community to integrate sequencing data with physical, geological, and geochemical datasets. Planet Microbe is a web-based platform that enables data discovery from curated historical and on-going oceanographic sequencing efforts. In Planet Microbe, each 'omics sample is linked with other biological and physiochemical measurements collected for the same water samples or during the same sample collection event, to provide a broader environmental context. This work highlights the need for curated aggregation efforts that can enable new insights into high-quality metagenomic datasets.Bonnie Hurwitzbhurwitz@arizona.eduhttp://www.hurwitzlab.org/https://orcid.org/0000-0001-8699-957XPersonPrimary contactProfessor at the University of Arizona known for her work in cyberinfrastructure development.Alise Ponseroaponsero@arizona.eduhttps://orcid.org/0000-0002-4125-7561PersonContributorKai Blumbergkblumberg@arizona.eduhttps://orcid.org/0000-0002-3410-4655PersonContributorMatthew Millermattmiller899@arizona.eduhttps://orcid.org/0000-0002-3491-8763PersonDeveloperMatthew Bomhoffmbomhoff@arizona.eduhttps://orcid.org/0000-0002-8014-9184PersonDeveloperKen Youens-Clarkkyclark@arizona.eduhttps://orcid.org/0000-0001-9961-144XPersonDeveloperlineagespotLineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).https://github.com/BiodataAnalysisGroup/lineagespotlineagespotbiotools:lineagespot1.0Libraryhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_3299Evolutionary biologyhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0199Genetic variationMacLinuxWindowsRMITCOVID-19EmergingFree of chargeOpen accessGreecehttp://edamontology.org/operation_3227Variant calling10.1038/s41598-022-06625-635177697PMC88546251.0Fotis E. Psomopoulosfpsom@certh.grhttps://orcid.org/0000-0002-0222-4273PersonPrimary contactNikolaos Pechlivanis,https://orcid.org/0000-0003-2502-612XMaria Tsagiopoulouhttps://orcid.org/0000-0002-1653-0327Meta-SNPMeta-predictor of disease causing variants.http://snps.biofold.org/meta-snpmeta-snpbiotools:meta-snp1.0Web servicehttp://edamontology.org/topic_0123Protein propertieshttp://edamontology.org/topic_0634PathologyLinuxWindowsMacMatureFree of chargeItalyhttp://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2209Mutation IDhttp://edamontology.org/format_2330Textual formathttp://snps.biofold.org/meta-snp/pages/help.htmlGeneral10.1186/1471-2164-14-s3-s223819846PMC3839641Primary1.0ELIXIR-ITA-BOLOGNAhttp://www.biocomp.unibo.itDivisionSupportEmidio Capriottiemidio.capriotti@gmail.comhttp://orcid.org/0000-0002-2323-0963PersonDeveloperPrimary contactplantRNAThe PlantRNA database compiles tRNA gene sequences retrieved from fully annotated nuclear, plastidial and mitochondrial genomes of photosynthetic organisms.http://plantrna.ibmp.cnrs.fr/plantrnabiotools:plantrna2.0Database portalhttp://edamontology.org/topic_0780Plant biologyCC-BY-SA-4.0MatureFree of chargeOpen access10.1111/tpj.1599736196656Primary1.010.1093/nar/gks93523066098PMC3531208Primary1.0Valerie Cognatvalerie.cognat@cnrs.frhttps://orcid.org/0000-0001-9337-2767PersonContributorMetaPathwaysMetaPathways is a meta’omic analysis pipeline for the annotation and analysis for environmental sequence information. MetaPathways include metagenomic or metatranscriptomic sequence data. The pipeline consists of four operational stages including: Quality Control, Feature Prediction, Functional Annotation, Pathway Inference.https://metapathways.readthedocs.io/en/dev/index.htmlmetapathwaysbiotools:metapathways3.5Command-line toolhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_3697Microbial ecologyhttp://edamontology.org/topic_3796Population genomicsLinuxPythonMPL-2.0Free of chargeOpen accesshttp://edamontology.org/operation_3672Gene functional annotationhttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAUse MetaPathways to annotate a metagenome.metapathways run \
-i $[input_metagenome.fa] \
-d ${path/to/save/reference_databases} \
-o ${path/to/output} \
-t ${threads}https://metapathways.readthedocs.io/en/dev/index.htmlOtherhttps://anaconda.org/Hallamlab/metapathwaysTool wrapper (Other)3.5https://quay.io/repository/hallamlab/metapathwaysContainer file3.5https://bitbucket.org/BCB2/metapathways/src/dev/Source code3.5https://metapathways.readthedocs.io/en/dev/index.htmlGeneral10.1101/2024.06.04.5974601.010.1093/bioinformatics/btv36126076725PMC45958962.510.1186/1471-2105-14-20223800136PMC36958371.0shallam@mail.ubc.cahttps://hallam.microbiology.ubc.ca/PersonPrimary contactREDItoolsPython scripts to detect RNA editing in deep transcriptome sequencing data (RNAseq)https://github.com/BioinfoUNIBA/REDItoolsreditoolsbiotools:reditools1.32.0RRID:SCR_012133rridCommand-line toolhttp://edamontology.org/topic_0622GenomicsLinuxMacPythonMITELIXIR-ITA-CNRMatureFree of chargehttp://edamontology.org/operation_2945Analysishttp://edamontology.org/data_1916Alignmenthttp://edamontology.org/format_2572BAMRun REDItools on RNA sequencesREDItoolDnaRna.py -i rnaseq.bam -f myreference.fa -o myoutputfolderhttps://github.com/BioinfoUNIBA/REDItoolsGeneral10.1093/bioinformatics/btt28723742983Primary1.0-1.310.1186/s12859-020-03562-x32838738PMC74461882.010.1038/s41596-019-0279-73199684410.1007/978-1-0716-1307-8_1433835447Usage10.1002/0471250953.bi1212s4925754992UsageELIXIR-ITA-CNRhttps://orcid.org/0000-0002-6549-0114InstituteProviderErnesto Picardiernesto.picardi@uniba.ithttps://www.uniba.it/docenti/picardi-ernesto/enhttps://orcid.org/0000-0002-6549-0114PersonPrimary contactMass DynamicsA software platform for analysis and visualization of label-free and tandem mass tag (TMT) data-dependent acquisition (DDA) bottom-up proteomics data, including pathway and gene set enrichment analyses.https://massdynamics.com/mass_dynamicsbiotools:mass_dynamics1.02.0http://edamontology.org/operation_2945Analysishttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/data_2536Mass spectrometry data10.1021/acs.jproteome.1c0068334647461Primary1.010.1101/2022.12.12.517480Primary2.0MISTICMISTIC (MISsense deleTeriousness predICtor), a prediction tool to reveal disease-relevant deleterious missense variants based on an original combination of two complementary machine learning algorithms using a soft voting system that integrates 113 missense features, ranging from multi-ethnic minor allele frequencies and evolutionary conservation, to physiochemical and biochemical properties of amino acids.http://lbgi.fr/misticmistic_predictorbiotools:mistic_predictor1.0Web applicationWeb APIScripthttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3063Medical informaticshttp://edamontology.org/topic_3325Rare diseaseshttp://edamontology.org/topic_3676Exome sequencingLinuxMacWindowsPythonMITRare DiseaseMatureFree of chargeOpen accessRare DiseasesFrancehttp://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/operation_3226Variant prioritisationhttp://edamontology.org/operation_0331Variant effect predictionhttp://lbgi.fr/mistic/downloadDownloads page1.0https://lbgi.fr/api/index.rvt?api=misticAPI specification1.010.1371/journal.pone.023696232735577PMC7394404Primary1.0Kirsley Chennenkchennen@unistra.frhttps://orcid.org/0000-0001-9268-6748PersonPrimary contactDeveloperMaintainerThomas Weberhttps://orcid.org/0000-0002-0807-6363PersonDeveloperOlivier Pocholivier.poch@unistra.frhttps://orcid.org/0000-0002-7134-3217PersonPrimary contactContributorEDAM-BrowserThe EDAM Browser is a client-side web-based visualization javascript widget of the EDAM ontology.
The EDAM Browser provides users a simple and performant interface to explore EDAM when annotating or searching for bioinformatics resources.
Its goals are to help describing bio-related resources and service with EDAM, and to facilitate and foster community contributions to EDAM.https://github.com/IFB-ElixirFr/edam-browseredam-browserbiotools:edam-browser2.0Plug-inWeb applicationhttp://edamontology.org/topic_0605Informaticshttp://edamontology.org/topic_0092Data visualisationLinuxWindowsMacJavaScriptMITMatureFree of chargeOpen accessInteroperabilityFrancehttp://edamontology.org/operation_3559Ontology visualisationhttp://edamontology.org/data_0582Ontologyhttp://edamontology.org/format_3464JSONhttps://github.com/IFB-ElixirFr/edam-browserRepositoryhttps://ifb-elixirfr.github.io/edam-browser/Servicehttps://github.com/IFB-ElixirFr/edam-browser/issuesIssue trackerhttps://ifb-elixirfr.github.io/edam-browser/demo.htmlTraining materialA demo on how to use it; Tutorialhttps://github.com/IFB-ElixirFr/edam-browser/blob/master/paper_resources/long_paper_version.mdOther10.21105/joss.00698Primary1.0Bryan Brancottehttps://orcid.org/0000-0001-8669-5525DeveloperHervé Ménagerhttps://orcid.org/0000-0002-7552-1009MaintainerChristophe BlanchetContributorHager Eldakrouryhttps://github.com/HagerDakrouryDeveloperVarGeniusVarGenius is a platform for analysis of variants from DNA sequencing data. Currently it can be used for WES and Panels. Starting from fastq files it can execute the GATK Best Practices pipeline doing both single calling and joint calling. Then it executes Annovar for variant annotation and generates a readable output in tabular and XLS format. All the data extracted from the samples (variants, genotypes, etc..) are uploaded into a Postgres database which can be used for further downstream analyses.https://github.com/frankMusacchia/VarGeniusVarGeniusbiotools:VarGenius1.0Command-line toolhttp://edamontology.org/topic_2533DNA mutationLinuxRPerlMatureFree of chargeOpen accessToolsItalyhttps://groups.google.com/forum/#!forum/VarGeniusHelpdeskhttps://github.com/frankMusacchia/VarGeniusSource code1.0https://github.com/frankMusacchia/VarGenius/tree/master/GUIDEInstallation instructionsvargenius-hzdincludes10.1186/s12859-018-2532-430541431PMC6291943PrimaryBenchmarking study1.0ELIXIR-ITA-TELETHONf.musacchia@tigem.ithttps://orcid.org/0000-0001-9440-1080PersonPrimary contactmetaQuantomemetaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.https://github.com/galaxyproteomics/metaquantomemetaQuantomebiotools:metaQuantome1.0Suitehttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3941Metatranscriptomicshttp://edamontology.org/topic_3697Microbial ecologyhttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/operation_2939Principal component visualisationhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3459Functional clusteringhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_3741Differential protein expression analysishttp://edamontology.org/operation_0531Heat map generationhttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_0227Indexinghttp://edamontology.org/operation_3695Filteringhttp://edamontology.org/operation_3658Statistical inferencehttp://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_2603Expression datahttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_1872Taxonomic classificationhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_2583GO concept ID (molecular function)http://edamontology.org/format_2330Textual formathttp://edamontology.org/data_1011EC numberhttp://edamontology.org/format_2330Textual format10.1074/mcp.RA118.00124031235611PMC6692774Method1.0https://www.mcponline.org/content/18/8_suppl_1/S8210.1021/ACS.JPROTEOME.0C0096033683127ARADEEPOPSISARADEEPOPSIS is a software tool that enables plant researchers to non-invasively score plant growth, biomass accumulation and senescence from image data in a highly parallelized, high throughput, yet easy to use manner.https://github.com/Gregor-Mendel-Institute/aradeepopsisaradeepopsisbiotools:aradeepopsis1.31.2.11.21.11.01.3.1doi:10.5281/zenodo.3946320doiCommand-line toolWorkflowhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_0780Plant biologyhttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_3298PhenomicsPythonRGroovyGPL-3.0Free of chargeOpen accesshttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_3443Image analysishttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_2428Validationhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3603PNGhttp://edamontology.org/format_3579JPGhttps://github.com/Gregor-Mendel-Institute/aradeepopsisRepositoryhttps://quay.io/beckerlab/aradeepopsis-baseContainer file1.3https://quay.io/beckerlab/aradeepopsis-shinyContainer file1.3https://zenodo.org/record/3946618Downloads pageTrained modelshttps://zenodo.org/record/3946393Downloads pageTraining datahttps://github.com/Gregor-Mendel-Institute/aradeepopsis#readmeGeneral10.1105/tpc.20.0031833037149PMC77213231.2.110.1101/2020.04.01.0181921.0Patrick Hütherpatrick.huether@gmail.comhttps://orcid.org/0000-0003-3315-2484PersonMaintainerClaude Beckerclaude.becker@gmi.oeaw.ac.atPersonPICKLEPICKLE (Protein InteraCtion KnowLedgebasE) is a meta-database for the direct protein-protein interactome of the human and the mouse proteomes, integrating publicly available source protein-protein interaction (PPI) databases via genetic information ontology. PICKLE integrates the primary PPI datasets by superimposing them on the UniProtKB/Swiss-Prot reviewed complete proteome of the human (RHCP) and the mouse (RMCP) ontology network without any a priori transformations.http://www.pickle.grpicklebiotools:pickle3.0Web applicationDatabase portalhttp://edamontology.org/topic_2259Systems biologyhttp://edamontology.org/topic_2815Human biologyhttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_3574Human geneticshttp://edamontology.org/topic_3396Systems medicineWindowsC#EmergingOpen accessDataGreecehttp://edamontology.org/operation_0276Protein interaction network analysishttp://edamontology.org/operation_3802Sortinghttp://edamontology.org/operation_3695Filteringhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_3083Pathway or network visualisationhttp://edamontology.org/data_1009Protein namehttp://edamontology.org/data_1025Gene identifierhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_2338Ontology identifierhttp://www.pickle.grOtherContent available to any user with no restrictions
Copyright: University of Patras & FORTH/ICE-HT, Greecehttp://www.pickle.gr/DownloadsBiological dataThe current and archived PICKLE PPI datasets at the UniProt and gene levels can be freely downloaded from the PICKLE webpage.active and archived versionshttp://www.pickle.gr/DownloadsBiological dataThe current and archived PICKLE genetic information ontology networks are available in owl format.active and archived versionshttp://www.pickle.grGeneralThe web portal of the meta-database10.1186/1752-0509-7-9624088582PMC5638325Primary1.010.1371/journal.pone.018603929023571Primary2.010.13140/RG.2.2.16985.21608OtherPoster Presentation in the ELIXIR All Hands Meeting10.1093/bioinformatics/btaa107033367505PMC8034533Method3.0The PICKLE 3.0 upgrade refers to the enrichment of this human protein–protein interaction (PPI) meta-database with the mouse protein interactome.Nicholas Moschonasn_moschonas@med.upatras.grhttp://www.pickle.grPersonPrimary contactMaria Klapamklapa@iceht.forth.grhttp://www.iceht.forth.gr/staff/klapa.htmlPersonPrimary contactrPredictorDBA web database for prediction, analysis and storage of secondary structures of RNAs.http://rpredictordb.elixir-czech.czrpredictorbiotools:rpredictor1.0Web applicationhttp://edamontology.org/topic_0097Nucleic acid structure analysishttp://edamontology.org/topic_0099RNALinuxWindowsMacMATLABC++C#JavaScriptPHPBashPythonJavaSQLFreewareCzech RepublicELIXIR-CZMatureFree of chargeOpen accessDataToolsCzech Republichttp://edamontology.org/operation_0278RNA secondary structure predictionhttp://edamontology.org/operation_0361Sequence annotationhttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/data_2080Database search resultsSearch in the databasehttp://edamontology.org/operation_0278RNA secondary structure predictionhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/data_3495RNA sequencehttp://edamontology.org/format_1929FASTAPredict secondary structure for own sequences using templates in the databasehttps://github.com/handrbaal/cppredict/RepositoryPrediction algorithmhttp://rpredictordb.elixir-czech.cz/contactMailing listhttp://rpredictordb.elixir-czech.cz/searchServicehttp://rpredictordb.elixir-czech.cz/predict#cppredict2Servicehttps://github.com/handrbaal/cppredict/Source codehttp://rpredictordb.elixir-czech.cz/downloadDownloads pagehttp://rpredictor.ms.mff.cuni.cz/documentation/GeneralCitation instructionsRelease notesQuick start guidehttp://rpredictordb.elixir-czech.cz/documentation/terms.htmlCode of conductTerms of usehttp://rpredictordb.elixir-czech.cz/documentation/rDoc-User/FAQ.htmlFAQhttp://rpredictordb.elixir-czech.cz/documentation/rDoc-Technical/setup.htmlInstallation instructionshttp://rpredictordb.elixir-czech.cz/documentation/rDoc-User/index.htmlUser manualtravelerusesenausesncbi_taxonomy_databaseusesrfamusessilvausesblastusesfastausesvienna_rna_packageusesblastuses10.1093/database/baz04731032840PMC6482342Primary10.1109/BIBM.2014.6999394Method0.1Early version of the prediction algorithm10.3389/fgene.2017.0014729067038PMC5641303Method1.0Final version of the prediction algorithm10.1186/s12859-017-1885-429141608PMC5688744MethodVisualisation toolELIXIR-CZhttps://www.elixir-czech.cz/InstituteProviderDavid Hokszadavid.hoksza@gmail.comPersonPrimary contactJosef Pánekpanek@biomed.cas.czPersonPrimary contactDeveloperOntoBrowserThe tool was developed to manage ontologies (and controlled terminologies e.g. CDISC SEND). The primary goal of the tool is to provide an online collaborative solution for expert curators to map code list terms (sourced from multiple systems/databases) to preferred ontology terms. Other key features include visualisation of ontologies in hierarchical/graph format, advanced search capabilities, peer review/approval workflow and web service access to data.https://github.com/Novartis/ontobrowserontobrowserbiotools:ontobrowser1Web APIWeb applicationhttp://edamontology.org/topic_0089Ontology and terminologyhttp://edamontology.org/topic_3345Data identity and mappingLinuxMacSQLApache-2.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_3559Ontology visualisationhttp://edamontology.org/operation_3436Aggregationhttp://edamontology.org/operation_2429Mappinghttp://edamontology.org/data_3028Taxonomyhttp://edamontology.org/format_2549OBOhttp://edamontology.org/data_0966Ontology termWeb based collaborative ontology curation
Interactive hierarchical/graph visualisation
Cross ontology searching
Synonym mapping
Automated mapping of similar matching synonyms
Central database for all ontologies
Version tracking
Review/Approve workflow
Email notification
Full curator audit trail/history Ontologies can be loaded into OntoBrowser using the /ontobrowser/ontologies RESTful web service. The web service only supports the PUT method for loading ontologies and only accepts OBO formatted data.
https://github.com/Novartis/ontobrowser/blob/master/doc/INSTALL.md Verbatim terms (to be reconcilated) are loaded from remote source database.
Controlled vocabularies are loaded via SQL. The following Internet Media Types are supported by the web service for GET requests:
application/rdf+xml
application/owl+xml
text/owl-manchester
text/turtle
text/obo
application/obo
application/json
https://github.com/Novartis/ontobrowser/blob/master/doc/web_services.mdhttps://github.com/Novartis/ontobrowserRepositoryhttps://github.com/Novartis/ontobrowser/blob/master/LICENSE.txtTerms of usehttps://github.com/Novartis/ontobrowser/tree/master/docGeneral10.1093/bioinformatics/btw57927605099PMC5408772Primary1.0Carlo Ravaglihttp://opensource.nibr.comgrid.419481.102f9zrr09PersonDeveloperFrancois Pognanhttp://opensource.nibr.comhttps://orcid.org/0000-0001-7033-2033grid.419481.102f9zrr09PersonContributorPhilippe Marcphilippe.marc@novartis.comhttp://opensource.nibr.comhttps://orcid.org/0000-0002-0064-0572grid.419481.102f9zrr09PersonContributorPrimary contactInnovative Medicines Initiative (IMI)https://www.imi.europa.eugrid.454814.8019af4n30Funding agencyContributorInnovative Medicines Initiative Joint Undertaking under grant agreement n° 115002. Part of the eTOX project (http://www.etoxproject.eu)StPeterA tool for analyzing proteomics data acquired by mass spectrometry. Quantifies proteins from shotgun MS/MS data using normalized spectral count or normalized spectral index techniques. Incorporates distributed techniques to account for peptide sequence degeneracy.http://tppms.orgstpeterbiotools:stpeter1.4.0Command-line toolhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimentLinuxWindowsMacC++Apache-2.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_3637Spectral countinghttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_3630Protein quantificationhttp://edamontology.org/operation_3634Label-free quantificationhttp://edamontology.org/data_0896Protein reporthttp://edamontology.org/format_3747protXMLOutput file is the same protXML input file, but with protein quantification results appended to each protein group.StPeter myProteins.prot.xmltpp_spcincludedIn10.1021/acs.jproteome.7b0078629400476PMC5891225Primary1.0pbg-ldLinked Data platform for Plant Breeding & Genomicshttps://www.research-software.nl/software/pbg-ldpbg-ldbiotools:pbg-ld1.0.0Web applicationSPARQL endpointWeb APIhttp://edamontology.org/topic_0780Plant biologyhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_0797Comparative genomicshttp://edamontology.org/topic_0089Ontology and terminologyLinuxMacOtherApache-2.0EmergingOpen accessDataNetherlandshttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_3436Aggregationhttp://edamontology.org/operation_0361Sequence annotationhttp://edamontology.org/operation_3282ID mappinghttp://edamontology.org/data_0842Identifierhttp://edamontology.org/format_2330Textual formathttps://www.research-software.nl/software/pbg-ldRepositoryhttps://github.com/candYgene/pbg-ldSource codehttps://github.com/candYgene/pbg-ld/blob/master/README.mdInstallation instructions10.18174/FAIRdata2018.16287Method10.3390/app10196813Primary1.010.5281/zenodo.1458168OtherArnold Kuzniara.kuzniar@esciencecenter.nlhttps://orcid.org/0000-0003-1711-7961PersonDeveloperMaintainerPrimary contactCarlos Martinez-Ortizhttps://orcid.org/0000-0001-5565-7577PersonContributorGurnoor Singhhttps://orcid.org/0000-0003-1615-4197PersonContributorRichard VIsserrichard.visser@wur.nlhttps://orcid.org/0000-0002-0213-4016PersonRichard Finkersrichard.finkers@wur.nlhttps://orcid.org/0000-0002-4368-8058Person