Epitope Generation GatewayA modular Snakemake pipeline for personalised neonatigen discovery and prioritisation using Patient Specific Functional Interaction Networkshttps://github.com/fhaive/epitope_generation_gatewayepitope_generation_gatewaybiotools:epitope_generation_gatewayv1.0https://github.com/fhaive/epitope_generation_gatewaySoftware packageGithub repository.
Main workflow is a servies of snakemake pipelines.
Automatically insstalls needed packages and dockers.
Needs snakemake, docker and conda isntalled.1.0https://github.com/fhaive/epitope_generation_gateway/blob/main/README.mdUser manualIQA DCE toolThe purpose of the tool is to provide a complete framework for automatic detection of image quality for Breast DCE MR images. The assessment is performed on the first post-contrast dynamic phase in order to assess the most clinically relevant sequence among a number of identical acquisitions. Two categories are available for image classification, i.e. high and low quality, depending on the level of noise, degree of blurring and presence of artifacts.https://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/iqa_dce_tool/info-tabiqa_dce_toolbiotools:iqa_dce_tool1.0Command-line toolhttp://edamontology.org/topic_3444MRIhttp://edamontology.org/topic_3572Data quality managementhttp://edamontology.org/topic_2640OncologyWindowsMacLinuxPythonEUPL-1.2EUCAIMMatureFree of chargeOpen accesshttps://harbor.eucaim.cancerimage.eu/harbor/projects/3/repositories/iqa_dce_toolContainer file1.0https://drive.eucaim.cancerimage.eu/s/NeAGoB5GGjSXeinUser manualhttps://www.youtube.com/watch?v=z2sSu1eIXTg&list=PL3Q1XjQpjfg_GEmwPDrQeESh6nqCMnYyR&index=5Training material10.3390/jimaging11110417Computational BioMedicine Laboratory, Foundation for Research and Technology Hellas (FORTH)https://www.ics.forth.gr/cbml/?lang=enInstituteProviderProcess CurationProcessCurated is a set of tools to process curated genome assemblies. In combination with gfastats and mashmap, it reconciliates the AGP file manually curated in PretextView to rename, reorient, and sort the assemblies to get them ready for submission.https://github.com/vgl-hub/vgl-curationvgp-processcurationbiotools:vgp-processcuration1.0Command-line toolhttp://edamontology.org/topic_0196Sequence assemblyMIThttps://github.com/vgl-hub/vgl-curation/archive/refs/tags/postcuration_1.0.zipSoftware package1.0ProfilerProfiler 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 proteomicHBATHBAT (Hydrogen Bond Analysis Tool) is a package to automate the analysis of potential hydrogen bonds and similar type of weak interactions in macromolecular structures, available in Protein Data Bank (PDB) file format. HBAT uses a geometric approach to identify molecular interactions by analysing distance and angular criteria.
HBAT 1.1 was released in 2007 as closed source Windows binary and continue to be available via SourceForge.
HBAT 2.0 was introduced in 2025 and a completed rewrite of original implementation with cross-platform support. HBAT 2.0 is open sourced under MIT License.https://hbat.abhishek-tiwari.comhbatbiotools:hbat2.x1.1, 1.0Command-line toolDesktop applicationhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0078ProteinsLinuxWindowsMacPerlPythonMITMatureFree of chargeOpen accesshttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhbat input.pdbhttps://github.com/abhishektiwari/hbatRepositoryIssue trackerhttp://www.mybiosoftware.com/hbat-1-1-hydrogen-bond-analysis-tool.htmlSoftware cataloguehttps://pypi.org/project/hbat/Software packageCross-platform PyPI Python Package2.xhttps://github.com/abhishektiwari/hbat/releasesBinariesMac and Linux Binaries including AppImage, .deb, standalone executables.2.xhttps://sourceforge.net/projects/hbat/BinariesWindows Binaries download from SourceForge1.0, 1.1https://hbat.abhishek-tiwari.comGeneralAPI documentationCitation instructionsCommand-line optionsInstallation instructionsQuick start guide10.3233/ISI-2007-0033718467777PrimaryPeer-reviewed paper for HBAT 1.010.5281/zenodo.17645321OtherPreprint for HBAT 2.x softwareAbhishek Tiwarihttps://www.abhishek-tiwari.comhttps://orcid.org/0000-0003-2222-2395PersonPrimary contactComplexBrowserComplexBrowser is a R based software for supervised analysis of changes in protein complex abundance and subunit co-expression in proteomic datasets. It uses information contained in CORUM and EBI Complex Portal databases to provide the user with visualizations helping with biological interpretation of obtained results. ComplexBrowser also incorporates a normalization and quality control steps.https://computproteomics.bmb.sdu.dk/app_direct/ComplexBrowser/ComplexBrowserbiotools:ComplexBrowser1.0Web applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_2269Statistics and probabilityWindowsMacLinuxRProteomicsOpen accesshttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/operation_2939Principal component visualisationhttp://edamontology.org/operation_2495Expression analysishttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_2428Validationhttp://edamontology.org/operation_3083Pathway or network visualisationhttp://edamontology.org/operation_2940Scatter plot plottinghttp://edamontology.org/operation_3282ID mappinghttp://edamontology.org/operation_2938Dendrogram visualisationhttp://edamontology.org/operation_0276Protein interaction network analysishttp://edamontology.org/operation_0531Heat map generationhttp://edamontology.org/operation_3659Regression analysishttp://edamontology.org/operation_3463Expression correlation analysishttp://edamontology.org/operation_3435Standardisation and normalisationhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_0571Expression data visualisationhttp://edamontology.org/data_2603Expression datahttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_0906Protein interaction datahttp://edamontology.org/format_3752CSVhttp://computproteomics.bmb.sdu.dk/Software cataloguehttps://bitbucket.org/michalakw/complexbrowser/src/master/Repositoryhttps://bitbucket.org/michalakw/complexbrowser/Source code1.0https://bitbucket.org/michalakw/complexbrowser/raw/dc9d8f0c8dff610e2f58e3cb5f5087d050df26f2/Manual.pdfUser manual10.1101/573774PrimaryVeit Schwämmleveits@bmb.sdu.dkPersonETENLNCETENLNC (End-To-End-Novel-NonCoding) is a lncRNA identification and analysis frameworkhttps://github.com/EvolOMICS-TU/ETENLNCetenlncbiotools:etenlnc1.0Command-line toolhttp://edamontology.org/topic_0659Functional, regulatory and non-coding RNALinuxMacWindowsGPL-3.0EmergingFree of chargeOpen accesshttp://edamontology.org/operation_3219Read pre-processinghttp://edamontology.org/operation_3218Sequencing quality controlhttp://edamontology.org/operation_3258Transcriptome assemblyhttp://edamontology.org/operation_0415Nucleic acid feature detectionhttp://edamontology.org/operation_3800RNA-Seq quantificationhttp://edamontology.org/operation_3223Differential gene expression profilinghttp://edamontology.org/operation_0531Heat map generationhttp://edamontology.org/operation_0278RNA secondary structure predictionhttp://edamontology.org/operation_3472k-mer countinghttp://edamontology.org/operation_0389Protein-nucleic acid interaction analysishttp://edamontology.org/operation_3901RNA-binding protein predictionhttp://edamontology.org/operation_2437Gene regulatory network predictionhttp://edamontology.org/data_2603Expression datahttp://edamontology.org/format_1930FASTQhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1288Genome maphttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3002Annotation trackhttp://edamontology.org/format_2306GTFhttp://edamontology.org/format_2305GFFRun ETENLNC on paired-end raw RNA-Seq (.fastq) databash ETENLNC_docker.shhttps://github.com/EvolOMICS-TU/ETENLNCRepositoryGitHub Repohttps://zenodo.org/records/14325721?token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6ImVmYTllNWJkLWE4ODUtNGM3OC05YTAxLWM4ZDk5YTljZDZjMCIsImRhdGEiOnt9LCJyYW5kb20iOiI4M2I1YjBlZDQ4MmUyZTIxNDg2YmI0YTFkMWE5MTI1OCJ9.HeB3WrsPduNzMyXjH4x5HfCgmIp4NzYv0P_11XU9lcXC_ZxEaVndP-kD0LDkxwufHVNlroeAhdK33PR51F6jnwBiological dataSample/demo data for ETENLNC. A detailed guide on running ETENLNC using the demo data can be found in the ETENLNC manual (supplementary to our publication).1.0https://github.com/EvolOMICS-TU/ETENLNCCommand-line optionsA detailed guide on running ETENLNC using the demo data can be found in the ETENLNC manual (supplementary to our publication)hisat2usessalmonusesfastqcusesfastpusesstringtieusesgffcompareusescpc2usesncbi_blast_plususestximportusesdeseq2useslnctarusescapsule-lpiusesseekruses10.1016/j.compbiolchem.2024.10814038996755Primary.0Pankaj Barahbarah@tezu.ernet.inhttps://www.tezu.ernet.in/dmbbt/profile/34https://orcid.org/0000-0001-7039-7996PersonPrimary contactMaintainerAssistant Professor at Department of Molecular Biology and Biotechnology, Tezpur University.Prangan Nathprangannathofficial@gmai.comhttps://orcid.org/0000-0002-9451-7822PersonDeveloperMaintainerColoPola dataset for colorectal cancer detectionThe dataset consists of 572 slices (specimens) with 20,592 images. There are 284 cancer samples and 288 normal samples. The lists of samples for training (train+val) set and testing set are provided in the Zenodo repository. Source code in Github is to train and validate five deep learning models using ColoPola dataset.https://github.com/haile493/Colorectal-cancer-detection-using-ColoPola-datasetcolopola_dataset_for_colorectal_cancer_detectionbiotools:colopola_dataset_for_colorectal_cancer_detection1.0Scripthttp://edamontology.org/topic_3316Computer scienceWindowsPythonCC0-1.0DatasetMatureFree of charge (with restrictions)Open access (with restrictions)https://github.com/haile493/Colorectal-cancer-detection-using-ColoPola-datasetRepositorySource codehttps://github.com/haile493/Colorectal-cancer-detection-using-ColoPola-dataset/issuesIssue trackerhttps://github.com/haile493/Colorectal-cancer-detection-using-ColoPola-datasetSource codePython language1.0https://zenodo.org/records/10554304Test dataDataset for running source code1.2compareMS2compareMS2 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/0000-0002-1220-9173PersonDeveloperopenVREThe Open Virtual Research Environment is a general purpose analysis platform that can be tailored for domain specific analyses.https://github.com/inab/openVRE/wikiopenvrebiotools:openvre1.0Bioinformatics portalWorkbenchhttp://edamontology.org/topic_0091BioinformaticsLinuxPHPPythonJavaScriptApache-2.0EUCAIMMatureFree of chargeOpen accessToolsSpainhttp://edamontology.org/operation_3760Service managementhttps://github.com/inab/openVRESource code1.0http://vre.multiscalegenomics.eu/help/starting.phpQuick start guideGetting Started GuidemugvreisNewVersionOfLaia Codólaia.codo@bsc.eshttps://www.bsc.es/codo-laiahttps://orcid.org/0000-0002-6797-8746grid.10097.3f05sd8tv9610.13039/501100006433PersonPrimary contactSenior Researcher at Barcelona Supercomputing Center. Lead of Trusted Research Environments and Cloud Computing at INB Lab.Josep Lluís Gelpígelpi@ub.eduhttps://webgrec.ub.edu/webpages/000011/ang/gelpi.ub.edu.htmlhttp://orcid.org/0000-0002-0566-7723grid.5841.8021018s5710.13039/501100005774PersonContributorProfessor at University of Barcelona and Team Leader at BSC's INB LaboratoryPinMolApplication for designing molecular beacons for live cell imaging of endogenous mRNAs.https://bratulab.wordpress.com/software/PinMolbiotools:PinMolbeta 1.0Command-line toolhttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_0632Probes and primershttp://edamontology.org/topic_3382ImagingWindowsMacPythonGPL-3.0EmergingFree of chargeOpen accesshttp://edamontology.org/operation_0278RNA secondary structure predictionhttp://edamontology.org/operation_0502RNA secondary structure alignmenthttp://edamontology.org/operation_0279Nucleic acid folding analysishttps://github.com/icatrina/PinMol_Win/releases/tag/v1.0-betaSource codebeta 1.0https://github.com/icatrina/PinMol_Mac/releases/tag/v1.0-betaSource codebeta 1.0https://bratulab.wordpress.com/tutorial-pinmol-mac/Training materialTutorial material10.1261/rna.069542.11830573696PMC6380279PrimaryIrina E. Catrinaiecatrina@gmail.comPersonPrimary contactPROTEOFORMERProteogenomic 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/DivisioniS-CellRiS-CellR (Interactive platform for Single-cell RNAseq) is a web-based Shiny application designed to provide a comprehensive analysis of single-cell RNA sequencing data.https://github.com/immcore/iS-CellRiS-CellRbiotools:iS-CellRDesktop applicationhttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_0099RNAhttp://edamontology.org/topic_3308TranscriptomicsLinuxWindowsMacRGPL-3.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_0337Visualisationhttps://github.com/immcore/iS-CellR/issuesIssue trackerhttps://github.com/immcore/iS-CellR/releases/tag/v1.1Source code1.1https://github.com/immcore/iS-CellR/releases/tag/v1.0Source code1.0https://github.com/immcore/iS-CellR/blob/master/README.mdGeneral10.1093/bioinformatics/bty51729982379PMC6289135PrimaryMitulkumar V. Patelmitul.patel@immunocore.comPersonPrimary contactAdjutantR-based tool to support topic discovery for systematic and literature reviews.https://github.com/amcrisan/AdjutantAdjutantbiotools:AdjutantLibraryhttp://edamontology.org/topic_3068Literature and languageLinuxWindowsMacRMITMatureFree of chargeOpen accesshttp://edamontology.org/operation_0306Text mininghttps://github.com/amcrisan/Adjutant/issuesIssue trackerhttps://github.com/amcrisan/Adjutant/releasesSource code1.0https://github.com/amcrisan/Adjutant/blob/master/README.mdGeneral10.1093/bioinformatics/bty72230875428PrimaryAnamaria Crisanacrisan@cs.ubc.caPersonPrimary contactDNAtoolsIncludes predicting DNA curvature; plotting physicochemical, statistical, or locally computed paramaters along DNA sequences; producing a 3-D model of a DNA sequence; searching an intron database.http://pongor.itk.ppke.hu/?q=bioinfoservicesdnatoolsbiotools:dnatoolsWeb applicationhttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_0654DNAhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_2269Statistics and probabilityLinuxWindowsMacUnlicenseMatureFree of chargeOpen accesshttp://edamontology.org/operation_0550DNA substitution modellinghttp://edamontology.org/operation_0433Splice site predictionhttp://edamontology.org/operation_2499Splicing model analysishttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_2238Statistical calculationhttp://pongor.itk.ppke.hu/dna/plot_it.html#/plotit_formServiceplot.it® Server: The Formhttp://pongor.itk.ppke.hu/dna/bend_it.html#/bendit_formServicebend.it® Serverhttp://pongor.itk.ppke.hu/dna/model_it.html#/modelit_formServicemodel.it® Serverhttps://github.com/r78v10a07/bendit/archive/1.0.tar.gzSoftware packageBend.it® Standalone version1.0http://pongor.itk.ppke.hu/dna/bend_it.html#/bendit_introGeneralbend.it® Serverhttp://pongor.itk.ppke.hu/dna/plot_it.html#/plotit_introGeneralplot.it® Serverhttp://pongor.itk.ppke.hu/dna/model_it.html#/modelit_introGeneral10.1093/nar/gkg55912824394PMC168966Sándor Pongorpongor.sandor@itk.ppke.huPersonPrimary contactIsodyn“C++”-program simulating the dynamics of metabolites and their isotopic isomers in the central metabolic network using a corresponding kinetic model. Supports the final step of 13C assisted the fluxomic analysis: evaluation of metabolic fluxes consistent with a given mass isotopomer distribution. The previous steps are supported by Ramid, Midcor, Isoform.https://github.com/seliv55/isodynIsodynbiotools:Isodyn1.0Command-line toolhttp://edamontology.org/topic_3955FluxomicsLinuxRFreewareOpen accessToolsSpainhttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/data_0943Mass spectrumhttp://edamontology.org/format_3835TIDE TXThttp://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3835TIDE TXTfiso="SW620-Glucose" # input data: file indicating 13C labeling of metabolites
fcon=xglc # input data: file with measured concentrations
inpar="glc/1" # input data: initial set of parameters to start
oudir="glc/" # output directory
fstat="glc/statfl" # path to write the results of fitting: mean and confidence intervals
fcmpr="glc/statfl" # results of fitting for the conditions used for comparison.
manfi=77 # number of files to be saved during fitting
FNCKAS # various options for the fitting./isodyn.out $fiso $fcon $inpar $oudir $fstat $fcmpr $manfi $FNCKAShttps://github.com/seliv55/isodynRepositoryCode and examplehttps://github.com/seliv55/isodynDownloads page1.0https://github.com/seliv55/isodynGeneralUsage instruction and example10.1007/978-1-0716-0159-4_1231893378Method10.1093/bioinformatics/bth41215256408Method10.1093/bioinformatics/bti57316002431Method10.1093/bioinformatics/btl48417000750MethodRAISSsoftware package enabling the imputation of SNP summary statistics from the neighboring SNPs by taking advantage of the Linkage desiquilibrium.http://statistical-genetics.pages.pasteur.fr/raiss/raissbiotools:raiss1.0, 2.0Command-line toolhttp://edamontology.org/topic_3517GWAS studyhttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_3053GeneticsLinuxPythonMITInstitut PasteurMatureFree of chargeOpen accessFrancehttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/data_0006Datahttp://edamontology.org/format_3475TSVhttps://gitlab.pasteur.fr/statistical-genetics/raissRepositoryhttps://gitlab.pasteur.fr/statistical-genetics/raiss/issuesIssue trackerhttps://biocontainers.pro/#/tools/raissContainer file1.0, 2.0http://statistical-genetics.pages.pasteur.fr/raiss/General10.1093/bioinformatics/btz46631173064PMC6853677PrimaryHugues Aschardhugues.aschard@pasteur.frhttps://research.pasteur.fr/fr/member/hugues-aschard/http://orcid.org/0000-0002-7554-6783PersonPrimary contactHanna Juliennehanna.julienne@pasteur.frhttps://research.pasteur.fr/fr/member/hanna-julienne/https://orcid.org/0000-0001-8214-9412PersonDeveloperBogdan Pasaniuchttps://orcid.org/0000-0002-0227-2056Huwenbo Shihttps://orcid.org/0000-0001-9886-877XPredictSNP2A 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 agencyContributorWHISCYWHISCY is a program to predict protein-protein interfaces. It is primarily based on conservation, but it also takes into account structural information. A sequence alignment is used to calculate a prediction score for each surface residue of your protein.https://bianca.science.uu.nl/whiscy/WHISCYbiotools:WHISCY1.0Web applicationhttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_3534Protein binding sitesLinuxWindowsMacBioExcelWeNMRINSTRUCTEGIMature3D-BioInfoNetherlandshttps://github.com/haddocking/whiscy/releasesDownloads page1.0https://github.com/haddocking/whiscyUser manual10.1002/prot.2084216450362PrimaryBonvin Laba.m.j.j.bonvin@uu.nlhttp://www.bonvinlab.orghttp://orcid.org/0000-0001-7369-1322DivisionProviderMaintainerDeveloperPrimary contactUtrecht Universityhttps://www.uu.nlNetherlands Organization for Scientific Research (NWO), VICI grant no. 700.96.442European H2020 e-Infrastructure grant, EOSC-Hub, grant no.7775363D-BioInfo + BioExcel: Protein Conformational Ensembles GenerationThis workflow illustrates the process of generating protein conformational ensembles from 3D structures and analysing its molecular flexibility, step by step, using the BioExcel Building Blocks library (biobb). Workflow included in the ELIXIR 3D-Bioinfo Implementation Study: Building on PDBe-KB to chart and characterize the conformation landscape of native proteinshttps://mmb.irbbarcelona.org/biobb/workflows#protein-conformational-ensembles-generation3d-bioinfo_bioexcel_protein_conformational_ensembles_generationbiotools:3d-bioinfo_bioexcel_protein_conformational_ensembles_generation1.0Workflowhttp://edamontology.org/topic_3892Biomolecular simulationhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_0092Data visualisationMacLinuxWindowsPythonApache-2.0BioExcel3D-BioInfo3D-BioInfo-Protein-ComplexEmergingFree of chargeOpen accessInteroperabilityTools3D-BioInfoSpainNorwayFranceBelgiumEMBLHungaryDenmarkhttp://edamontology.org/operation_0474Protein structure predictionhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/operation_3891Essential dynamicshttp://edamontology.org/operation_3890Trajectory visualizationhttp://edamontology.org/operation_0250Protein property calculationhttp://edamontology.org/operation_2939Principal component visualisationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttps://mmb.irbbarcelona.org/biobb/workflows#protein-conformational-ensembles-generationOtherMain web site (BioBB workflows)https://mmb.irbbarcelona.org/biobb/workflows/tutorials/flexdynOtherTutorial in HTMLhttps://biobb-wf-flexdyn.readthedocs.io/en/latest/index.htmlOtherTutorial in Read The Docshttps://github.com/bioexcel/biobb_wf_flexdynRepositorySource Code in GitHubhttps://github.com/bioexcel/biobb_wf_flexdynSource code1.0https://bioexcel-binder.tsi.ebi.ac.uk/v2/gh/bioexcel/biobb_wf_md_setup/master?filepath=biobb_wf_md_setup%2Fnotebooks%2Fbiobb_MDsetup_tutorial.ipynbVM imageBioExcel Binder1.0https://biobb-wf-flexdyn.readthedocs.io/en/latest/?badge=latestOtherRead The Docs Workflow Documentationbiobbusesimodusesflexservusesprodyusesnglviewuses10.1038/s41597-019-0177-431506435PMC6736963OtherBioExcel Building Blocks (BioBB)10.12688/f1000research.20559.132566135PMC7284151Other3D-BioInfo, ELIXIR Structural CommunityAdam Hospitaladam.hospital@irbbarcelona.orghttps://www.irbbarcelona.org/en/research/adam-hospitalPersonPrimary contactDeveloperDocumentorMaintainerGenís Bayarrigenis.bayarri@irbbarcelona.orghttps://www.irbbarcelona.org/en/research/genis-bayarriPersonContributorMaintainer3D-BioInfokatharina.heil@elixir-europe.orghttps://elixir-europe.org/communities/3d-bioinfoConsortiumProviderSuchTreeA Python library for doing fast, thread-safe computations with phylogenetic trees.https://github.com/ryneches/SuchTreesuchtreebiotools:suchtreeLibraryhttp://edamontology.org/topic_0084PhylogenyMacLinuxWindowsPythonBSD-3-ClauseEmergingFree of chargeOpen accesshttp://edamontology.org/operation_0557Phylogenetic tree distances calculationhttp://edamontology.org/operation_0551Phylogenetic tree topology analysishttp://edamontology.org/operation_0567Phylogenetic tree visualisationhttp://edamontology.org/data_3271Gene treehttp://edamontology.org/format_1910newickSuchTree.distances_by_name()https://github.com/ryneches/SuchTreeRepositoryhttps://github.com/ryneches/SuchTree/issuesIssue trackerhttps://pypi.org/project/SuchTree/Software package1.0https://github.com/ryneches/SuchTree#readmeGeneral10.21105/joss.00678Primary0.7Russell Y. Necheshttps://vort.orghttps://orcid.org/0000-0002-2055-8381PersonPrimary contactCamille Scotthttp://www.camillescott.org/https://orcid.org/0000-0001-8822-8779PersonContributorKojakA 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.2c0067036629399PMC10234491Primary2.0.0BioExcel Building Blocks tutorials: Macromolecular Coarse-Grained FlexibilityThis tutorial aims to illustrate the process of generating protein conformational ensembles from 3D structures using Coarse-Grained tools from the FlexServ server and analysing its molecular flexibilityhttps://mmb.irbbarcelona.org/biobb/workflows/tutorials/flexservbioexcel_building_blocks_tutorials_macromolecular_coarse-grained_flexibilitybiotools:bioexcel_building_blocks_tutorials_macromolecular_coarse-grained_flexibility1.0Workflowhttp://edamontology.org/topic_3892Biomolecular simulationhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_0092Data visualisationMacLinuxWindowsPythonApache-2.0BioExcelEmergingFree of chargeOpen accessToolsInteroperabilitySpainUKhttp://edamontology.org/operation_0474Protein structure predictionhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/operation_3891Essential dynamicshttp://edamontology.org/operation_3890Trajectory visualizationhttp://edamontology.org/operation_0250Protein property calculationhttp://edamontology.org/operation_2939Principal component visualisationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttps://mmb.irbbarcelona.org/biobb/workflows#macromolecular-coarse-grained-flexibilityOtherMain web site (BioBB Workflows)https://mmb.irbbarcelona.org/biobb/workflows/tutorials/flexservOtherTutorial in HTMLhttps://biobb-wf-flexserv.readthedocs.io/en/latest/index.htmlOtherTutorial in Read The Docshttps://github.com/bioexcel/biobb_wf_flexservRepositorySource Code in GitHubhttps://github.com/bioexcel/biobb_wf_flexservSource code1.0https://bioexcel-binder.tsi.ebi.ac.uk/v2/gh/bioexcel/biobb_wf_flexserv/main?filepath=biobb_wf_flexserv%2Fnotebooks%2Fbiobb_wf_flexserv.ipynbVM imageBioExcel Binder1.0https://biobb-wf-flexserv.readthedocs.io/en/latest/index.htmlOtherRead The Docs workflow documentationbiobbusesflexservusesnglviewusespcasuiteuses10.1038/s41597-019-0177-431506435PMC6736963OtherBioExcel Building Blocks (BioBB)Adam Hospitaladam.hospital@irbbarcelona.orghttps://www.irbbarcelona.org/en/research/adam-hospitalhttps://orcid.org/0000-0002-8291-8071PersonPrimary contactDeveloperDocumentorMaintainerGenís Bayarrigenis.bayarri@irbbarcelona.orghttps://www.irbbarcelona.org/es/research/genis-bayarrihttps://orcid.org/0000-0003-0513-0288PersonContributorDeveloperMaintainerBioExcel CoEhttps://bioexcel.eu/ConsortiumProviderBioExcel Building Blocks tutorials: Molecular Interaction PotentialsThis tutorial aims to illustrate the process of computing classical molecular interaction potentials from protein structures step by step, using the BioExcel Building Blocks library (biobb)https://mmb.irbbarcelona.org/biobb/workflows/tutorials/cmipbioexcel_building_blocks_tutorials_molecular_interaction_potentialsbiotools:bioexcel_building_blocks_tutorials_molecular_interaction_potentials1.0Workflowhttp://edamontology.org/topic_3892Biomolecular simulationhttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0092Data visualisationMacLinuxWindowsPythonApache-2.0BioExcelEmergingFree of chargeOpen accessToolsInteroperabilitySpainUKhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_2480Structure analysishttp://edamontology.org/operation_2949Protein-protein interaction analysishttp://edamontology.org/operation_0272Residue contact predictionhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_3870Trajectory datahttp://edamontology.org/format_1476PDBhttps://mmb.irbbarcelona.org/biobb/workflows/tutorials/cmipOtherTutorial in HTMLhttps://biobb-wf-cmip.readthedocs.io/en/latest/index.htmlOtherTutorial in Read The Docshttps://github.com/bioexcel/biobb_wf_cmipRepositorySource Code in GitHubhttps://github.com/bioexcel/biobb_wf_cmipSource code1.0https://bioexcel-binder.tsi.ebi.ac.uk/v2/gh/bioexcel/biobb_wf_cmip/main?filepath=biobb_wf_cmip%2Fnotebooks%2Fbiobb_wf_cmip.ipynbVM imageBioExcel Binderhttps://biobb-wf-cmip.readthedocs.io/en/latest/index.htmlOtherRead the Docs workflow documentationbiobbusesnglviewusesclassical_molecular_interaction_potentials_cmipuses10.1038/s41597-019-0177-431506435PMC6736963OtherBioExcel Building Blocks (BioBB)Adam Hospitaladam.hospital@irbbarcelona.orghttps://www.irbbarcelona.org/en/research/adam-hospitalhttps://orcid.org/0000-0002-8291-8071PersonPrimary contactDeveloperDocumentorMaintainerGenís Bayarrigenis.bayarri@irbbarcelona.orghttps://www.irbbarcelona.org/es/research/genis-bayarrihttps://orcid.org/0000-0003-0513-0288PersonContributorDeveloperMaintainerBioExcel CoEhttps://bioexcel.eu/ConsortiumProviderBioExcel Building Blocks tutorials: Protein Conformational TransitionsThis tutorial aims to illustrate the process of computing a conformational transition between two known structural conformations of a protein, step by step, using the BioExcel Building Blocks (biobb).https://mmb.irbbarcelona.org/biobb/workflows/tutorials/godmdbioexcel_building_blocks_tutorials_protein_conformational_transitionsbiotools:bioexcel_building_blocks_tutorials_protein_conformational_transitions1.0Workflowhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_3892Biomolecular simulationhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0092Data visualisationMacLinuxWindowsPythonApache-2.0BioExcelEmergingFree of chargeOpen accessToolsInteroperabilitySpainUKhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_2476Molecular dynamicshttp://edamontology.org/operation_2480Structure analysishttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_3890Trajectory visualizationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttps://mmb.irbbarcelona.org/biobb/workflows/tutorials/godmdOtherTutorial in HTMLhttps://biobb-wf-godmd.readthedocs.io/en/latest/index.htmlOtherTutorial in Read the Docshttps://github.com/bioexcel/biobb_wf_godmdRepositorySource Code in GitHubhttps://github.com/bioexcel/biobb_wf_godmdSource codeSource Code in GitHub1.0https://bioexcel-binder.tsi.ebi.ac.uk/v2/gh/bioexcel/biobb_wf_godmd/main?filepath=biobb_wf_godmd%2Fnotebooks%2Fbiobb_wf_godmd.ipynbVM imageBioExcel Binderhttps://biobb-wf-godmd.readthedocs.io/en/latest/index.htmlOtherDocumentation in Read the Docsbiobbusesgodmduseswateruses10.1038/s41597-019-0177-431506435PMC6736963OtherBioExcel Building Blocks (BioBB)10.1093/bioinformatics/btt32423740746OtherGOdMD methodAdam Hospital Gaschadam.hospital@irbbarcelona.orghttps://www.irbbarcelona.org/en/research/adam-hospitalhttps://orcid.org/0000-0002-8291-8071PersonPrimary contactDeveloperDocumentorMaintainerGenís Bayarrigenis.bayarri@irbbarcelona.orghttps://www.irbbarcelona.org/es/research/genis-bayarrihttps://orcid.org/0000-0003-0513-0288PersonContributorDeveloperMaintainerBioExcel CoEhttps://bioexcel.eu/ConsortiumProviderBioExcel Building Blocks tutorials: Protein-ligand DockingThis tutorial aims to illustrate the process of protein-ligand docking, step by step, using the BioExcel Building Blocks library (biobb).https://mmb.irbbarcelona.org/biobb/workflows/tutorials/vs_bsbioexcel_building_blocks_tutorials_protein-ligand_dockingbiotools:bioexcel_building_blocks_tutorials_protein-ligand_docking1.0Workflowhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_0092Data visualisationMacLinuxWindowsPythonApache-2.0BioExcelEmergingFree of chargeOpen accessInteroperabilityToolsSpainUKhttp://edamontology.org/operation_0482Protein-ligand dockinghttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3814SDFhttps://mmb.irbbarcelona.org/biobb/workflows/tutorials/vs_bsOtherTutorial in HTML (PDB Cluster90 Binding Site Version)https://biobb-wf-virtual-screening.readthedocs.io/en/latest/cluster_bs_tutorial.htmlOtherTutorial in Read The Docs (PDB Cluster90 Binding Site Version)https://github.com/bioexcel/biobb_wf_virtual-screeningRepositorySource Code in GitHubhttps://mmb.irbbarcelona.org/biobb/workflows/tutorials/vs_ebiOtherTutorial in HTML (PDBe REST-API Binding Site Version)https://biobb-wf-virtual-screening.readthedocs.io/en/latest/ebi_api_tutorial.htmlOtherTutorial in Read the Docs (PDBe REST-API Binding Site Version)https://mmb.irbbarcelona.org/biobb/workflows/tutorials/vs_fpocketOtherTutorial in HTML (Fpocket Binding Site Version)https://biobb-wf-virtual-screening.readthedocs.io/en/latest/fpocket_tutorial.htmlOtherTutorial in Read the Docs (Fpocket Binding Site Version)https://github.com/bioexcel/biobb_wf_virtual-screeningSource code1.0https://biobb-wf-virtual-screening.readthedocs.io/en/latest/cluster_bs_tutorial.htmlOtherRead the Docs Workflow Documentation (PDB Cluster90 Binding Site Version)https://biobb-wf-virtual-screening.readthedocs.io/en/latest/ebi_api_tutorial.htmlOtherRead the Docs Workflow Documentation (PDBe REST-API Binding Site Version)https://biobb-wf-virtual-screening.readthedocs.io/en/latest/fpocket_tutorial.htmlOtherRead the Docs Workflow Documentation (Fpocket Binding Site Version)biobbusesautodock_vinausesfpocketusespdbeuses10.1038/s41597-019-0177-431506435PMC6736963OtherBioExcel Center of Excellence for Computational Biomolecular Researchhttps://www.bioexcel.euConsortiumProviderGenís Bayarrigenis.bayarri@irbbarcelona.orghttps://www.irbbarcelona.org/en/research/genis-bayarrihttps://orcid.org/0000-0003-0513-0288PersonDeveloperDocumentorMaintainerAdam Hospitaladam.hospital@irbbarcelona.orghttps://www.irbbarcelona.org/en/research/adam-hospitalhttps://orcid.org/0000-0002-8291-8071PersonPrimary contactPlanet 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/0000-0001-9961-144XPersonDeveloperCoCoNatCoCoNat is a novel deep-learning based method for predicting coiled-coil regions, register annotation and oligomenrization state. CoCoNat adopts a sequence encoding based on two state-of-the-art protein language models and a deep-learning architetcure to perform prediction.https://coconat.biocomp.unibo.itcoconatbiotools:coconat1.0Web applicationCommand-line toolhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0736Protein folds and structural domainsMacLinuxWindowsPythonGPL-3.0Bologna Biocomputing GroupMatureFree of chargeOpen accessToolsItalyhttp://edamontology.org/operation_0268Protein super-secondary structure predictionhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttps://github.com/BolognaBiocomp/coconatSource code1.0https://github.com/BolognaBiocomp/coconatCommand-line optionshttps://coconat.biocomp.unibo.it/help/User manual10.1093/bioinformatics/btad49537540220PMC10425188Primary10.21769/BioProtoc.493538405078PMC10883893UsageELIXIR-ITA-BOLOGNAInstituteProviderCastrense Savojardocastrense.savojardo2@unibo.ithttps://orcid.org/0000-0002-7359-0633PersonPrimary contactDeveloperMaintainerPier Luigi Martellipierluigi.martelli@unibo.ithttps://orcid.org/0000-0002-0274-5669PersonPrimary contactPlasGOPlasGO: a Python library (Linux or Ubuntu only) for predicting cluster-level Gene Ontology (GO) terms of plasmid-encoded proteins.https://github.com/Orin-beep/PlasGOplasgobiotools:plasgo1.0https://github.com/Orin-beep/PlasGOSoftware package1.0get_MNVget_MNV is a tool designed to identify Multi-Nucleotide Variants (MNVs) within the same codon in genomic sequences. MNVs occur when multiple Single Nucleotide Variants (SNVs) are present within the same codon, leading to the translation of a different amino acid. This tool addresses limitations in current annotation programs like ANNOVAR or SnpEff, which are primarily designed to work with individual SNVs and might overlook the actual amino acid changes resulting from MNVs.https://github.com/PathoGenOmics-Lab/get_mnvget_mnvbiotools:get_mnv1.0.0Command-line toolhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_0077Nucleic acidshttp://edamontology.org/topic_3053GeneticsLinuxMacOtherGPL-3.0EmergingFree of chargeOpen accesshttp://edamontology.org/operation_0361Sequence annotationhttp://edamontology.org/operation_3661SNP annotationhttp://edamontology.org/data_1279Sequence maphttp://edamontology.org/format_3016VCFget_mnv [OPTIONS] --vcf <VCF_FILE> --fasta <FASTA_FILE> --genes <GENES_FILE>https://github.com/PathoGenOmics-Lab/get_mnvRepositoryhttps://github.com/PathoGenOmics-Lab/get_MNV/releases/download/1.0.0/get_mnvBinaries1.0https://github.com/PathoGenOmics-Lab/get_MNV/wikiUser manualDeepdefensesoftware tool for the annotation and discovery of novel immune systems in prokaryoteshttps://github.com/SvenHauns/Deepdefensedeepdefensebiotools:deepdefenseCommand-line toolhttp://edamontology.org/topic_3070BiologyPythonMITFree of chargeOpen accesshttp://edamontology.org/operation_2990Classificationhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttps://github.com/SvenHauns/DeepdefenseRepositoryhttps://github.com/SvenHauns/DeepdefenseSource code1.0ScanScanning sample-specific miRNA regulation from bulk and single-cell RNA-sequencing datahttps://github.com/zhangjunpeng411/ScanScanbiotools:Scan1.0Scripthttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0204Gene regulationhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_3308TranscriptomicsMacLinuxWindowsRMATLABAGPL-3.0CancerOpen accesshttp://edamontology.org/operation_2437Gene regulatory network predictionhttp://edamontology.org/operation_3792miRNA expression analysishttp://edamontology.org/data_3112Gene expression matrixhttps://github.com/zhangjunpeng411/ScanRepositoryhttps://github.com/zhangjunpeng411/ScanSource code1.0https://github.com/zhangjunpeng411/ScanQuick start guideJunpeng Zhangzhangjunpeng411@gmail.comhttps://orcid.org/0000-0001-6127-9701GERONIMOGERONIMO is a bioinformatics pipeline designed to conduct high-throughput homology searches of structural genes using covariance models. These models are based on the alignment of sequences and the consensus of secondary structures. The pipeline is built using Snakemake, a workflow management tool that allows for the reproducible execution of analyses on various computational platforms.https://github.com/amkilar/GERONIMO.gitGERONIMObiotools:GERONIMO1.0WorkflowCommand-line toolhttp://edamontology.org/topic_3299Evolutionary biologyhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3293PhylogeneticsWindowsLinuxPythonRBashMITMatureFree of chargeOpen accessToolshttps://github.com/amkilar/GERONIMO.gitSource code1.0https://github.com/amkilar/GERONIMO.gitUser manualinfernalusesAgata Kilaragata.kilar@gmail.comhttps://orcid.org/0000-0003-3876-6581DevelopermirKitmiRkit is an open source framework written in R, that allows for the comprehensive analysis of RT-PCR data, from the processing of raw data to a functional analysis of the produced results. The main goal of the tool is to provide an assessment of the samples’ quality, perform data normalization by endogenous and exogenous miRNAs, and facilitate differential and functional enrichment analysis. The tool offers fast execution times with low memory usage, can perform the full analysis from the raw RT-PCR data to functional analysis of targeted genes, and is specifically designed to support the popular miScript miRNA PCR Array (Qiagen) technology.https://github.com/BiodataAnalysisGroup/miRkitmirkitbiotools:mirkit1.0http://edamontology.org/topic_0659Functional, regulatory and non-coding RNAhttp://edamontology.org/topic_3518Microarray experimentMITMatureFree of chargeOpen accesshttp://edamontology.org/operation_2436Gene-set enrichment analysishttp://edamontology.org/operation_3792miRNA expression analysishttp://edamontology.org/data_2082Matrixhttp://edamontology.org/format_1957rawhttp://edamontology.org/format_3999R scripthttps://github.com/BiodataAnalysisGroup/miRkitSource code1.0https://github.com/BiodataAnalysisGroup/miRkit/blob/main/README.mdQuick start guideFotis Psomopoulosfpsom@certh.grhttps://orcid.org/0000-0002-0222-4273PersonPrimary contactBiobb Mutations WorkflowCWL VM environment is a repository which can be deployed on cloud to execute Biobb Mutations Workflow.https://github.com/EMBL-EBI-TSI/cpa-bioexcel-cwlCWL_VM_environmentbiotools:CWL_VM_environment1.0Workbenchhttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_0199Genetic variationLinuxBioExcelLegacyFree of charge (with restrictions)https://github.com/EMBL-EBI-TSI/cpa-bioexcel-cwlVM imageBioExcel_ECP_Application;name:CWL VM environment;teamName:BioExcel Embassy;config:CWL biobb_wf_mutations1.0Felix Xavier Amaladossfamaladoss@ebi.ac.ukDeveloperLindaThe web application Linda offers a complete tool for entering and managing metadata associated with a phenotyping experiment on plants. It thus makes it possible to intuitively describe experimental related information such as, for example, the experimental design, the growth protocols, the environmental variable measurements, etc. Linda is coupled with a database that stores this information in a structured manneer using oriented graphs. This database uses reference ontologies (e.g., Plant Ontology, Crop Ontology, etc.) and standards dedicated to this type of experiment such as the Minimal Information About Plant Phenotyping Experiment (MIAPPE) standard. Data sharing is facilitated on the one hand by respecting the FAIR principles (Findable Accessible Interoperable Reusable) and oon the other hand, by exporting this metadata relating to the experiment in tabulated formats or formatted for submission in the international databases (ISA-tab).https://services.cbib.u-bordeaux.fr/linda/xeml-labbiotools:xeml-lab1Web applicationhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0219Data submission, annotation and curationhttp://edamontology.org/topic_0089Ontology and terminologyLinuxMacJavaScriptBashPythonOtherMITEmergingFree of chargeOpen access (with restrictions)http://edamontology.org/operation_3431DepositionThe web application Linda offers a complete tool for entering and managing metadata associated with a phenotyping experiment on plants. It thus makes it possible to intuitively describe experimental related information such as, for example, the experimental design, the growth protocols, the environmental variable measurements, etc. Linda is coupled with a database that stores this information in a structured manneer using oriented graphs. This database uses reference ontologies (e.g., Plant Ontology, Crop Ontology, etc.) and standards dedicated to this type of experiment such as the Minimal Information About Plant Phenotyping Experiment (MIAPPE) standard. Data sharing is facilitated on the one hand by respecting the FAIR principles (Findable Accessible Interoperable Reusable) and oon the other hand, by exporting this metadata relating to the experiment in tabulated formats or formatted for submission in the international databases (ISA-tab).https://services.cbib.u-bordeaux.fr/linda/Repositoryhttps://services.cbib.u-bordeaux.fr/lindaTool wrapper (Other)1.0https://services.cbib.u-bordeaux.fr/lindaGeneralCitation instructionsGeneralBenjamin DartiguesPersonDeveloperPrimary contactYves GibonPersonContributorCecile CabassonPersonContributorUMR 1332 - Biologie du Fruit et PathologieInstituteProviderCentre de Bioinformatique de Bordeaux (CBiB)InstituteProviderMacha NikolskiPersonContributorAlexis GroppiPersonContributorMISTICMISTIC (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 contactContributorVIQoRVIQoR, is a user-friendly web service for Visually supervised protein Inference and protein Quantification implemented in R. The Shiny web interface integrates the post-identification processes involved in protein inference and relative protein abundance summarization, along with smart and novel interactive visualization modules to support the common researchers with a straight-forward tool for protein quantification, data browsing and data inspection.http://computproteomics.bmb.sdu.dk:443/app_direct/VIQoR/viqorbiotools:viqor1.0Web serviceScripthttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_0108Protein expressionhttp://edamontology.org/topic_0601Protein modificationsWindowsLinuxMacRJavaScriptApache-2.0ProteomicsMatureFree of chargeOpen accessProteomicsDenmarkhttp://edamontology.org/operation_1812Parsinghttp://edamontology.org/operation_3695Filteringhttp://edamontology.org/operation_3435Standardisation and normalisationhttp://edamontology.org/operation_2429Mappinghttp://edamontology.org/operation_3767Protein identificationhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_3630Protein quantificationhttp://edamontology.org/operation_3463Expression correlation analysishttp://edamontology.org/operation_0571Expression data visualisationhttp://edamontology.org/operation_0531Heat map generationhttp://edamontology.org/operation_2938Dendrogram visualisationhttp://edamontology.org/operation_3184Sequence assembly visualisationhttp://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_1233Sequence set (protein)http://edamontology.org/format_1929FASTAhttp://edamontology.org/format_2330Textual formathttps://bitbucket.org/vtsiamis/viqor/RepositoryRepository of source code and docker file.http://computproteomics.bmb.sdu.dk:8192/app_direct/VIQoR/Servicehttps://bitbucket.org/vtsiamis/viqor/downloads/Source code1.0https://bitbucket.org/vtsiamis/viqor/src/master/Manual.pdfUser manual10.1101/2021.06.01.446512PrimaryVasileios Tsiamisvasileios@bmb.sdu.dkhttps://orcid.org/0000-0003-1359-5253DeveloperDocumentorMaintainerPrimary contactSupportVeit Schwämmleveits@bmb.sdu.dkhttps://orcid.org/0000-0002-9708-6722Primary contactContributorProviderSPACNACSSPACNACS is a crowdsourcing initiative to provide information about Copy Number Variations of the Spanish population to the scientific/medical community.http://csvs.clinbioinfosspa.es/spacnacsspacnacsbiotools:spacnacsWeb applicationhttp://edamontology.org/topic_3056Population geneticshttp://edamontology.org/topic_3958Copy number variationJavaJavaScriptGPL-2.0https://github.com/babelomics/SPACNACSSource code1.0https://github.com/babelomics/SPACNACS/wikiUser manualJoaquín Dopazojoaquin.dopazo@juntadeandalucia.esBioExcel Building Blocks REST API (BioBB-API)BioBB REST API extends and complements the BioBB library offering programmatic access to the collection of biomolecular simulation tools included in the BioExcel Building Blocks library. Molecular Dynamics setup, docking, structure modeling, free energy simulations, and flexibility analyses are examples of functionalities included in the endpoints collection. All functionalities are accessible through standard REST API calls, eluding the need of tools installation.https://mmb.irbbarcelona.org/biobb-api/bioexcel_building_blocks_rest_api_biobb-apibiotools:bioexcel_building_blocks_rest_api_biobb-api1.0Web APIWeb servicehttp://edamontology.org/topic_3892Biomolecular simulationhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_2275Molecular modellingMacLinuxWindowsPythonApache-2.0BioExcelEmergingFree of chargeOpen accessInteroperabilityTools3D-BioInfoSpainhttp://edamontology.org/operation_2476Molecular dynamicshttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_0478Molecular dockinghttp://edamontology.org/operation_0475Nucleic acid structure predictionhttp://edamontology.org/operation_2481Nucleic acid structure analysishttp://edamontology.org/operation_2844Structure clusteringhttp://edamontology.org/operation_3893Forcefield parameterisationhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1459Nucleic acid structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3870Trajectory datahttp://edamontology.org/format_3650netCDFhttp://edamontology.org/format_3875XTChttp://edamontology.org/format_3876TNGhttp://edamontology.org/format_3878mdcrdhttp://edamontology.org/format_3885BinPoshttp://mmb.irbbarcelona.org/biobb-api/OtherBioBB-API Landing Websitehttps://mmb.irbbarcelona.org/biobb-api/restOtherBioBB-API OpenAPI Documentationhttps://mmb.irbbarcelona.org/biobb-api/tools-documentationOtherBioBB-API Endpoints Listhttps://mmb.irbbarcelona.org/biobb-api/tools-executionOtherBioBB-API Endpoints Exampleshttps://mmb.irbbarcelona.org/biobb-api/tutorials/restapiOtherBioBB-API Endpoints Tutorialshttps://mmb.irbbarcelona.org/biobb-api/tutorials/mdsetupOtherBioBB-API Protein MD Setup Workflow Tutorialhttps://biobb-rest-api-documentation.readthedocs.io/OtherBioBB-API Read-The-Docs Documentationhttp://mmb.irbbarcelona.org/biobb-api/restAPI specificationBioBB-API OpenAPI Documentation1.0https://mmb.irbbarcelona.org/biobb-api/tools-documentationAPI specificationBioBB-API Enpoints List1.0https://biobb-rest-api-documentation.readthedocs.io/API documentationQuick start guideBioBB-API Read The Docs DocumentationbiobbusesGenís Bayarrigenis.bayarri@irbbarcelona.orghttps://www.irbbarcelona.org/en/research/genis-bayarrihttps://orcid.org/0000-0003-0513-0288PersonPrimary contactDeveloperDocumentorMaintainerMain developerPau Andriopau.andrio@bsc.eshttps://www.bsc.es/andrio-balado-pauhttps://orcid.org/0000-0003-2116-3880PersonContributorDeveloperResearch Support Engineer in the Barcelona Supercomputing Center.Adam Hospitaladam.hospital@irbbarcelona.orghttps://www.irbbarcelona.org/en/research/adam-hospitalhttps://orcid.org/0000-0002-8291-8071PersonContributorResearch Software Engineer in the IRB-BarcelonaJosep Lluís Gelpígelpi@ub.eduhttps://www.bsc.es/gelpi-josephttps://orcid.org/0000-0002-0566-7723PersonContributorComputational Group Manager in the BSCBioExcel Center of Excellence for Computational Biomolecular Researchhttps://bioexcel.eu/ConsortiumProviderBioExcel Centre of Excellence for Computational Biomolecular Research is a consortium of European partners born as an H2020 project, giving support to academic and industrial researchers in the use of high-performance computing (HPC) and high-throughput computing (HTC) in biomolecular research.SUPERGNOVASUPERGNOVA (SUPER GeNetic cOVariance Analyzer) is a statistical framework to perform local genetic covariance analysis. SUPERGNOVA only needs GWAS summary data and a reference panel as input data.https://github.com/qlu-lab/SUPERGNOVAsupergnovabiotools:supergnovaCommand-line toolhttp://edamontology.org/topic_3517GWAS studyhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3676Exome sequencinghttp://edamontology.org/topic_2885DNA polymorphismMacLinuxPythonMITFree of chargeOpen accesshttp://edamontology.org/operation_3463Expression correlation analysishttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_3659Regression analysishttp://edamontology.org/operation_0335Formattinghttp://edamontology.org/operation_3557Imputationhttps://github.com/qlu-lab/SUPERGNOVA/releases/tag/1.0Source code1.010.1186/S13059-021-02478-W34493297PMC8422619Hongyu Zhaohongyu.zhao@yale.eduhttps://orcid.org/0000-0003-1195-9607PersonYiliang ZhangQiongshi LuYixuan YeVarGeniusVarGenius 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 contact3DRS3DRS, a web-based tool to share interactive representations of 3D biomolecular structures and Molecular Dynamics trajectorieshttps://mmb.irbbarcelona.org/3dRS/3drsbiotools:3drs1.0Web applicationhttp://edamontology.org/topic_1317Structural biologyhttp://edamontology.org/topic_3307Computational biologyhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_3892Biomolecular simulationMacLinuxWindowsJavaScriptPHPApache-2.0BioExcelEmergingFree of chargeOpen accessInteroperability3D-BioInfoSpainhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_3890Trajectory visualizationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_1459Nucleic acid structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_3870Trajectory datahttp://edamontology.org/format_3650netCDFhttp://edamontology.org/format_3885BinPoshttp://edamontology.org/format_3875XTChttp://edamontology.org/format_3910trrGenerate animated figures for macromolecular 3D structures and trajectories using NGL viewerhttps://mmb.irbbarcelona.org/3dRS/ServiceMain web serverhttps://github.com/gbayarri?tab=repositories&q=3drsRepositoryGitHub repositories for the projecthttps://3drs-documentation.readthedocs.io/en/latest/OtherDocumentation in Read The Docshttps://mmb.irbbarcelona.org/3dRS/OtherMain Web Site1.0https://3drs-documentation.readthedocs.io/en/latest/index.htmlUser manualRead The Docs documentationnglusesAdam Hospitaladam.hospital@irbbarcelona.orghttps://www.irbbarcelona.org/en/research/adam-hospitalhttps://orcid.org/0000-0002-8291-8071PersonContributorGenís Bayarrigenis.bayarri@irbbarcelona.orghttps://www.irbbarcelona.org/en/research/genis-bayarriPersonDeveloperDocumentorMaintainermetaXplormetaXplor is an interactive viral and microbial metagenomic data manager. It aims at storing large volumes of user-defined sample, sequence and assignment information while providing a user-friendly fine-filtering web-interface. This online GUI also offers means to share datasets with collaborators, BLAST external sequences against them, and confirm assignments by running phylogenetic placement. metaXplor is available as a set of Docker containers that make it simple to deploy on various infrastructures.https://github.com/SouthGreenPlatform/metaXplormetaxplorbiotools:metaxplor1.0-betaRRID:SCR_019025rridWeb applicationDatabase portalhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_3071Biological databasesLinuxAGPL-3.0MatureFree of chargeOpen access (with restrictions)https://github.com/SouthGreenPlatform/metaXplorRepositoryhttps://metaxplor.cirad.fr/metaXplor/OtherLive instance with public datahttps://raw.githubusercontent.com/SouthGreenPlatform/metaXplor/master/docker-compose.ymlContainer fileThis is a docker-compose file which upon execution automatically downloads required images1.0-betahttps://metaxplor.cirad.fr/metaXplor/docIndex.jspUser manualHTML documentation is embedded in the web applicationGuilhem Sempéréguilhem.sempere@cirad.frhttps://orcid.org/0000-0001-7429-2091metaxplor@cirad.frMendelIHT.jlImplements iterative hard thresholding as a multiple regression model for GWAS. Built-in support for handling PLINK and VCF files, parallel computing, fits a variety of GLM models, and handles group/weighting SNPs.https://github.com/OpenMendel/MendelIHT.jlmendeliht.jlbiotools:mendeliht.jlRRID:SCR_018292rridLibraryhttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_3053GeneticsLinuxWindowsMacJuliaMITMatureFree of chargeOpen accesshttp://edamontology.org/operation_3232Gene expression QTL analysishttp://edamontology.org/operation_3197Genetic variation analysishttps://github.com/OpenMendel/MendelIHT.jlAPI specificationStart Julia, press ] to enter package manager mode, and type the following (after pkg>):
(v1.0) pkg> add https://github.com/OpenMendel/SnpArrays.jl
(v1.0) pkg> add https://github.com/OpenMendel/MendelSearch.jl
(v1.0) pkg> add https://github.com/OpenMendel/MendelBase.jl
(v1.0) pkg> add https://github.com/OpenMendel/MendelIHT.jlJulia 1.0-1.3https://openmendel.github.io/MendelIHT.jl/latest/API documentationLyoPRONTOAn Open-Source Lyophilization Process Optimization Tool.
This work presents a new user-friendly lyophilization simulation and process optimization tool, freely available under the name LyoPRONTO. This tool comprises freezing and primary drying calculators, a design-space generator, and a primary drying optimizer. The freezing calculator performs 0D lumped capacitance modeling to predict the product temperature variation with time which shows reasonably good agreement with experimental measurements. The primary drying calculator performs 1D heat and mass transfer analysis in a vial and predicts the drying time with an average deviation of 3% from experiments. The calculator is also extended to generate a design space over a range of chamber pressures and shelf temperatures to predict the most optimal setpoints for operation.https://sites.google.com/view/rgdart/Research/lyopronto-lyophilization-processoptimization-toolLyoPRONTObiotools:LyoPRONTOCommand-line toolhttp://edamontology.org/topic_3068Literature and languagehttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/operation_3659Regression analysishttps://drive.google.com/file/d/12is--VvE1bUGAOoNz_UvjMQ4m-SyIEO5/viewSource code1.010.1208/S12249-019-1532-731673810PMC6823652Alina A. Alexeenkoalexeenk@purdue.eduPersonVISORHaplotype-aware structural variants simulator for short, long and linked readshttps://github.com/davidebolo1993/VISORVISORbiotools:VISOR1.0http://edamontology.org/topic_3511Nucleic acid sites, features and motifshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3175DNA structural variationShellRPythonLGPL-3.0MatureFree of chargeOpen accessToolsEMBLhttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/operation_2928Alignmenthttp://edamontology.org/operation_3208Genome visualisationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2914Sequence features metadatahttp://edamontology.org/format_3003BEDVISOR {HACk, SHORtS, LASeR, XENIA} --helphttps://github.com/davidebolo1993/VISORRepositoryhttps://github.com/davidebolo1993/VISORSource code1.0https://davidebolo1993.github.io/visordoc/User manualtricolorusedBy10.1093/BIOINFORMATICS/BTZ71931589307MethodDavide Bologninidavidebolognini7@gmail.comhttps://orcid.org/0000-0002-8735-8093PersonMaintainerDocumentorDeveloperRetroPath RLRetroPath RL performs bio-retrosynthesis using the Monte Carlo Tree Search Reinforcement Learning approach. It is compatible with mono-component reaction rules from RetroRules.https://github.com/brsynth/RetroPathRLretropath_rlbiotools:retropath_rlCommand-line toolhttp://edamontology.org/topic_3398Bioengineeringhttp://edamontology.org/topic_3895Synthetic biologyhttp://edamontology.org/topic_2258Cheminformaticshttp://edamontology.org/topic_0602Molecular interactions, pathways and networksLinuxMacPythonMITMatureFree of chargeOpen accesshttps://github.com/brsynth/RetroPathRLRepositoryhttps://github.com/brsynth/RetroPathRLSource code1.0retrorulesuses10.1021/acssynbio.9b0044731841626PrimaryMathilde Kochhttps://orcid.org/0000-0002-8924-3513Thomas Duigouhttps://orcid.org/0000-0002-2649-2950Jean-Loup Faulonhttps://orcid.org/0000-0003-4274-2953