RAiSD-AIRAiSD-AI is a tool for training, testing, and deploying Convolutional Neural Networks to detect selective sweeps in genomic data, extending the functionality of the original RAiSD software with machine learning capabilities. It supports SNP data processing, CNN model training with TensorFlow or PyTorch, and genome-wide selective sweep detection.https://github.com/alachins/RAiSD-AIRAiSD-AIbiotools:RAiSD-AI4.5Command-line toolhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3474Machine learningShellRPythonCNot licensedMatureFree of chargehttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/operation_3197Genetic variation analysishttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_3016VCFhttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_2048Report

10.1038/s42003-018-0085-830271960PMC6123745Method10.32942/x2gw9bPrimarytrieA generic C++ trie search tree library for small alphabets, allowing customizable leaf node structures and supporting approximate matching and word generation.https://github.com/jfjlaros/trietriebiotools:trieLibraryC++MITEmergingFree of chargehttp://edamontology.org/operation_0224Query and retrievalhttps://cpptrie.readthedocs.io/en/latest/User manualInstallation instructionsAPI documentationtosccatoscca is an R package to perform Thresholded Ordered Sparse Canonical Correlation Analysis (TOSCCA).https://github.com/nuria-sv/tosccatosccabiotools:toscca1.0Libraryhttp://edamontology.org/topic_2269Statistics and probabilityROtherEmergingFree of chargehttp://edamontology.org/operation_3935Dimensionality reductionhttp://edamontology.org/operation_3465Correlationhttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/data_3869Simulation

http://edamontology.org/data_1636Heat map

http://edamontology.org/data_2884Plot

https://github.com/nuria-sv/toscca/wikiGeneralggplot2uses10.1093/bioadv/vbae02138456127PMC10919946PrimaryOpenProteoOpenProteo is the open-source Rust stack for proteomics raw-file access. It reads Thermo, Bruker, and Waters acquisitions through a single API (via the sibling OpenTFRaw, OpenTimsTDF, and OpenWRaw readers), converts them to PSI-MS mzML 1.1.0 with a canonical writer, and provides a zero-copy read_arrow() API (enabled by default) that loads directly into Polars or Pandas via PyArrow. No vendor SDKs, no Windows-only DLLs, no binary blobs in the release pipeline. Includes a one-shot vendor2mzml CLI.https://github.com/Sigilweaver/OpenProteoOpenProteobiotools:OpenProteo1.0.3doi:10.5281/zenodo.20470595doiCommand-line toolLibraryhttp://edamontology.org/topic_0121ProteomicsWindowsMacLinuxPythonRustApache-2.0EmergingFree of chargehttp://edamontology.org/operation_0335Data formattinghttp://edamontology.org/operation_1812Data parsinghttp://edamontology.org/data_2536Mass spectrometry data

http://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3244mzML

https://github.com/Sigilweaver/OpenProteoRepositoryhttps://crates.io/crates/openproteo-ioSoftware packageRust cratehttps://pypi.org/project/openproteo/Software packagePython packagehttps://github.com/Sigilweaver/OpenProteo/releasesBinariesPre-built vendor2mzml CLI binarieshttps://sigilweaver.app/openproteo/docsUser manualNathan Rileyhttps://orcid.org/0009-0004-1579-7312PersonDeveloperMaintainerOpenWRawOpenWRaw is a standalone, cross-platform reader for Waters MassLynx .raw acquisition directories, implemented in pure Rust with no dependency on vendor DLLs. Python bindings built on PyO3 expose functions, scans, and ion-mobility data as native Python objects from Waters QTof and SYNAPT instrument families, ready to be assembled into a Pandas or Polars DataFrame.https://github.com/Sigilweaver/OpenWRawOpenWRawbiotools:OpenWRaw1.0.5doi:10.5281/zenodo.20470607doiLibraryhttp://edamontology.org/topic_0121ProteomicsWindowsMacLinuxPythonRustApache-2.0EmergingFree of chargehttp://edamontology.org/operation_1812Data parsinghttp://edamontology.org/data_2536Mass spectrometry data

http://edamontology.org/data_2536Mass spectrometry data

https://github.com/Sigilweaver/OpenWRawRepositoryhttps://crates.io/crates/openwrawSoftware packageRust cratehttps://pypi.org/project/openwraw/Software packagePython packagehttps://sigilweaver.app/openwraw/docsUser manualNathan Rileyhttps://orcid.org/0009-0004-1579-7312PersonDeveloperMaintainerOpenTimsTDFOpenTimsTDF is a standalone, cross-platform reader for Bruker timsTOF .tdf and .tdf_bin acquisition files, implemented in pure Rust with no dependency on vendor SDKs. Python bindings built on PyO3 expose frame, scan, and peak data as native Python objects, providing ion-mobility-aware access that can be assembled into a Pandas or Polars DataFrame.https://github.com/Sigilweaver/OpenTimsTDFOpenTimsTDFbiotools:OpenTimsTDF1.0.6doi:10.5281/zenodo.20470603doiLibraryhttp://edamontology.org/topic_0121ProteomicsWindowsMacLinuxPythonRustApache-2.0EmergingFree of chargehttp://edamontology.org/operation_1812Data parsinghttp://edamontology.org/data_2536Mass spectrometry data

http://edamontology.org/data_2536Mass spectrometry data

https://github.com/Sigilweaver/OpenTimsTDFRepositoryhttps://crates.io/crates/opentimstdfSoftware packageRust cratehttps://pypi.org/project/opentimstdf/Software packagePython packagehttps://sigilweaver.app/opentimstdf/docsUser manualNathan Rileyhttps://orcid.org/0009-0004-1579-7312PersonDeveloperMaintainerOpenTFRawOpenTFRaw is a standalone, cross-platform reader for Thermo Fisher Scientific .raw mass-spectrometry files, implemented in pure Rust with no dependency on vendor DLLs or .NET. Python bindings built on PyO3 return NumPy arrays for spectral data, straightforward to load into Pandas or Polars. Covers format versions 8 through 66 (LCQ Classic through Orbitrap Astral and modern TSQ instruments), supporting both centroid and profile spectra.https://github.com/Sigilweaver/OpenTFRawOpenTFRawbiotools:OpenTFRaw1.0.6doi:10.5281/zenodo.20470601doiLibraryhttp://edamontology.org/topic_0121ProteomicsWindowsLinuxMacPythonRustApache-2.0EmergingFree of chargehttp://edamontology.org/operation_1812Data parsinghttp://edamontology.org/data_2536Mass spectrometry data

http://edamontology.org/data_2536Mass spectrometry data

https://github.com/Sigilweaver/OpenTFRawRepositoryhttps://crates.io/crates/opentfrawSoftware packageRust cratehttps://pypi.org/project/opentfraw/Software packagePython packagehttps://sigilweaver.app/opentfraw/docsUser manualNathan Rileyhttps://orcid.org/0009-0004-1579-7312PersonDeveloperMaintainerHPO ExplorerInteractive browser for the complete Human Phenotype Ontology (~19,800 terms), with a graph-based term explorer and a clinical profile analyzer for phenotype similarity, differential diagnosis, and gene prioritization.https://hpoexplorer.comhpo_explorerbiotools:hpo_explorer0.1.0Web applicationhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3325Rare diseasesJavaScriptTypeScriptCC-BY-4.0EmergingFree of chargeOpen accesshttp://edamontology.org/operation_3559Ontology visualisationhttp://edamontology.org/data_3025Ontology concept identifier

http://edamontology.org/data_2353Ontology data

Browses the full HPO term graph via a synced tree and Cytoscape DAG view.http://edamontology.org/operation_3226Variant prioritisationhttp://edamontology.org/data_1081Genotype and phenotype annotation ID

http://edamontology.org/data_0920Genotype/phenotype report

https://hpoexplorer.com/aboutOtherhttps://hpoexplorer.com/abouthttps://hpoexplorer.com/articlesSoftware cataloguehttps://github.com/mchandrahasreddy/hpoexplorerRepositoryhttps://hpoexplorer.com/articlesGeneralguides and documentation.10.5281/zenodo.21178435Chandrahas Mallireddycontact@hpoexplorer.comhttps://hpoexplorer.comPersonDeveloperChandrahas Mallireddycontact@hpoexplorer.comhttps://hpoexplorer.comPersonPrimary contactBioCalculatorBioCalculator is a mobile toolkit for biology and laboratory calculations. It consolidates calculators and preparation guides for molecular biology, microbiology, virology, stock solutions, buffers, dilutions, unit conversions, and TCID50 endpoint dilution workflows for students and lab professionals.https://biocalculator.app/biocalculatorbiotools:biocalculatorMobile applicationiOSAndroidFreewareMatureFree of chargeOpen accesshttps://apps.apple.com/app/apple-store/id6498629520?pt=126896711&ct=website&mt=8Downloads pageiOS App Store listing for BioCalculator.https://play.google.com/store/apps/details?id=com.biocalculator.appDownloads pageGoogle Play listing for BioCalculator.SMILES-MapperSMILES-Mapper is a small web app that allows students to easily visualize how SMILES & InChI strings are created together with other mol-block file formats such as .mol and .sdf files.https://mol.tools/SMILES-Mapper/smiles-mapperbiotools:smiles-mapperWeb applicationhttp://edamontology.org/topic_3332Computational chemistryWindowsLinuxMacJavaScriptMITMatureFree of chargeOpen accesshttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/data_2301SMILES string

http://edamontology.org/data_2884Plothttp://edamontology.org/format_2331HTML

Produces an interactive visualization of how file formats are created from an input SMILES string.https://mol.tools/SMILES-Mapper/ServiceURL for web-app, where SMILES-Mapper can be used for free.https://github.com/KylleV/SMILES-MapperRepositorySMILES-Mapper source code GitHub repositoryhttps://github.com/KylleV/SMILES-MapperSource codeSource code download, application can be run by opening index.html1.0SQUARNASQUARNA is a tool for RNA secondary structure prediction. It can take a single RNA sequence or an alignment of sequences as input. SQUARNA handles pseudoknots and can predict alternative structures. SQUARNA allows structural restraints and chemical probing data as additional input and is available at https://github.com/febos/SQUARNA and https://larnal.imol.institute/.https://github.com/febos/SQUARNAsquarnabiotools:squarna3.22Command-line toolLibraryWeb applicationScripthttp://edamontology.org/topic_3307Computational biologyhttp://edamontology.org/topic_0077Nucleic acidshttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_0097Nucleic acid structure analysishttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_0099RNAhttp://edamontology.org/topic_0659Functional, regulatory and non-coding RNAhttp://edamontology.org/topic_3511Nucleic acid sites, features and motifsWindowsMacLinuxPythonApache-2.03D-BioInfo-Nucleic-AcidEmergingFree of chargeOpen accesshttp://edamontology.org/operation_0278RNA secondary structure predictionhttp://edamontology.org/data_3495RNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1961Stockholm formathttp://edamontology.org/data_1383Nucleic acid sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1961Stockholm formathttp://edamontology.org/data_0889Structural profile

http://edamontology.org/data_0880RNA secondary structurehttp://edamontology.org/format_2546FASTA-like

http://edamontology.org/data_1772Score

Input can be a single or several RNA sequences or an alignment of RNA sequences along with structural restraints and/or chemical probing data on base reactivitiesSQUARNA i=inputfile [OPTIONS]https://github.com/febos/SQUARNARepositoryGitHub repositoryhttps://pypi.org/project/SQUARNA/Software cataloguePyPi repository pagehttps://larnal.imol.institute/ServiceWeb serverhttps://doi.org/10.5281/zenodo.8292325Downloads page3.22https://pypi.org/project/SQUARNA/Software packagepip install SQUARNA3.22https://github.com/febos/SQUARNA/blob/main/README.mdUser manualhttps://pypi.org/project/SQUARNA/Installation instructionspip install SQUARNA10.64898/2026.06.30.735492Primary3.22biorxiv preprintEugene F Baulinefbaulin@gmail.comhttps://scholar.google.com/citations?user=sjfDaUwAAAAJ&hl=enhttps://orcid.org/0000-0003-4694-9783PersonDeveloperPrimary contactSupporthttps://imol.institute/leaders/baulin-group/miRcountsGenerates pre-miRNA and mature miRNA count tables from read alignments to pre-miRNA sequences and a gff file, both downloaded from mirBase. Produces also read coverage plots of pre-miRNAs.https://github.com/ARTbio/tools-artbio/tree/main/tools/mircountsmircountsbiotools:mircountsCommand-line toolhttp://edamontology.org/topic_3308TranscriptomicsShellPythonRMITGalaxy ToolsMatureFree of chargeOpen accesshttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/operation_0292Sequence alignmenthttps://github.com/ARTbio/tools-artbio/tree/main/tools/mircountsRepositoryhttp://artbio.frOtherClustVisWeb tool which allows users to upload their own data and easily create Principal Component Analysis (PCA) plots and heatmaps. Data can be uploaded as a file or by copy-pasteing it to the text box.http://biit.cs.ut.ee/clustvisclustvisbiotools:clustvis1RRID:SCR_017133rridWeb applicationhttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_2269Statistics and probabilityLinuxWindowsMacRGPL-3.0Elixir-EEFree of chargeToolsEstoniahttp://edamontology.org/operation_0313Gene expression clusteringhttp://edamontology.org/operation_2942Treemap visualisationhttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/operation_2939Principal component plottinghttp://edamontology.org/operation_0531Heat map generationhttp://edamontology.org/data_3111Processed microarray datahttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_3033Matrix formathttp://edamontology.org/data_3113Sample annotationhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_3033Matrix formathttp://edamontology.org/data_0928Gene expression profilehttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_3033Matrix format

http://edamontology.org/data_1636Heat maphttp://edamontology.org/format_3466EPShttp://edamontology.org/format_3604SVGhttp://edamontology.org/format_3508PDF

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3466EPShttp://edamontology.org/format_3604SVGhttp://edamontology.org/format_3508PDF

https://github.com/taunometsalu/ClustVisRepositoryA code repository in github.https://hub.docker.com/r/taunometsalu/clustvis/Container fileDocker imagehttps://biit.cs.ut.ee/clustvis/General10.1093/nar/gkv46825969447PMC4489295PrimaryELIXIR-EEInstituteProviderTauno Metsalutauno.metsalu@ut.eePersonPrimary contactbiit.support@ut.eePersonPrimary contactSequenceMatrixConcatenation software for the fast assembly of multi-gene datasets with character set and codon information.http://www.ggvaidya.com/taxondna/sequencematrixbiotools:sequencematrixCommand-line toolhttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_2229Cell biologyhttp://edamontology.org/topic_3053GeneticsMacLinuxWindowsJavaGPL-2.0Free of chargeOpen accesshttp://edamontology.org/operation_0310Sequence assemblyhttps://github.com/gaurav/taxondnaRepositoryhttp://taxondna.sourceforge.netOther10.1111/J.1096-0031.2010.00329.X34875773Rudolf Meiermeier@nus.edu.sgDavid J. LohmanGaurav VaidyaBIGR xnattoolsxnattools is a python package with a set of modules for performing various operations on data stored in XNAT servers. The main purpose is to provide one standardized platform for running operations on XNAT servers. The package currently contains four tools that use this platform: dicom to nifty conversion, thumbnail generation from dicom, DICOM header data collection, in bulk downloading of a project.https://gitlab.com/radiology/radiomics/xnattoolsbigr_xnattoolsbiotools:bigr_xnattoolsv1.0.0LibraryWindowsLinuxMacPythonApache-2.0EUCAIMEmergingFree of chargeOpen accesshttp://edamontology.org/operation_3096Data editinghttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/operation_3436Aggregationhttps://gitlab.com/radiology/radiomics/xnattoolsSource codev1.0.0xnatpyusesxnatusesMartijn PA Starmansm.starmans@erasmusmc.nlhttps://bigr.nl/member/martijn/https://orcid.org/0000-0001-5086-7153PersonPrimary contactErasmus MCInstituteProviderDeepTaxaDeepTaxa is a hybrid CNN-BERT deep learning framework for multi-rank taxonomic classification of 16S rRNA gene sequences. It predicts all seven Linnaean ranks from domain to species in a single forward pass and provides pre-trained checkpoints for full-length 16S and V3-V4 amplicons.https://github.com/systems-genomics-lab/deeptaxadeeptaxabiotools:deeptaxa1.0.1Command-line toolLibraryhttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_0637Taxonomyhttp://edamontology.org/topic_3697Microbial ecologyWindowsMacLinuxPythonMITEmergingFree of chargeOpen accesshttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1929FASTAhttps://github.com/systems-genomics-lab/deeptaxaRepositorySource codehttps://github.com/systems-genomics-lab/deeptaxa/issuesIssue trackerBug reports and feature requestshttps://huggingface.co/systems-genomics-lab/deeptaxaOtherPre-trained model checkpointshttps://pypi.org/project/deeptaxa-rrna/Software packagePyPI: pip install deeptaxa-rrnahttps://anaconda.org/bioconda/deeptaxa-rrnaSoftware packageBioconda: conda install -c bioconda deeptaxa-rrnahttps://systems-genomics-lab.github.io/deeptaxa/User manualTutorials: prediction, training, analysis, architecture10.1093/bioadv/vbag16642381921PMC13316423PrimaryAhmed Moustafaamoustafa@aucegypt.eduhttps://ahmedmoustafa.github.io/https://orcid.org/0000-0002-0111-3555PersonPrimary contactDeveloperMaintainerProfessor at the American University in CairoRana Salahrana_salah@aucegypt.eduhttps://orcid.org/0000-0003-2344-0714PersonDeveloperKhlood R. AbdElaalkhlood.ramadan@aucegypt.eduhttps://orcid.org/0009-0009-0054-9283PersonDeveloperLobna Ghonaimlobnaghonaim@aucegypt.eduhttps://orcid.org/0009-0003-6158-0029PersonDeveloperBabelHand-curated Snakemake pipelines to combine identifier cross-references from multiple sources across dozens of biomedical types, including anatomical entities, diseases and phenotypes, genes and proteins and many others.https://github.com/NCATSTranslator/Babelbabelbiotools:babel1.17PythonMITMatureFree of chargehttps://github.com/NCATSTranslator/Babel/issuesIssue trackerhttps://lists.renci.org/mailman3/lists/babel-tools.lists.renci.org/Mailing listhttps://github.com/NCATSTranslator/BabelRepositorynodenormusedBynameresusedBy10.48550/arXiv.2601.10008PreprintPanAbyssPanAbyss is a tool for exploring and visualizing pangenome graphs. It allows users to search for and display regions of a pangenome using coordinates on a reference individual or based on annotations. It also enables searching for regions associated with a selected set of individuals (for example, those linked to a phenotype), computing proximity trees, and retrieving sequences from a given region.https://github.com/Pange31/PanAbysspanabyssbiotools:panabyss1.4.0Web applicationhttp://edamontology.org/topic_0080Sequence analysisWindowsMacLinuxGPL-3.0EmergingFree of chargeOpen accessFrancehttps://github.com/Pange31/PanAbyss/wikiGeneralGrazianifabien.graziani@inrae.frhttps://orcid.org/0009-0002-3966-0906InstitutePrimary contactPathBench-MILPathBench-MIL is a comprehensive, flexible benchmarking/AutoML framework for multiple instance learning in histopathologyhttps://github.com/Sbrussee/PathBench-MILPathBench-MILbiotools:PathBench-MILhttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_3474Machine learningLinuxPythonShellGPL-3.0MatureFree of chargehttp://edamontology.org/operation_3659Regression analysishttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_2425Optimisation and refinementhttp://edamontology.org/operation_2990Classificationhttp://edamontology.org/data_2093Data referencehttp://edamontology.org/format_3752CSVhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3591TIFF

http://edamontology.org/data_3905Histogramhttp://edamontology.org/format_2331HTML

http://edamontology.org/data_2048Reporthttp://edamontology.org/format_2331HTML

10.48550/arXiv.2512.17517ab1lensBrowser-based tool for viewing, comparing, and inspecting Sanger sequencing ab1 / ABIF chromatogram files. Files are processed locally in the browser.https://fishka.bio/ab1lensab1lensbiotools:ab1lensWeb applicationhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_3673Whole genome sequencingFreewareMatureFree of chargeOpen accessRAMENRegional Association of Methylome variability with the Exposome and geNome (RAMEN) is an R package whose goal is to identify genome-wide Variable Methylated Loci (VML) from microarray DNA methylation data; then, using genomic and exposomic data, it can identify which model out of the following explains best the DNA methylation variability at each VML: genetic (G), environmental (E), additive (G+E) or interactive (GxE).https://ericknavarrod.github.io/RAMEN/ramenbiotools:ramenLibraryhttp://edamontology.org/topic_3173Epigenomicshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3391OmicsRGPL-3.0-or-laterMatureFree of chargeOpen accesshttp://edamontology.org/operation_3659Regression analysishttps://github.com/ErickNavarroD/RAMENRepositoryhttps://github.com/ErickNavarroD/RAMENSoftware package2https://ericknavarrod.github.io/RAMEN/articles/RAMEN.htmlQuick start guide10.1186/s13059-025-03864-441372765PMC12690895Primary1Erick Navarro-Delgadoerick.navarrodelgado@bcchr.cahttps://erick-navarrodelgado.netlify.apphttps://orcid.org/0000-0003-1040-3519PersonPrimary contactDanteDANTE (Da Amazing NucleoTide Exposer) is an algorithm for genotyping STR (short tandem repeat) alleles from NGS reads. It accounts for natural deviations from the expected sequence including repeat count variation, sequencing errors, ambiguous bases, and complex multi-motif loci. Provides evidence for expanded alleles too long to be captured by a single NGS read, as well as allelic point mutations, small insertions and deletions relevant for diagnostic evaluation. Includes both command-line and graphical user interface.https://github.com/dante-tr/dante-trdante-trbiotools:dante-trCommand-line toolDesktop applicationhttp://edamontology.org/topic_0199Genetic variationLinuxPythonRustCC-BY-NC-SA-4.0MatureFree of chargeOpen access (with restrictions)http://edamontology.org/operation_3196Genotypinghttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_2200FASTA-like (text)http://edamontology.org/format_2182FASTQ-like format (text)http://edamontology.org/format_2572BAM

http://edamontology.org/data_0920Genotype/phenotype reporthttp://edamontology.org/format_2331HTML

https://github.com/dante-tr/dante-trRepositoryhttps://github.com/dante-tr/dante-trSource codehttps://github.com/dante-tr/dante-tr/blob/main/README.mdGeneral10.1093/bioinformatics/bty79130203023PMC6166771PrimaryJaroslav Budišjaroslav.budis@geneton.skhttps://orcid.org/0000-0002-8667-6655PersonDeveloperPrimary contactAndrej Balážandrej.balaz@geneton.skhttps://orcid.org/0000-0002-3113-3389PersonDeveloperAgentic Target EvidenceMulti-agent system for drug-discovery gene target validation. LangGraph agents over an MCP data layer (~26 data sources, ~44 tools) score evidence across six independent lenses (genetics, biology, safety, clinical, commercial, regulatory) into a provenanced dossier. Configurable local/cloud LLM routing with full Langfuse/OTEL traceability.https://github.com/athril/agentic-target-evidenceagentic-target-evidencebiotools:agentic-target-evidenceCommand-line toolScriptWorkflowhttp://edamontology.org/topic_2815Human biologyhttp://edamontology.org/topic_3295Epigeneticshttp://edamontology.org/topic_3297Biotechnologyhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0218Natural language processinghttp://edamontology.org/topic_3303MedicineWindowsLinuxMacPythonApache-2.0EmergingFree of chargeOpen accesshttp://edamontology.org/operation_3436Aggregationhttp://edamontology.org/operation_3561Database comparisonhttp://edamontology.org/operation_2945Data analysishttp://edamontology.org/operation_3908Information retrievalhttps://github.com/athril/agentic-target-evidenceRepositoryBioExcel Building Blocks tutorials: Protein MD Setup tutorial through REST APIThis tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks (biobb) REST API. The particular example used is the Lysozyme protein (PDB code 1AKI).https://mmb.irbbarcelona.org/biobb/availability/tutorials/rest-apibioexcel_building_blocks_tutorials_protein_md_setup_tutorial_through_rest_apibiotools:bioexcel_building_blocks_tutorials_protein_md_setup_tutorial_through_rest_api1.0Web APIWorkflowhttp://edamontology.org/topic_0176Molecular dynamicshttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_2814Protein structure analysisLinuxMacWindowsPythonApache-2.0BioExcelEmergingFree of chargeOpen accessToolsInteroperabilitySpainUKhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_2476Molecular dynamicshttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_3872Topology datahttp://edamontology.org/format_3880GROMACS tophttp://edamontology.org/format_3883GROMACS itp

http://edamontology.org/data_3870Trajectory datahttp://edamontology.org/format_3910trr

https://mmb.irbbarcelona.org/biobb/availability/tutorials/rest-apiOtherTutorial in HTMLhttps://biobb-wf-md-setup-api.readthedocs.io/en/latest/index.htmlOtherTutorial in Read the Docshttps://github.com/bioexcel/biobb_wf_md_setup_apiOtherSource Code in GitHubhttps://github.com/bioexcel/biobb_wf_md_setup_apiSource codeMarch 2020https://biobb-wf-md-setup-api.readthedocs.io/en/latest/index.htmlOtherBioExcel Building Blocks API Tutorial documentationhttp://mmb.irbbarcelona.org/biobb-api/restAPI documentationBioExcel Building Blocks Swagger API documentationbiobbusesgromacsuses10.1038/s41597-019-0177-431506435PMC6736963OtherBetaBioExcel Building Blocks (BioBB)10.1371/journal.pcbi.101217338900779PMC11189206Usage1.0Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflowsGenís Bayarrigenis.bayarri@irbbarcelona.orgPersonDeveloperDocumentorPrimary contactMaintainerSupportBioExcel Building Blocks tutorials: ABC MD SetupThis BioExcel Building Blocks library (BioBB) workflow provides a pipeline to setup DNA structures for the Ascona B-DNA Consortium (ABC) members. It follows the work started with the NAFlex tool to offer a single, reproducible pipeline for structure preparation, ensuring reproducibility and coherence between all the members of the consortium.https://mmb.irbbarcelona.org/biobb/workflows/#abc-md-setupbioexcel_building_blocks_tutorials_abc_md_setupbiotools:bioexcel_building_blocks_tutorials_abc_md_setup1.0Workflowhttp://edamontology.org/topic_0176Molecular dynamicshttp://edamontology.org/topic_0097Nucleic acid structure analysisMacWindowsLinuxPythonApache-2.0BioExcelEmergingFree of chargeOpen accessInteroperabilityTools3D-BioInfoSpainUKhttp://edamontology.org/operation_2476Molecular dynamicshttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_3872Topology datahttp://edamontology.org/format_3881AMBER top

http://edamontology.org/data_3870Trajectory datahttp://edamontology.org/format_3878mdcrdhttp://edamontology.org/format_3650NetCDF

https://biobb-wf-amber-md-setup.readthedocs.io/en/latest/abcsetup_tutorial.htmlOtherTutorial in Read the Docshttps://github.com/bioexcel/biobb_wf_amber_md_setupRepositorySource code in GitHubhttps://github.com/bioexcel/biobb_wf_amber_md_setupSource codehttps://biobb-wf-amber-md-setup.readthedocs.io/en/latest/abcsetup_tutorial.htmlOtherWorkflow Documentation in Read the Docsbiobbusesambertoolsuses10.1038/s41597-019-0177-431506435PMC6736963OtherBioExcel Building Blocks (BioBB)10.1371/journal.pcbi.101217338900779PMC11189206Usage1.0Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflowsBioExcel Center of Excellence for Computational Biomolecular Researchhttps://www.bioexcel.euConsortiumProviderAdam 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/en/research/genis-bayarrihttps://orcid.org/0000-0003-0513-0288PersonDeveloperDocumentorMaintainerBioExcel Building Blocks tutorials: Protein-Ligand Complex MD Setup (Amber Version)This tutorial aims to illustrate the process of setting up a simulation system containing a protein in complex with a ligand, step by step, using the BioExcel Building Blocks library (biobb) wrapping the AmberTools utility from the AMBER package. The particular example used is the T4 lysozyme protein (PDB code 3HTB) with two residue modifications L99A/M102Q complexed with the small ligand 2-propylphenol (3-letter code JZ4).https://mmb.irbbarcelona.org/biobb/workflows/#amber-protein-ligand-complex-md-setupbioexcel_building_blocks_tutorials_protein-ligand_complex_md_setup_amber_versionbiotools:bioexcel_building_blocks_tutorials_protein-ligand_complex_md_setup_amber_version1.0Workflowhttp://edamontology.org/topic_0176Molecular dynamicshttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_2814Protein structure analysisMacWindowsLinuxPythonApache-2.0BioExcelEmergingFree of chargeOpen accessInteroperabilityTools3D-BioInfoSpainUKhttp://edamontology.org/operation_2476Molecular dynamicshttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_3872Topology datahttp://edamontology.org/format_3881AMBER top

http://edamontology.org/data_3870Trajectory datahttp://edamontology.org/format_3878mdcrdhttp://edamontology.org/format_3650NetCDF

https://biobb-wf-amber-md-setup.readthedocs.io/en/latest/mdsetup_lig_tutorial.htmlOtherTutorial in Read the Docshttps://github.com/bioexcel/biobb_wf_amber_md_setupRepositorySource Codehttps://github.com/bioexcel/biobb_wf_amber_md_setupSource codehttps://biobb-wf-amber-md-setup.readthedocs.io/en/latest/mdsetup_lig_tutorial.htmlOtherRead the Docs workflow documentationbiobbusesambertoolsuses10.1038/s41597-019-0177-431506435PMC6736963OtherBioExcel Building Blocks (BioBB)10.1371/journal.pcbi.101217338900779PMC11189206Usage1.0Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflowsBioExcel Center of Excellence for Computational Biomolecular Researchhttps://www.bioexcel.euConsortiumProviderAdam 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/en/research/genis-bayarrihttps://orcid.org/0000-0003-0513-0288PersonDeveloperDocumentorMaintainerBioExcel Building Blocks tutorials: Structural DNA helical parameters from MD trajectoryThis tutorial aims to illustrate the process of extracting structural and dynamical properties from a DNA MD trajectory helical parameters, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Drew Dickerson Dodecamer sequence -CGCGAATTCGCG- (PDB code 1BNA). The trajectory used is a 500ns-long MD simulation taken from the BigNASim database (NAFlex_DDD_II entry).https://mmb.irbbarcelona.org/biobb/workflows/#structural-dna-helical-parametersbioexcel_building_blocks_tutorials_structural_dna_helical_parameters_from_md_trajectorybiotools:bioexcel_building_blocks_tutorials_structural_dna_helical_parameters_from_md_trajectory1.0Workflowhttp://edamontology.org/topic_0097Nucleic acid structure analysisWindowsLinuxMacPythonApache-2.0BioExcelEmergingFree of chargeOpen accessInteroperabilityTools3D-BioInfoSpainUKhttp://edamontology.org/operation_0262Nucleic acid property calculationhttp://edamontology.org/operation_2481Nucleic acid structure analysishttp://edamontology.org/data_3870Trajectory datahttp://edamontology.org/format_3650NetCDFhttp://edamontology.org/format_3878mdcrd

http://edamontology.org/data_3905Histogramhttp://edamontology.org/format_1637dat

http://edamontology.org/data_0912Nucleic acid propertyhttp://edamontology.org/format_1637dat

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3603PNG

https://biobb-wf-dna-helparms.readthedocs.io/en/latest/tutorial.htmlOtherTutorial in Read the Docshttps://github.com/bioexcel/biobb_wf_dna_helparmsRepositorySource code in GitHubhttps://github.com/bioexcel/biobb_wf_dna_helparmsSource codehttps://biobb-wf-dna-helparms.readthedocs.io/en/latest/tutorial.htmlOtherWorkflow documentation in Read the Docsbiobbusescurvesuses10.1038/s41597-019-0177-431506435PMC6736963OtherBioExcel Building Blocks (BioBB)10.1371/journal.pcbi.101217338900779PMC11189206Usage1.0Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflowsBioExcel Center of Excellence for Computational Biomolecular Researchhttps://www.bioexcel.euConsortiumProviderAdam 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/en/research/genis-bayarrihttps://orcid.org/0000-0003-0513-0288PersonDeveloperDocumentorMaintainerBioExcel Building Blocks tutorials: AMBER Constant pH MD setupThis tutorial aims to illustrate the process of setting up a simulation system to run constant pH Molecular Dynamics simulations with AMBER, step by step, using the BioExcel Building Blocks library (biobb) wrapping the AmberTools utility from the AMBER package. The particular example used is the Bovine Pancreatic Trypsin Inhibitor (BPTI) protein (PDB code 6PTI).https://mmb.irbbarcelona.org/biobb/workflows/#amber-constant-ph-md-setupbioexcel_building_blocks_tutorials_amber_constant_ph_md_setupbiotools:bioexcel_building_blocks_tutorials_amber_constant_ph_md_setup1.0Workflowhttp://edamontology.org/topic_0176Molecular dynamicshttp://edamontology.org/topic_2814Protein structure analysisMacLinuxWindowsPythonApache-2.0BioExcelEmergingFree of chargeOpen accessInteroperabilityTools3D-BioInfoSpainUKhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_2476Molecular dynamicshttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_3872Topology datahttp://edamontology.org/format_3881AMBER top

http://edamontology.org/data_3870Trajectory datahttp://edamontology.org/format_3878mdcrdhttp://edamontology.org/format_3650NetCDF

https://biobb-wf-amber-md-setup.readthedocs.io/en/latest/mdsetup_ph_tutorial.htmlOtherTutorial in Read the Docshttps://github.com/bioexcel/biobb_wf_amber_md_setupRepositorySource Code in GitHubhttps://github.com/bioexcel/biobb_wf_amber_md_setupSource codehttps://biobb-wf-amber-md-setup.readthedocs.io/en/latest/mdsetup_ph_tutorial.htmlOtherRead the Docs workflow documentationbiobbusesambertoolsuses10.1038/s41597-019-0177-431506435PMC6736963OtherBioExcel Building Blocks (BioBB)10.1371/journal.pcbi.101217338900779PMC11189206Usage1.0Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflowsBioExcel Center of Excellence for Computational Biomolecular Researchhttps://www.bioexcel.euConsortiumProviderAdam 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/en/research/genis-bayarrihttps://orcid.org/0000-0003-0513-0288PersonDeveloperDocumentorMaintainerBioExcel Building Blocks tutorials: Protein MD Setup (Amber Version)This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb) wrapping the AmberTools utility from the AMBER package. The particular example used is the Lysozyme protein (PDB code 1AKI).https://mmb.irbbarcelona.org/biobb/workflows/#amber-protein-md-setupbioexcel_building_blocks_tutorials_protein_md_setup_amber_versionbiotools:bioexcel_building_blocks_tutorials_protein_md_setup_amber_version1.0Workflowhttp://edamontology.org/topic_0176Molecular dynamicshttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0092Data visualisationWindowsLinuxMacPythonApache-2.0BioExcelEmergingFree of chargeOpen accessToolsInteroperabilitySpainhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/operation_2476Molecular dynamicshttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_3890Trajectory visualizationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_3872Topology datahttp://edamontology.org/format_3881AMBER top

http://edamontology.org/data_3870Trajectory datahttp://edamontology.org/format_3650NetCDFhttp://edamontology.org/format_3878mdcrd

https://biobb-wf-amber-md-setup.readthedocs.io/en/latest/mdsetup_tutorial.htmlOtherTutorial in Read the Docshttps://github.com/bioexcel/biobb_wf_amber_md_setupRepositorySource Code in GitHubhttps://github.com/bioexcel/biobb_wf_amber_md_setupSource codehttps://biobb-wf-amber-md-setup.readthedocs.io/en/latest/mdsetup_tutorial.htmlOtherRead the Docs Workflow Documentationambertoolsusesbiobbuses10.1038/s41597-019-0177-431506435PMC6736963OtherBioExcel Building Blocks (BioBB)10.1371/journal.pcbi.101217338900779PMC11189206Usage1.0Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflowsBioExcel Center of Excellence for Computational Biomolecular Researchhttps://www.bioexcel.euConsortiumProviderAdam 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/en/research/genis-bayarrihttps://orcid.org/0000-0003-0513-0288PersonDeveloperDocumentorMaintainerBioExcel 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/#macromolecular-coarse-grained-flexibilitybioexcel_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 visualisationWindowsLinuxMacPythonApache-2.0BioExcelEmergingFree of chargeOpen accessToolsInteroperabilitySpainUKhttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/operation_0474Protein structure predictionhttp://edamontology.org/operation_2939Principal component visualisationhttp://edamontology.org/operation_0250Protein property calculationhttp://edamontology.org/operation_3890Trajectory visualizationhttp://edamontology.org/operation_3891Essential dynamicshttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_3870Trajectory datahttp://edamontology.org/format_3874PCAziphttp://edamontology.org/format_3464JSONhttp://edamontology.org/format_1476PDB

https://mmb.irbbarcelona.org/biobb/workflows#macromolecular-coarse-grained-flexibilityOtherMain web site (BioBB Workflows)https://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://biobb-wf-flexserv.readthedocs.io/en/latest/index.htmlOtherRead The Docs workflow documentationbiobbusesflexservusesnglviewusespcasuiteuses10.1038/s41597-019-0177-431506435PMC6736963OtherBioExcel Building Blocks (BioBB)10.1371/journal.pcbi.101217338900779PMC11189206Usage1.0Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflowsAdam 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-Ligand Complex MD Setup (Gromacs Version)This tutorial aims to illustrate the process of setting up a simulation system containing a protein in complex with a ligand, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the T4 lysozyme L99A/M102Q protein (PDB code 3HTB), in complex with the 2-propylphenol small molecule (3-letter Code JZ4).http://mmb.irbbarcelona.org/biobb/workflows/#gromacs-protein-ligand-complex-md-setupbioexcel_building_blocks_tutorials_protein-ligand_complex_md_setupbiotools:bioexcel_building_blocks_tutorials_protein-ligand_complex_md_setup1.0Workflowhttp://edamontology.org/topic_0176Molecular dynamicshttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0128Protein interactionsMacLinuxWindowsPythonApache-2.0BioExcelEmergingFree of chargeOpen accessToolsInteroperabilitySpainUKhttp://edamontology.org/operation_2476Molecular dynamicshttp://edamontology.org/operation_2480Structure analysishttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDB

http://edamontology.org/data_3872Topology datahttp://edamontology.org/format_3880GROMACS tophttp://edamontology.org/format_3883GROMACS itp

http://edamontology.org/data_3870Trajectory datahttp://edamontology.org/format_3910trr

https://biobb-wf-protein-complex-md-setup.readthedocs.io/en/latest/index.htmlOtherTutorial in Read the Docshttps://github.com/bioexcel/biobb_wf_protein-complex_md_setupRepositorySource code in GitHubhttps://github.com/bioexcel/biobb_wf_protein-complex_md_setupSource codeMarch 2020https://biobb-wf-protein-complex-md-setup.readthedocs.io/en/latest/index.htmlOtherRead the Docs workflow documentationbiobbusesgromacsusesopen_babelusesacpypeuses10.1038/s41597-019-0177-431506435PMC6736963OtherBetaBioExcel Building Blocks (BioBB)10.1371/journal.pcbi.101217338900779PMC11189206Usage1.0Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflowsGenís Bayarrigenis.bayarri@irbbarcelona.orghttps://www.irbbarcelona.org/en/profile/genis-bayarriPersonDeveloperDocumentorMaintainerAdam Hospitaladam.hospital@irbbarcelona.orghttps://www.irbbarcelona.org/en/profile/adam-hospitalhttps://orcid.org/0000-0002-8291-8071PersonPrimary contactPau Andriopau.andrio@bsc.eshttps://www.bsc.es/andrio-balado-pauPersonDeveloperDocumentorMaintainerSupportBioExcel Centre of Excellencehttps://bioexcel.eu/ConsortiumProviderBioExcel Building Blocks tutorials: Mutation Free Energy CalculationsThis tutorial aims to illustrate how to compute a fast-growth mutation free energy calculation, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Staphylococcal nuclease protein (PDB code 1STN), a small, minimal protein, appropriate for a short tutorial.http://mmb.irbbarcelona.org/biobb/workflows/#mutation-free-energy-calculationsbioexcel_building_blocks_tutorials_mutation_free_energy_calculationsbiotools:bioexcel_building_blocks_tutorials_mutation_free_energy_calculations1.0Workflowhttp://edamontology.org/topic_0176Molecular dynamicshttp://edamontology.org/topic_3120Protein variantsMacLinuxWindowsPythonApache-2.0BioExcelEmergingFree of chargeOpen accessToolsInteroperabilitySpainUKhttp://edamontology.org/operation_0331Variant effect predictionhttp://edamontology.org/operation_2476Molecular dynamicshttp://edamontology.org/operation_2406Protein structure analysishttp://edamontology.org/data_3870Trajectory datahttp://edamontology.org/format_3875XTChttp://edamontology.org/data_3872Topology datahttp://edamontology.org/format_3880GROMACS tophttp://edamontology.org/format_3883GROMACS itp

http://edamontology.org/data_3779Annotated texthttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_3905Histogramhttp://edamontology.org/format_3603PNG

http://edamontology.org/data_3870Trajectory datahttp://edamontology.org/format_3910trr

https://biobb-wf-pmx-tutorial.readthedocs.io/en/latest/index.htmlOtherTutorial in Read the Docshttps://github.com/bioexcel/biobb_wf_pmx_tutorialOtherSource code in GitHubhttps://github.com/bioexcel/biobb_wf_pmx_tutorialSource codeMarch 2020https://biobb-wf-pmx-tutorial.readthedocs.io/en/latest/index.htmlOtherRead the Docs workflow documentationbiobbusesgromacsusespmxuses10.1038/s41597-019-0177-431506435PMC6736963OtherBetaBioExcel Building Blocks (BioBB)10.1371/journal.pcbi.101217338900779PMC11189206Usage1.0Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflowsGenís Bayarrigenis.bayarri@irbbarcelona.orghttps://www.irbbarcelona.org/en/profile/genis-bayarriPersonDeveloperDocumentorMaintainerAdam Hospitaladam.hospital@irbbarcelona.orghttps://www.irbbarcelona.org/en/profile/adam-hospitalhttps://orcid.org/0000-0002-8291-8071PersonPrimary contactPau Andriopau.andrio@bsc.eshttps://www.bsc.es/andrio-balado-pauPersonDeveloperDocumentorMaintainerSupportBioExcel Centre of Excellencehttps://bioexcel.eu/ConsortiumProviderBioExcel Building Blocks tutorials: Automatic Ligand parameterizationThis tutorial aims to illustrate the process of ligand parameterization for a small molecule, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Ibuprofen small compound (3-letter code IBP, Drugbank code DB01050), a non-steroidal anti-inflammatory drug (NSAID) derived from propionic acid.http://mmb.irbbarcelona.org/biobb/workflows/#automatic-ligand-parameterizationbioexcel_building_blocks_tutorials_automatic_ligand_parameterizationbiotools:bioexcel_building_blocks_tutorials_automatic_ligand_parameterization1.0Workflowhttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_0176Molecular dynamicsLinuxMacWindowsPythonApache-2.0BioExcelEmergingFree of chargeOpen accessToolsInteroperabilitySpainUKhttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/data_1463Small molecule structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_3872Topology datahttp://edamontology.org/format_3880GROMACS tophttp://edamontology.org/format_3883GROMACS itp

https://biobb-wf-ligand-parameterization.readthedocs.io/en/latest/index.htmlOtherTutorial in Read the Docshttps://github.com/bioexcel/biobb_wf_ligand_parameterizationRepositorySource Code in GitHubhttps://github.com/bioexcel/biobb_wf_ligand_parameterizationSource codeMarch 2020https://biobb-wf-ligand-parameterization.readthedocs.io/en/latest/index.htmlOtherRead the Docs workflow documentationbiobbusesacpypeusesopen_babeluses10.1038/s41597-019-0177-431506435PMC6736963OtherBeta10.1371/journal.pcbi.101217338900779PMC11189206Usage1.0Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflowsGenís Bayarrigenis.bayarri@irbbarcelona.orghttps://www.irbbarcelona.org/en/profile/genis-bayarriPersonDeveloperDocumentorMaintainerAdam Hospitaladam.hospital@irbbarcelona.orghttps://www.irbbarcelona.org/en/profile/adam-hospitalhttps://orcid.org/0000-0002-8291-8071PersonPrimary contactPau Andriopau.andrio@bsc.eshttps://www.bsc.es/andrio-balado-pauPersonDeveloperDocumentorMaintainerSupportBioExcel Centre of Excellencehttps://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/#protein-ligand-docking-(fpocket)bioexcel_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 visualisationMacWindowsLinuxPythonApache-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_3814SDFhttp://edamontology.org/format_1476PDB

http://edamontology.org/data_1461Protein-ligand complexhttp://edamontology.org/format_1476PDB

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://biobb-wf-virtual-screening.readthedocs.io/en/latest/ebi_api_tutorial.htmlOtherTutorial in Read the Docs (PDBe REST-API 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/s41597-019-0177-431506435PMC6736963Other10.1371/journal.pcbi.101217338900779PMC11189206Usage1.0Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflowsBioExcel 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 contactBioExcel Building Blocks tutorials: Molecular Structure CheckingThis tutorial aims to illustrate the process of checking a molecular structure before using it as an input for a Molecular Dynamics simulation, step by step, using the BioExcel Building Blocks (biobb).https://mmb.irbbarcelona.org/biobb/workflows/#molecular-structure-checkingbioexcel_building_blocks_tutorials_molecular_structure_checkingbiotools:bioexcel_building_blocks_tutorials_molecular_structure_checking1.0Workflowhttp://edamontology.org/topic_3892Biomolecular simulationhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_0092Data visualisationMacLinuxWindowsPythonApache-2.0BioExcelEmergingFree of chargeOpen accessToolsInteroperabilitySpainUKhttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_2048Reporthttp://edamontology.org/format_3464JSON

https://biobb-wf-structure-checking.readthedocs.io/en/latest/index.htmlOtherTutorial in Read the Docshttps://github.com/bioexcel/biobb_wf_structure_checkingRepositorySource Code in GitHubhttps://github.com/bioexcel/biobb_wf_structure_checkingSource codeSource Code in GitHubhttps://biobb-wf-structure-checking.readthedocs.io/en/latest/index.htmlOtherDocumentation in Read the Docsbiobbuses10.1038/s41597-019-0177-431506435PMC6736963OtherBioExcel Building Blocks (BioBB)10.1371/journal.pcbi.101217338900779PMC11189206Usage1.0Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflowsAdam 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/0000-0003-0513-0288PersonContributorDeveloperMaintainerJosep Lluís Gelpígelpi@ub.eduhttps://www.bsc.es/es/gelpi-josephttps://orcid.org/0000-0002-0566-7723PersonDeveloperMaintainerSupportBioExcel 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/#protein-conformational-transitions-calculationsbioexcel_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 visualisationWindowsLinuxMacPythonApache-2.0BioExcelEmergingFree of chargeOpen accessToolsInteroperabilitySpainUKhttp://edamontology.org/operation_2476Molecular dynamicshttp://edamontology.org/operation_2480Structure analysishttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_3890Trajectory visualizationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_3870Trajectory datahttp://edamontology.org/format_3878mdcrdhttp://edamontology.org/format_3874PCAzip

https://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://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: 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/#molecular-interaction-potentialsbioexcel_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 visualisationLinuxMacWindowsPythonApache-2.0BioExcelEmergingFree of chargeOpen accessToolsInteroperabilitySpainUKhttp://edamontology.org/operation_0248Residue interaction calculationhttp://edamontology.org/operation_0272Residue contact predictionhttp://edamontology.org/operation_2480Structure analysishttp://edamontology.org/operation_2949Protein-protein interaction analysishttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/data_3870Trajectory datahttp://edamontology.org/format_1476PDB

http://edamontology.org/data_0906Protein interaction datahttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_2330Textual format

https://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://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)10.1371/journal.pcbi.101217338900779PMC11189206Usage1.0Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflowsAdam 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 MD Setup (Gromacs Version)This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI).http://mmb.irbbarcelona.org/biobb/workflows/#gromacs-protein-md-setupbioexcel_building_blocks_tutorials_protein_md_setupbiotools:bioexcel_building_blocks_tutorials_protein_md_setup1.0Workflowhttp://edamontology.org/topic_0176Molecular dynamicshttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_2814Protein structure analysisMacWindowsLinuxPythonApache-2.0BioExcelEmergingFree of chargeOpen accessInteroperabilityToolsSpainUKhttp://edamontology.org/operation_2476Molecular dynamicshttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_3872Topology datahttp://edamontology.org/format_3883GROMACS itphttp://edamontology.org/format_3880GROMACS top

http://edamontology.org/data_3870Trajectory datahttp://edamontology.org/format_3910trr

https://biobb-wf-md-setup.readthedocs.io/en/latest/index.htmlOtherTutorial in Read the Docshttps://github.com/bioexcel/biobb_wf_md_setupRepositorySource code in GitHubhttps://github.com/bioexcel/biobb_wf_md_setupSource codehttps://biobb-wf-md-setup.readthedocs.io/en/latest/?badge=latestOtherRead the Docs workflow documentationbiobbusesgromacsuses10.1038/s41597-019-0177-431506435PMC6736963OtherBetaBioExcel Building Blocks (BioBB)10.1371/journal.pcbi.101217338900779PMC11189206Usage1.0Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflowsGenís Bayarrigenis.bayarri@irbbarcelona.orghttps://www.irbbarcelona.org/en/profile/genis-bayarriPersonDeveloperDocumentorMaintainerAdam Hospitaladam.hospital@irbbarcelona.orghttps://www.irbbarcelona.org/en/profile/adam-hospitalhttps://orcid.org/0000-0002-8291-8071PersonPrimary contactBioExcel Centre of Excellencehttps://bioexcel.eu/ConsortiumProviderPau Andriopau.andrio@bsc.eshttps://www.bsc.es/andrio-balado-pauPersonDeveloperDocumentorSupportBioExcel Building Blocks tutorials: Protein-Protein DockingThis tutorial aims to illustrate the process of protein-protein docking, step by step, using HADDOCK3 and the BioExcel Building Blocks (biobb)https://mmb.irbbarcelona.org/biobb/workflows/#protein-protein-dockingbioexcel_building_blocks_tutorials_protein-protein_dockingbiotools:bioexcel_building_blocks_tutorials_protein-protein_docking1.0Workflowhttp://edamontology.org/topic_2275Molecular modellingWindowsLinuxMacPythonApache-2.0BioExcelEmergingFree of chargeOpen accessInteroperabilityTools3D-BioInfoSpainhttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/operation_0478Molecular dockinghttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDB

http://edamontology.org/data_2884Plot

https://github.com/bioexcel/biobb_wf_haddockRepositorySource Code in GitHubhttps://github.com/bioexcel/biobb_wf_haddockSource codeSource Code1.0https://github.com/bioexcel/biobb_workflows/tree/main/biobb_wf_haddock/dockerContainer fileDocker Container1.0https://github.com/bioexcel/biobb_wf_haddockGeneralInstallation instructionsWorkflow Documentationbiobbuseshaddock3usesnglviewuses10.1038/s41597-019-0177-431506435PMC6736963Primary1.0BioExcel Building Blocks (BioBB)10.1371/journal.pcbi.101217338900779PMC11189206Usage1.0Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflowsAdam Hospitaladam.hospital@irbbarcelona.orghttps://www.irbbarcelona.org/en/research/adam-hospitalhttps://orcid.org/0000-0002-8291-8071PersonPrimary contactGenís Bayarrigenis.bayarri@irbbarcelona.orghttps://www.irbbarcelona.org/en/research/genis-bayarrihttps://orcid.org/0000-0003-0513-0288PersonMaintainerRubén Chavesruben.chaves@irbbarcelona.orghttps://www.irbbarcelona.org/en/research/ruben-chaveshttps://orcid.org/0009-0005-6656-2991PersonDeveloperDocumentorMaintainerBioExcel Building Blocks tutorials: Protein-Membrane MD analysisThis tutorial aims to illustrate the process of analyzing a membrane molecular dynamics (MD) simulation, step by step, using the BioExcel Building Blocks (biobb)https://mmb.irbbarcelona.org/biobb/workflows/#protein-membrane-md-analysisbioexcel_building_blocks_tutorials_protein-membrane_md_analysisbiotools:bioexcel_building_blocks_tutorials_protein-membrane_md_analysis1.0Workflowhttp://edamontology.org/topic_3892Biomolecular simulationhttp://edamontology.org/topic_0820Membrane and lipoproteinshttp://edamontology.org/topic_2814Protein structure analysisMacWindowsLinuxPythonApache-2.0BioExcelEmergingFree of chargeOpen accessInteroperabilityTools3D-BioInfoSpainhttp://edamontology.org/operation_2241Transmembrane protein visualisationhttp://edamontology.org/operation_0250Protein property calculationhttp://edamontology.org/operation_2476Molecular dynamicshttp://edamontology.org/operation_0270Transmembrane protein analysishttp://edamontology.org/data_3872Topology datahttp://edamontology.org/format_3881AMBER tophttp://edamontology.org/format_3882PSFhttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3880GROMACS tophttp://edamontology.org/data_3870Trajectory datahttp://edamontology.org/format_3875XTChttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3650NetCDF

http://edamontology.org/data_0897Protein property

http://edamontology.org/data_2884Plot

http://edamontology.org/data_1277Protein features

https://github.com/bioexcel/biobb_wf_memRepositorySource Code in GitHubhttps://github.com/bioexcel/biobb_wf_memSource codeSource Code1.0https://github.com/bioexcel/biobb_workflows/tree/main/biobb_wf_mem/dockerContainer fileDocker Container1.0https://github.com/bioexcel/biobb_workflows/tree/main/biobb_wf_mem/cwlTool wrapper (CWL)CWL Specification1.0https://github.com/bioexcel/biobb_wf_memGeneralInstallation instructionsWorkflow Documentationbiobbusesnglviewusesmdanalysisuses10.1038/s41597-019-0177-431506435PMC6736963Primary1.0BioExcel Building Blocks (BioBB)10.1371/journal.pcbi.101217338900779PMC11189206Usage1.0Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflowsAdam Hospitaladam.hospital@irbbarcelona.orghttps://www.irbbarcelona.org/en/research/adam-hospitalhttps://orcid.org/0000-0002-8291-8071PersonPrimary contactGenís Bayarrigenis.bayarri@irbbarcelona.orghttps://www.irbbarcelona.org/en/research/genis-bayarrihttps://orcid.org/0000-0003-0513-0288PersonMaintainerRubén Chavesruben.chaves@irbbarcelona.orghttps://www.irbbarcelona.org/en/research/ruben-chaveshttps://orcid.org/0009-0005-6656-2991PersonDeveloperDocumentorMaintainerBioExcel Building Blocks tutorials: AutoEncoders for Anomaly DetectionThis tutorial involves the use of a multilayer AutoEncoder (AE) for feature extraction and pattern recognition by analyzing Molecular Dynamic Simulations, step by step, using the BioExcel Building Blocks library (biobb)https://mmb.irbbarcelona.org/biobb/workflows/#autoencoders-for-anomaly-detectionbioexcel_building_blocks_tutorials_autoencoders_for_anomaly_detectionbiotools:bioexcel_building_blocks_tutorials_autoencoders_for_anomaly_detection1.0Workflowhttp://edamontology.org/topic_3892Biomolecular simulationhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_3474Machine learningMacWindowsLinuxPythonApache-2.0BioExcelEmergingFree of chargeOpen accessInteroperabilityTools3D-BioInfoSpainhttp://edamontology.org/operation_3890Trajectory visualizationhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/operation_0250Protein property calculationhttp://edamontology.org/operation_2476Molecular dynamicshttp://edamontology.org/data_3870Trajectory datahttp://edamontology.org/data_3872Topology data

http://edamontology.org/data_3842Molecular simulation datahttp://edamontology.org/format_3875XTChttp://edamontology.org/format_1476PDB

http://edamontology.org/data_2884Plothttp://edamontology.org/format_2330Textual format

https://github.com/bioexcel/biobb_wf_autoencoderRepositorySource Code in GitHubhttps://github.com/bioexcel/biobb_wf_autoencoderSource codeSource Code1.0https://github.com/bioexcel/biobb_workflows/tree/main/biobb_wf_autoencoder/dockerContainer fileDocker Container1.0https://github.com/bioexcel/biobb_workflows/tree/main/biobb_wf_autoencoder/cwlTool wrapper (CWL)CWL specification1.0https://github.com/bioexcel/biobb_wf_autoencoderGeneralInstallation instructionsWorkflow Documentationbiobbusesnglviewusespytorchusesmdtrajusesmatplotlibusesnumpyuses10.1038/s41597-019-0177-431506435PMC6736963Primary1.0BioExcel Building Blocks (BioBB)10.1371/journal.pcbi.101217338900779PMC111892061.0Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflowsAdam Hospitaladam.hospital@irbbarcelona.orghttps://www.irbbarcelona.org/en/research/adam-hospitalhttps://orcid.org/0000-0002-8291-8071PersonPrimary contactGenís Bayarrigenis.bayarri@irbbarcelona.orghttps://www.irbbarcelona.org/en/research/genis-bayarrihttps://orcid.org/0000-0003-0513-0288PersonMaintainerDeveloperPieter Zanderspieter.zanders@bsc.eshttps://www.bsc.es/zanders-marxuach-pieterhttps://orcid.org/0009-0000-3463-6806PersonDeveloperDocumentorMaintainermetagWGSmetagWGS is a workflow dedicated to the analysis of metagenomic data. It allows assembly, taxonomic annotation, and functional annotation of predicted genes. Since release 2.3, binning step with the possibility of cross-alignment is included. It has been developed in collaboration with several CATI BIOS4biol agents. Funded by Antiselfish Project (Labex Ecofect), ExpoMicoPig project (France Futur elevage) and SeqOccIn project (CPER - Occitanie Toulouse / FEDER), ATB_Biofilm funded by PNREST Anses, France genomique (ANR-10-INBS-09-08) and Resalab Ouest.https://forge.inrae.fr/genotoul-bioinfo/metagwgsmetagwgsbiotools:metagwgs2.32.5.02.6.0Workflowhttp://edamontology.org/topic_3174MetagenomicsLinuxPythonGPL-3.0MatureFree of chargeOpen accessFrancehttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQ

http://edamontology.org/data_3028Taxonomyhttp://edamontology.org/format_1915Format

http://edamontology.org/operation_3672Gene functional annotationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_3917Count matrixhttp://edamontology.org/format_1915Format

http://edamontology.org/operation_0524De-novo assemblyhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1930FASTQ

http://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTA

https://forge.inrae.fr/genotoul-bioinfo/metagwgsRepositorySee documentation, source code and functionnal test documentation.https://forge.inrae.fr/genotoul-bioinfo/metagwgs-test-datasetsTest dataFunctional tests data and scripthttps://genotoul-bioinfo.pages-forge.inrae.fr/metagwgs/master/index.htmlUser manualWe provide up to date installation documentation, usage documentation, output description and functionnal test datasets and procedure.10.1101/2024.09.13.612854PreprintmetagWGS, a comprehensive workflow to analyze metagenomic data using Illumina or PacBio HiFi reads Jean Mainguy, Maïna Vienne, Joanna Fourquet, Vincent Darbot, Céline Noirot, Adrien Castinel, Sylvie Combes, Christine Gaspin, Denis Milan, Cécile Donnadieu, Carole Iampietro, Olivier Bouchez, Géraldine Pascal, Claire Hoede bioRxiv 2024.09.13.612854Claire Hoedeclaire.hoede@inrae.frhttps://orcid.org/0000-0001-5054-7731PersonPrimary contactGenoToul bioinformatics facilityhttp://bioinfo.genotoul.fr/DivisionProviderURGIURGI (Unit Resources Genomics-Info) is a bioinformatics facility who support various research activities on plants of agronomic and forestry interest for INRAE. The platform has federated with 3 other INRAE ​​bioinformatics platforms to form the BioinfOmics research infrastructure. It is part of the French Institute of Bioinformatics which is the French node of the European infrastructure ELIXIR . URGI is part of the Saclay Plant Science network and of the Graduate School Biosphera . URGI is labeled by GIS IBiSA and is ISO-9001 certified.https://urgi.versailles.inrae.fr/urgibiotools:urgiBioinformatics portalhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0780Plant biologyhttp://edamontology.org/topic_3175Structural variationhttp://edamontology.org/topic_3943Paleogenomicshttp://edamontology.org/topic_0108Protein expressionhttp://edamontology.org/topic_0797Comparative genomicshttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0089Ontology and terminologyMacWindowsLinuxOtherURGIFree of chargePlant SciencesFrancehttp://edamontology.org/operation_3745Ancestral reconstructionhttp://edamontology.org/operation_2421Database searchRaphaël Floresraphael.flores@inrae.frhttps://orcid.org/0000-0002-0278-5441PersonDeveloperURGIurgi-support@inrae.frDivisionMaintainerSyntenyViewerComparative genomics-driven translational research tool.https://urgi.versailles.inrae.fr/syntenysyntenyviewerbiotools:syntenyviewerWeb applicationhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0780Plant biologyhttp://edamontology.org/topic_3175Structural variationhttp://edamontology.org/topic_3943Paleogenomicshttp://edamontology.org/topic_0108Protein expressionhttp://edamontology.org/topic_0797Comparative genomicsMacLinuxWindowsJavaJSPOtherURGILegacyFree of chargeFrance10.1093/database/baad02737159239PMC10167986Jerome Salsejerome.salse@inrae.frhttps://orcid.org/0000-0003-2942-1098PersonPrimary contactRaphaël Floresraphael.flores@inrae.frhttps://orcid.org/0000-0002-0278-5441PersonDeveloperURGIurgi-support@inrae.frDivisionSupportPy-HLA-MatchPy-HLA-Match is a Python library for standardised, rule-based HLA (Human Leukocyte Antigen) matching in retrospective analyses, method development, benchmarking, and in-silico studies in immunogenetics and related fields.https://github.com/fraunhofer-izi/py-hla-matchpy-hla-matchbiotools:py-hla-matchLibraryhttp://edamontology.org/topic_3948Immunoinformaticshttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3063Medical informaticsMacWindowsLinuxPythonApache-2.0EmergingFree of chargeOpen accesshttp://edamontology.org/operation_2990Classificationhttp://edamontology.org/data_0920Genotype/phenotype report

http://edamontology.org/data_2048Report

https://github.com/fraunhofer-izi/py-hla-matchRepositoryhttps://pypi.org/project/py-hla-match/Repositoryhttps://github.com/fraunhofer-izi/py-hla-match/releases/tag/v0.1.0Source code0.1.0https://fraunhofer-izi.github.io/py-hla-match/API documentationhttps://github.com/fraunhofer-izi/py-hla-match/releasesRelease noteshttps://github.com/fraunhofer-izi/py-hla-match/blob/main/demo/demo_validation.ipynbQuick start guidehttps://github.com/fraunhofer-izi/py-hla-match/blob/main/README.mdInstallation instructionshttps://github.com/fraunhofer-izi/py-hla-match/blob/main/CITATION.cffCitation instructionsGeorg Poppgeorg.popp@izi.fraunhofer.dehttps://orcid.org/0009-0003-4251-4093PersonMaintainerTim Adamstim.adams@scai.fraunhofer.dehttps://orcid.org/0000-0002-2823-0102PersonMaintainercompareMS2compareMS2 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:comparems21.02.02.2Desktop applicationCommand-line toolhttp://edamontology.org/topic_0084Phylogenyhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_3520Proteomics experimentMacLinuxWindowsJavaScriptGoCMITProteomicsms-utilsMatureFree of chargeProteomicsNetherlandshttp://edamontology.org/operation_0567Phylogenetic tree visualisationhttp://edamontology.org/operation_2424Comparisonhttp://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3651MGF

http://edamontology.org/data_3272Species treehttp://edamontology.org/format_3603PNGhttp://edamontology.org/format_3604SVG

http://edamontology.org/data_2855Distance matrixhttp://edamontology.org/format_1912Nexus formathttp://edamontology.org/format_1991megahttp://edamontology.org/format_1910newick

https://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/0000-0002-1220-9173PersonDeveloperpico_galaxyGalaxy tools and wrappers for sequence analysishttps://github.com/peterjc/pico_galaxypico_galaxybiotools:pico_galaxyv0.0.15Command-line toolhttp://edamontology.org/topic_3307Computational biologyShellPythonNot licensedMatureFree of chargehttp://edamontology.org/operation_3695Data filteringmcquantModule for single-cell data extraction given a segmentation mask and multi-channel image.https://github.com/labsyspharm/mcmicromcquantbiotools:mcquant1.6.0Command-line toolhttp://edamontology.org/topic_3307Computational biologyPythonNot licensedMatureFree of chargehttp://edamontology.org/operation_3443Image analysishttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3591TIFFhttp://edamontology.org/data_0883Structurehttp://edamontology.org/format_3590HDF5

http://edamontology.org/data_2082Matrixhttp://edamontology.org/format_3752CSV

mcquant --masks ./segmentation/cellMask.tif ./segmentation/membraneMask.tif --image ./registration/Exemplar_001.h5 --output ./feature_extraction --channel_names ./my_channels.csvgff3sortGFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix toolshttps://github.com/tao-bioinfo/gff3sortgff3sortbiotools:gff3sortv1.0.0Command-line toolhttp://edamontology.org/topic_3307Computational biologyLinuxPerlGPL-3.0MatureFree of chargehttp://edamontology.org/operation_3802Data sortinghttp://edamontology.org/data_1255Sequence featureshttp://edamontology.org/format_1975GFF3

http://edamontology.org/data_1255Sequence featureshttp://edamontology.org/format_1975GFF3

gff3sort.pl [input GFF3 file] >output.sort.gff310.1186/s12859-017-1930-329137598PMC5686826enrichMToolbox for comparative genomics of MAGshttps://github.com/geronimp/enrichMenrichMbiotools:enrichM0.5.0Command-line toolhttp://edamontology.org/topic_3307Computational biologyPythonNot licensedMatureFree of chargehttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/data_2044Sequence

http://edamontology.org/data_2048Reporthttp://edamontology.org/format_2305GFF

https://github.com/geronimp/enrichM/wikiGeneral