REFUTEREFUTE is an open benchmark for scientific critique honesty and epistemic calibration on recent life-science and biomedical literature. It tests whether models keep claims inside what the evidence allows (overclaim / planted-flaw / falsifier selection) and whether stated confidence is calibrated, with judge-free MCQ axes plus open-ended critique scoring.https://bgpt.pro/refutebgpt-refutebiotools:bgpt-refuteWeb applicationPythonMITFree of chargeOpen accesshttps://github.com/connerlambden/refute-inspectRepositoryhttps://huggingface.co/datasets/BGPT-OFFICIAL/refuteOtherHugging Face datasethttps://doi.org/10.5281/zenodo.21542238OtherZenodo preprint DOIhttps://www.openml.org/d/47266OtherOpenML REFUTE-knowledge-v3https://www.openml.org/d/47268OtherOpenML REFUTE-soundness-v3https://doi.org/10.7910/DVN/IGAJWOOtherHarvard Dataverse datasethttps://ascl.net/code/v/4795OtherASCL software entryhttps://www.wikidata.org/wiki/Q140690703OtherWikidata itemhttps://osf.io/qxyfe/OtherOSF projecthttps://www.saashub.com/refuteOtherSaaSHub listinghttps://bgpt.pro/refuteGeneral10.5281/zenodo.21542238PrimaryInterim preprint deposit on Zenodo (v3.0.0-preprint).Conner Lambdencontact@bgpt.prohttps://bgpt.prohttps://orcid.org/0000-0003-0162-6622PersonDeveloperCBRAWorkflow optimized for the analysis of rare diseases, designed to detect SNVs, INDELs , CNVs and SVs in targeted sequencing data (CES/WES) and whole genome sequencing (WGS), built on Nextflow and following nf-core standards. It has an advanced variant annotation optimized for rare diseases diagnosis and discovery.https://github.com/CIBERER/CBRAnf-cbra-snvsbiotools:nf-cbra-snvsWorkflowhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0091BioinformaticsLinuxMITIMPaCT-ISCIIIIMPaCT-DataEmergingFree of chargeOpen accesshttps://github.com/CIBERER/CBRARepositoryhttps://github.com/CIBERER/CBRAUser manualRosin-Rammler Diagram plotting toolThis tool plots the Rosin-Rammler Diagram (RRSB) and calculates various related parameters.https://www.mathworks.com/matlabcentral/fileexchange/28013-rosin-rammler-diagram-plotting-toolrrsb-plotbiotools:rrsb-plot1.16.0.0Libraryhttp://edamontology.org/topic_3344Biomedical sciencehttp://edamontology.org/topic_3070Biologyhttp://edamontology.org/topic_3382ImagingWindowsLinuxMacMATLABMATLABFile ExchangeFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_0337Visualisationhttps://www.mathworks.com//matlabcentral/mlc-downloads/downloads/submissions/28013/versions/17/screenshot.pngScreenshotIvan Brezanihttps://www.mathworks.com/matlabcentral/profile/2241235-ivan-brezaniPersonPrimary contactPangolinPangolin is a deep-learning based method for predicting splice site strengths (for details, see Zeng and Li, Genome Biology 2022). It is available as a command-line tool that can be run on a VCF or CSV file containing variants of interest; Pangolin will predict changes in splice site strength due to each variant, and return a file of the same format. Pangolin's models can also be used with custom sequences.https://github.com/tkzeng/Pangolinpangolinbiotools:pangolinCommand-line toolhttp://edamontology.org/topic_3320RNA splicinghttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_3676Exome sequencingMacLinuxWindowsPythonGPL-3.0Free of chargeOpen accesshttp://edamontology.org/operation_0433Splice site predictionhttp://edamontology.org/operation_0232Sequence merginghttp://edamontology.org/operation_0264Alternative splicing predictionhttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_3016VCFhttp://edamontology.org/format_3752CSV10.1186/s13059-022-02664-435449021PMC9022248Yang I Liyangili1@uchicago.eduhttps://orcid.org/0000-0002-0736-251XPersonTony ZengArrayAnalysisArrayAnalysis is a web-based application for transcriptomic data analysis. It supports the analysis of both microarray and RNA-seq data. The tool may also be installed locally as a desktop app, Docker image, or R package.https://www.arrayanalysis.orgarrayanalysis.orgbiotools:arrayanalysis.orgWeb applicationhttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_3365Data architecture, analysis and designhttp://edamontology.org/topic_0091BioinformaticsLinuxWindowsMacRCC-BY-4.0Free of chargeOpen accesshttps://www.arrayanalysis.orgGeneral10.1093/nar/gkt29323620278PMC369204910.1186/s12864-015-1689-826122086PMC448612610.64898/2026.07.13.738193PreprintJarno Koetsierhttps://orcid.org/0000-0002-7981-1345PersonDeveloperMaintainerLars Eijssenhttps://orcid.org/0000-0002-6473-2839PersonDeveloperPinPathPinPath enables flexible visualization of (omics) data onto pathways diagrams, allowing users to pinpoint where the relevant changes occur. It supports pathway diagrams from WikiPathways and KEGG, as well as custom GPML and KGML files. Data can be displayed on both native pathway layouts and network representationshttps://synum-lab.github.io/PinPath-web/pinpathbiotools:pinpathWeb applicationLibraryCommand-line toolhttp://edamontology.org/topic_3391Omicshttp://edamontology.org/topic_0602Molecular interactions, pathways and networksRMITBioconductorFree of chargeOpen accesshttps://github.com/SyNUM-lab/PinPathRepositoryhttps://synum-lab.github.io/PinPath-web/Generalhttps://doi.org/doi:10.18129/B9.bioc.PinPathUser manualJarno Koetsierjarno.koetsier@maastrichtuniversity.nlhttps://orcid.org/0000-0002-7981-1345PersonPrimary contactDeveloperMaintainerLars Eijssenhttps://orcid.org/0000-0002-6473-2839PersonContributorEgon Willighagenhttps://orcid.org/0000-0001-7542-0286PersonContributorpickletBrowser-based tool to open almost any sequence file — FASTA, FASTQ, GenBank, EMBL, Swiss-Prot, AB1/ABIF, SCF, Clustal, Stockholm, PHYLIP, NEXUS, MSF, PIR and more — see every sequence inside, pick the ones you want, and save them as FASTA. The format is detected from the file content, not from the extension, so unlabelled or misnamed files still open. Runs entirely in the browser — files are never uploaded.https://fishka.bio/pickletpickletbiotools:pickletDesktop applicationWeb applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3071Data managementWindowsMacLinuxTypeScriptFreewareMatureFree of chargeOpen accesshttp://edamontology.org/operation_2121Sequence file editinghttp://edamontology.org/operation_0233Sequence conversionhttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_1632SCFhttp://edamontology.org/format_3000AB1http://edamontology.org/format_1963UniProtKB formathttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1947GCG MSFhttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1961Stockholm formathttp://edamontology.org/format_1912Nexus format

http://edamontology.org/data_0850Sequence sethttp://edamontology.org/format_1929FASTA

https://fishka.bioSoftware cataloguefishka.bio — the tool collection picklet belongs tohttps://fishka.bio/downloadDownloads pageOffline build — the same application as a self-contained archive, runs from local files with no server10.5281/zenodo.21444547Other2026.07.19Software deposit (concept DOI — resolves to the latest version) covering the fishka.bio tools, including picklet.Fishka Bioswim@fishka.biohttps://fishka.bioProjectPrimary contactDeveloperMaintainerab1lensBrowser-based viewer for Sanger sequencing chromatograms in AB1/ABIF and SCF format. Opens .ab1/.abi/.fsa files, shows raw and analysed traces, basecalls, quality values and the ABIF directory, and puts two reads side by side for comparison. Aligns a read against a reference sequence to highlight mismatches. Exports the read as FASTA, FASTQ or ABIF and the chromatogram as a high-resolution image. Runs entirely in the browser — files are never uploaded.https://fishka.bio/ab1lensab1lensbiotools:ab1lensWeb applicationDesktop applicationhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0092Data visualisationWindowsMacLinuxTypeScriptFreewareMatureFree of chargeOpen accesshttp://edamontology.org/operation_3203Chromatogram visualisationhttp://edamontology.org/data_0924Sequence tracehttp://edamontology.org/format_1632SCFhttp://edamontology.org/format_3000AB1

http://edamontology.org/data_2168Sequence trace imagehttp://edamontology.org/format_3603PNG

http://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTA

http://edamontology.org/operation_0491Pairwise sequence alignmenthttp://edamontology.org/data_0924Sequence tracehttp://edamontology.org/format_3000AB1http://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTA

https://fishka.bioSoftware cataloguefishka.bio — the tool collection ab1lens belongs tohttps://fishka.bio/downloadDownloads pageOffline build — the same application as a self-contained archive, runs from local files with no server10.5281/zenodo.21444547Other2026.07.19Software deposit (concept DOI — resolves to the latest version) covering the fishka.bio tools, including ab1lens.Fishka Bioswim@fishka.biohttps://fishka.bioProjectPrimary contactDeveloperMaintainergbatlasBrowser-based viewer for GenBank and GenPept files. Renders an interactive linear and circular feature map, the annotated source text, and the nucleotide/protein sequence side by side. Translates CDS features using the record's own genetic code and translation qualifiers, flags where the stored /translation disagrees with a plain translation, and adds optional computed layers: ORF prediction and restriction-site mapping. Handles multi-record files. Runs entirely in the browser — files are never uploaded.https://fishka.bio/gbatlasgbatlasbiotools:gbatlasWeb applicationDesktop applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_3511Nucleic acid sites, features and motifsWindowsMacLinuxTypeScriptFreewareMatureFree of chargeOpen accesshttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_0431Restriction site recognitionhttp://edamontology.org/operation_0436Coding region predictionhttp://edamontology.org/operation_0371DNA translationhttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/format_1937genpept

http://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_1929FASTA

https://fishka.bioSoftware cataloguefishka.bio — the tool collection gbatlas belongs tohttps://fishka.bio/downloadDownloads pageOffline build — the same application as a self-contained archive, runs from local files with no server10.5281/zenodo.21444547Other2026.07.19Software deposit (concept DOI — resolves to the latest version) covering the fishka.bio tools, including gbatlas.Fishka Bioswim@fishka.biohttps://fishka.bioProjectPrimary contactDeveloperMaintainerkMetaShotThe application of 2nd and 3rd generation High Throughput Sequencing (HTS) technologies has deeply reshaped experimental method to investigate microbial communities and obtain a taxonomic and functional profile of the invetigated community. Shotgun Metagenomics allow to quickly obtain a representation of microorganisms genomes characterizing a particular environment. In order to obtain a fast e reliable taxonomic classification of microorganisms genomes we present kMetaShot, an alignment-free taxonomic classifier based on k-mer/minimizer counting.https://github.com/gdefazio/kMetaShotkMetaShotbiotools:kMetaShotCommand-line toolhttp://edamontology.org/topic_3174MetagenomicsLinuxPythonGPL-3.0EmergingFree of chargeOpen accessToolsMarine MetagenomicsItalyhttps://github.com/gdefazio/kMetaShotOther10.1093/bib/bbae680Giuseppe Defaziogiuseppe.defazio@uniba.ithttps://persone.ict.uniba.it/rubrica/@@cerca?advanced_search=False&sort_on=&SearchableText=defaziohttps://orcid.org/0000-0002-9356-5224PersonDeveloperPost-Doc Researcher at University of BariTranscriptoScopeLocal Windows-friendly R Shiny application for RNA-seq differential expression using DESeq2, normalized-expression testing, over-representation analysis, fgsea-ranked pathway analysis, and WGCNA coexpression-network analysis. It supports input validation, additive and interaction designs, built-in human, fruit-fly, and yeast annotations, publication-quality plots, and reproducibility bundles containing results, settings, and executable R and R Markdown rerun code.https://github.com/Shettima123/TranscriptoScopetranscriptoscopebiotools:transcriptoscope0.5.0WorkbenchDesktop applicationhttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_3170RNA-SeqWindowsRMITMatureFree of chargeOpen accesshttp://edamontology.org/operation_3680RNA-Seq analysishttp://edamontology.org/operation_3928Pathway analysishttp://edamontology.org/operation_2436Gene-set enrichment analysishttp://edamontology.org/operation_3766Weighted correlation network analysishttp://edamontology.org/operation_3223Differential gene expression profilinghttps://github.com/Shettima123/TranscriptoScopeRepositoryhttps://github.com/Shettima123/TranscriptoScope/issuesIssue trackerhttps://github.com/Shettima123/TranscriptoScope/releases/download/v0.5.0/TranscriptoScope_Windows_Store_v0.5.0.exeBinariesStandalone x64 Windows installer that bundles R and the required package library.0.5.0https://github.com/Shettima123/TranscriptoScope/releases/download/v0.5.0/TranscriptoScope_Windows_v0.5.0.zipSoftware packageManual Windows package for users who already have R.0.5.0https://github.com/Shettima123/TranscriptoScope/archive/refs/tags/v0.5.0.zipSource code0.5.0https://github.com/Shettima123/TranscriptoScope/releases/tag/v0.5.0Downloads page0.5.0https://github.com/Shettima123/TranscriptoScope/blob/v0.5.0/README.mdGeneralhttps://github.com/Shettima123/TranscriptoScope/blob/v0.5.0/INSTALL_WINDOWS.mdInstallation instructionsQuick start guidehttps://github.com/Shettima123/TranscriptoScope/blob/v0.5.0/RELEASE_NOTES.mdRelease noteshttps://github.com/Shettima123/TranscriptoScope/blob/v0.5.0/CITATION.cffCitation instructionshttps://github.com/Shettima123/TranscriptoScope/blob/v0.5.0/SUPPORT.mdGeneralSupport and issue-reporting instructions.10.5281/zenodo.21409091Primary0.5.0Version-specific archived software release.Abubakar Abdulkadirhttps://github.com/Shettima123PersonDeveloperMaintainerDocumentorPrimary contactDr. Rosby's LabProjectProviderSupportSouthern University A and MInstituteProviderFAIR EVA for EUCAIMFAIR EVA: Evaluator, Validator & Advisor has been developed to check the FAIRness level of digital objects from different repositories or data portals. It requires the object identifier (preferably persistent and unique identifier) and the repository to check. It also provides a generic and agnostic way to check digital objects. This software started to be developed within IFCA-Advanced-Computing receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 857647.https://github.com/IFCA-Advanced-Computing/FAIR_evafair_eva_4_eucaimbiotools:fair_eva_4_eucaimEUCAIM_plugin_0.3EUCAIM_plugin_0.3.1EUCAIM_plugin_0.4.0EUCAIM_0.4.2v0.6.1Command-line toolPlug-inWeb servicehttp://edamontology.org/topic_4012FAIR dataLinuxPythonApache-2.0EUCAIMMatureFree of chargeOpen accesshttp://edamontology.org/operation_0336Format validationhttp://edamontology.org/operation_2428Validationhttp://edamontology.org/data_1048Database ID

http://edamontology.org/data_1772Score

fair-eva-cli batch -p eucaim_legacyhttps://github.com/IFCA-Advanced-Computing/FAIR_evaRepositoryRepository for FAIR EVA, without the EUCAIM specific pluginhttps://gitlab.ifca.es/eucaim/fair_eucaimRepositoryRepository for FAIR-EVA for eucaim plugin. Currently not public.https://github.com/IFCA-Advanced-Computing/FAIR_eva/blob/main/docs/index.mdGeneralDocumentation for the main package, EUCAIM plugin specific documentation not included.https://gitlabpages.ifca.es/fair-eva-guide-608baa/User manualWiki page with FAIR EVA for EUCAIM specific instructions.10.1038/s41597-023-02652-8Fernando Aguilarhttps://orcid.org/0000-0001-9462-4831PersonDeveloperMaintainerDocumentorCreator and devloper of the main package FAIR EVA. This software started to be developed within IFCA-Advanced-Computing receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 857647.David Rodríguezhttps://orcid.org/0000-0002-9160-5106PersonDeveloperPrimary contactDeveloper of the EUCAIM plugin.Inés Victoriahttps://orcid.org/0009-0003-7950-3937PersonDeveloperDeveloper of the EUCAIM plugin.InflexaInflexa is an open-source, agentic orchestration platform for computational biology and translational medicine. It is designed to assist researchers in analyzing multi-omics, cheminformatics, and imaging data by reading published literature, designing multi-step analysis plans, and executing experiments with full reproducibility.https://inflexa.aiinflexabiotools:inflexaCommand-line toolhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_2258Cheminformaticshttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_0218Natural language processinghttp://edamontology.org/topic_3391OmicsLinuxMacWindowsPythonTypeScriptGoApache-2.0Free of chargeOpen accesshttp://edamontology.org/operation_2945Data analysishttps://github.com/inflexa-ai/inflexaRepositoryGitHub repohttps://public.inflexa.ai/GSE110256/pharmacogenomic-mouse-cerebrocortical-culturesOtherPharmacogenomic Drug Screen in Mouse Cerebrocortical Cultures (Re-analysis of GSE110256)https://public.inflexa.ai/GSE282861/il-33-il-4ra-blockade-hdm-airway-inflammationOtherGenome-wide Dissection of IL-33 and IL-4Rα Blockade in HDM-driven Airway Inflammation (Re-analysis of GSE282861)https://public.inflexa.ai/33558495/breast-cancer-african-arab-european-ancestryOtherHow Genetic Ancestry Shapes Breast Cancer Biology (Re-analysis of Roelands et al. 2021 (npj Breast Cancer) )https://public.inflexa.ai/GSE286094-GSE286095/atg7-deficiency-reshapes-microglia-biology-alzheimers-diseaseOtherATG7 Deficiency Reshapes Microglia Biology in Alzheimer’s Disease (Re-analysis of GSE286094 / GSE286095)https://public.inflexa.ai/GSE157194/atopic-dermatitis-dupilumab-cyclosporineOtherAtopic Dermatitis Transcriptome Under Dupilumab and Cyclosporine (Re-analysis of GSE157194)https://github.com/inflexa-ai/inflexa/releasesBinariesSupportsupport@inflexa.aiSupportREACTRReactr is an modularized, Snakemake workflow for automated, species-agnostic characterization of gene families from sequence to experimental design. Given a query protein sequence and NCBI taxonomy IDs (or RefSeq assembly accessions), reactr retrieves genomic data and runs comprehensive analysis across 4 integrated tiers: (1) evolutionary analysis, including homolog detection, domain-based clustering, multiple sequence alignment, and phylogenetic inference; (2) synteny and selection analysis, detecting collinear blocks and calculating Ka/Ks ratios; (3) structural and regulatory characterization, including motif discovery, chromosomal mapping, biochemical property prediction, subcellular localization prediction, and promoter analysis; and (4) experimental design tools, generating PCR primers and scored CRISPR gRNAs for lab validation. Reactr bridges computational prediction and experimental validation, thus enabling rapid transition from genomic discovery to functional studies.https://zenodo.org/records/21125109reactrbiotools:reactr3Command-line toolhttp://edamontology.org/topic_0091BioinformaticsMacPythonMITBiocondaFree of chargeOpen accesshttp://edamontology.org/operation_2422Data retrievalLoads genomic data and prepares it for query analysis`snakemake -s LoadDatasets.smk --cores 8`http://edamontology.org/operation_0226Annotationhttp://edamontology.org/operation_2424Comparisonhttp://edamontology.org/operation_3429Generationhttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/operation_2928Alignmenthttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_0227Indexinghttp://edamontology.org/operation_2945Data analysishttp://edamontology.org/operation_0250Protein property calculationhttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_2428Validationhttp://edamontology.org/operation_2990ClassificationRuns query analysis`snakemake -s MainPipeline.smk`DanteDANTE is a software tool for genotyping and characterizing tandem repeats (TRs) from both second- and third-generation sequencing data. It supports the analysis of short-read massively parallel sequencing (sr-MPS) and long-read massively parallel sequencing (lr-MPS), enabling accurate repeat characterization across a wide range of loci. A key feature of DANTE is its ability to determine genotypes at nucleotide resolution, including the characterization and phasing of complex repeat motifs. For sr-MPS data, the tool determines allele size and sequence composition of alleles for which spanning reads are generated. In addition, it identifies alleles that exceed the sequencing read length by estimating their presence from partial read evidence and supports the visualisation of the sequence composition of partial reads. For lr-MPS data, where complete repeat regions are typically sequenced, DANTE determines the allele size and sequence composition of identified alleles.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_2182FASTQ-like format (text)http://edamontology.org/format_2572BAMhttp://edamontology.org/format_2200FASTA-like (text)

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/bty79130203023PMC6166771Primary10.1016/j.ab.2025.11579339894140Usage10.1016/j.mcp.2024.10200539710066UsageJaroslav Budišjaroslav.budis@geneton.skhttps://orcid.org/0000-0002-8667-6655PersonDeveloperPrimary contactAndrej Balážandrej.balaz@geneton.skhttps://orcid.org/0000-0002-3113-3389PersonDeveloperMarcel Kucharikmarcel.kucharik@geneton.skhttps://orcid.org/0000-0002-5373-8282DeveloperIngrid Lojováingrid.lojova@savba.skhttps://orcid.org/0000-0001-7659-0850ContributorJán Radvánszkyjan.radvanszky@savba.skhttps://orcid.org/0000-0001-9657-1198ContributorAgentomicsAutonomous ML experimentation for biomedical data.https://www.agentomicsml.com/agentomicsbiotools:agentomicsMITFree of chargeOpen accesshttps://www.agentomicsml.com/Otherhttps://github.com/BioGeMT/agentomics-mlRepositoryhttps://biogemt.github.io/agentomics-ml/User manual10.1093/bioinformatics/btag25042412783NIM-StudioNIM Studio is a local-first platform for neuroinformatics, BIDS organization, metadata generation, duplicate auditing, and scalable research data management.https://nim-studio.readthedocs.io/en/latest/index.htmlnim-studiobiotools:nim-studio0.1.0-betaDesktop applicationhttp://edamontology.org/topic_3071Data managementhttp://edamontology.org/topic_4010Open scienceWindowsMacPythonProprietaryEmergingFree of chargeOpen access (with restrictions)http://edamontology.org/operation_2409Data handling10.5281/zenodo.21296290.0.1.0-betaGAIn (Genomic Annotation Infrastructure)GAIn is a platform for annotating genetic variants, genomic positions, and regions with reproducible, declarative pipelines using curated Genomic Resource Repositories.https://gain.iossifovlab.com/gain_genomic_annotation_infrastructurebiotools:gain_genomic_annotation_infrastructureWeb applicationCommand-line toolhttp://edamontology.org/topic_0622GenomicsLinuxMacPythonMITMatureFree of chargeOpen accesshttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/data_1016Sequence positionhttp://edamontology.org/data_1276Nucleic acid featureshttp://edamontology.org/data_1017Sequence range

http://edamontology.org/data_1276Nucleic acid features

Annotates tabular files containing genetic variants, genomic positions, or genomic regions using a declarative YAML pipeline and configured Genomic Resource Repositories.annotate_tabular variants.tsv pipeline.yaml -o annotated_variants.tsvhttps://github.com/iossifovlab/gainRepositoryhttps://github.com/iossifovlab/mini-GRRRepositoryhttps://github.com/iossifovlab/gain/archive/refs/heads/master.zipSource codehttps://iossifovlab.com/gaindocs/General10.64898/2026.07.08.737273PreprintMurat Cokolmuratcokol@gmail.comVigyanllmVigyanLLM is a sovereign, on-premises biomedical AI platform designed for computational biology. It provides autonomous primer design, evaluating melting temperature (Tm) and GC content; CRISPR guide RNA analysis with off-target scoring; BLAST sequence similarity searching; multiple sequence alignment (MSA); and GPU-accelerated molecular docking for drug discovery. Unlike cloud-based SaaS, VigyanLLM deploys via Docker to ensure institutional genomic data sovereigntyhttps://www.vigyanllm.in/vigyanllmbiotools:vigyanllmBioinformatics portalhttp://edamontology.org/topic_4019BiosciencesProprietaryEmergingFree of charge (with restrictions)Open accessfigtracerPlain-text, git-tracked electronic lab notebook (ELN) for reproducible bioinformatics — threads your R & Python figures into living lab notes with full provenance. Built for single-cell / CyTOF / flow cytometry; works with Obsidian, Quarto & Jupyter.https://github.com/david-priest/figtracerfigtracerbiotools:figtracer0.1.0LibraryCommand-line toolhttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_3934Cytometryhttp://edamontology.org/topic_3071Data managementhttp://edamontology.org/topic_3372Software engineeringPythonMITEmergingFree of chargeOpen access10.5281/zenodo.21288980David Priesthttps://orcid.org/0000-0003-0095-6718InstituteHPO 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.frOtherSequenceMatrixConcatenation 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/0009-0003-6158-0029PersonDeveloperConspectaConspecta is a browser-based research platform that brings microscopy image analysis, flow cytometry, molecular biology, sample tracking, and publication-ready figures into one connected workspace. It replaces the patchwork of disconnected tools most labs assemble, so a lab's data, samples, and results stay linked from experiment to figure with full traceability. Built for imaging-heavy and flow-heavy biology labs, new PIs, and early-stage biotech. Research-focused, not regulated or clinical. Free for individuals. Paid team plans add shared workspaces.https://conspecta.bioconspectabiotools:conspectaRRID:SCR_028623rridWeb applicationhttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_3385Light microscopyhttp://edamontology.org/topic_3934Cytometryhttp://edamontology.org/topic_3047Molecular biologyMacLinuxWindowsProprietaryEmergingFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_3443Image analysishttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3935Dimensionality reductionPanAbyssPanAbyss 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 contactRAMENRegional 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 contactAgentic 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/0009-0000-3463-6806PersonDeveloperDocumentorMaintainer