pyBiodatafusePython package for biodatafuse project.https://biodatafuse.org/pyBiodatafusebiotools:pyBiodatafusev1.3.0Database portalhttp://edamontology.org/topic_3344Biomedical sciencePythonC++MITMaturehttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/data_1052URLhttps://biodatafuse.github.io/pyBiodatafuseGeneralhttps://pybiodatafuse.readthedocs.io/en/latest/index.htmlInstallation instructionsUser manual10.1093/bioinformatics/btag06441692987PMC12949461PrimaryAmsterdamUMCdbAmsterdamUMCdb is a database of de-identified health data related to tens of thousands of intensive care unit admissions, including demographics, vital signs, laboratory tests and medications.https://amsterdammedicaldatascience.nl/AmsterdamUMCdbbiotools:AmsterdamUMCdb1.5.0Database portalhttp://edamontology.org/topic_3303MedicinePythonMITMaturehttp://edamontology.org/operation_0224Query and retrievalhttps://github.com/AmsterdamUMC/AmsterdamUMCdb/wikiGeneral10.1097/ccm.000000000000491633625129PMC8132908PrimaryRAiSD-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_1929FASTA10.1038/s42003-018-0085-830271960PMC6123745Method10.32942/x2gw9bPrimaryValidSenseValidSense is a toolbox for assessing agreement between two quantitative methods or devices measuring the same quantity using the Limits of Agreement (LoA) analysis, also known as the Bland-Altman analysis.https://github.com/umcu/ValidSenseValidSensebiotools:ValidSensePythonMITEmerginghttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/operation_2424Comparisonhttp://edamontology.org/data_3108Experimental measurementhttp://edamontology.org/format_3620xlsxhttp://edamontology.org/format_3752CSV10.1016/s0140-6736(86)90837-82868172Method10.1177/09622802990080020410501650Method10.1080/1054340070132942217613642MethodtrieA 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_3869Simulationhttps://github.com/nuria-sv/toscca/wikiGeneralggplot2uses10.1093/bioadv/vbae02138456127PMC10919946PrimaryminibwaMinibwa aligns short reads against a reference genome. It is the successor of bwa-mem with a different algorithm. Minibwa is over three times as fast as the original bwa-mem and twice as fast as bwa-mem2 at comparable accuracy. While minibwa works with accurate long reads, minimap2 is more robust under high error rate.https://github.com/lh3/minibwaminibwabiotools:minibwaGONetA Molecular Interaction-Guided Graph Learning Framework for Multi-Omics Cancer Classificationhttps://github.com/EayonYang/GONetGONet-v1biotools:GONet-v1http://edamontology.org/topic_4021Multiomicshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3474Machine learningPythonApache-2.0OpenProteoOpenProteo 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 datahttps://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 datahttps://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 datahttps://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 datahttps://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 identifierBrowses 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 IDhttps://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 stringProduces 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.html1.0PlatformaIntegrated software platform for biologics discovery and NGS analysis, supporting antibody discovery, peptide discovery, TCR/BCR repertoire profiling, and multi-omics data integration. Built on MiXCR, a widely adopted tool for adaptive immune repertoire sequencing, and other open-source bioinformatics algorithms.
In vitro antibody discovery: Computational analysis of display-based selection (e.g., phage/yeast display) NGS datasets to identify enriched antibody sequences, perform clonotype clustering, and prioritize candidates using sequence-derived features and developability metrics, supported by ML-based ranking workflows.
In vivo antibody discovery: Integration of immune repertoire sequencing with functional assay outputs and developability annotations to characterize adaptive immune responses, identify antigen-associated clonotypes, and prioritize lead antibody candidates through multi-parameter computational scoring and repertoire-level analysis.https://platforma.bioplatformabiotools:platformaBioinformatics portalDesktop applicationhttp://edamontology.org/topic_1317Structural biologyhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_4021MultiomicsWindowsMacLinuxMaturehttps://github.com/milaboratory/platformaRepositoryhttps://platforma.bio/downloadsDownloads pageFree for academic accesshttps://docs.platforma.bioUser manualSQUARNASQUARNA 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 profileInput 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/PLIP - Protein-Ligand Interaction ProfilerPLIP is a tool for fast identification of non-covalent interactions between biological macromolecules and their ligands. It predicts protein-ligand interactions based on essential dynamics, providing valuable insights for drug discovery and structural biology.https://plip-tool.biotec.tu-dresden.de/plip-web/plip/indexplin2_plin3biotools:plin2_plin3http://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_3407Endocrinology and metabolismhttp://edamontology.org/topic_3360Biomarkershttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_4028Single-cell sequencinghttp://edamontology.org/operation_0478Molecular dockinghttp://edamontology.org/operation_2940Scatter plot plottinghttp://edamontology.org/operation_3891Essential dynamicshttp://edamontology.org/operation_0314Gene expression profilinghttp://edamontology.org/operation_2492Protein interaction prediction10.3389/FIMMU.2025.168198941246346PMC12611683Gang Lianzhenligang@163.comPersonpMLSTpMLST is a tool developed by the Center for Genomic Epidemiology for plasmid Multi-Locus Sequence Typing, used to classify IncF plasmids based on sequence comparisons against a database to create plasmid sequence types. It aims to improve the accuracy of plasmid typing, particularly in cases with multiple variants.https://bitbucket.org/genomicepidemiology/pmlst/pmlstbiotools:pmlsthttp://edamontology.org/topic_0798Mobile genetic elementshttp://edamontology.org/topic_4056Long-read sequencinghttp://edamontology.org/topic_3305Public health and epidemiologyhttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_3500ZoologyPythonhttp://edamontology.org/operation_0578Plasmid map drawinghttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/operation_3840Multilocus sequence typing10.1128/MSYSTEMS.01010-2440197103PMC12090814Monika Dolejskamonika.dolejska@gmail.comhttps://orcid.org/0000-0001-7877-483XPersonmiRcountsGenerates 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 formathttps://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 VaidyaSnapGeneTool to intuitively design, simulate, and visualise plasmids, primers, and DNA constructs.https://www.snapgene.com/snapgenebiotools:snapgene8.2MDWebWeb-based platform to help access to molecular dynamics (MD). The platform provides tools to prepare systems from PDB structures mimicking the procedures followed by human experts. It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs). Tools for analysis of trajectories are also incorporated.http://mmb.irbbarcelona.org/MDWeb2mdwebbiotools:mdweb2.0Web applicationWorkbenchhttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_3306Biophysicshttp://edamontology.org/topic_0176Molecular dynamicshttp://edamontology.org/topic_2275Molecular modellingLinuxPHPBioExcelIRB-BSCELIXIR-ESMatureFree of charge (with restrictions)http://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_2476Molecular dynamicshttp://edamontology.org/data_1127PDB IDhttp://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/data_0883Structurehttp://edamontology.org/format_1476PDBPlatform for setup and analysis of molecular dynamics simulationshttp://mmb.irbbarcelona.org/MDWeb2/help.php?id=baseUser manualTraining material10.1093/bioinformatics/bts13922437851PrimaryInstitute of Research in Biomedicine - BarcelonaInstituteInstitute for Research in Biomedicine Barcelonamdweb@mmb.irbbarcelona.orgPersonPrimary contactBIGR 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/0009-0003-6158-0029PersonDevelopermiRNAProtPredA powerful, high-performance bioinformatics framework for discovering, evaluating, and verifying microRNA (miRNA) interactions across DNA, RNA, and protein target sequences.
The mirnaprotpred package provides two core modules:
SeqFinder: A discovery engine to find all potential miRNA interactions across a genome or target sequence.
Validator: A targeted verification engine to test specific, user-provided miRNAs against a target sequence.
Both modules are powered by a shared, rigorous biological engine that evaluates exact seed matching, wobble pairing, AU-rich context, and RNAduplex thermodynamic stability.https://mirnaprotpred.biounfold.in/mirnaprotpredbiotools:mirnaprotpredCommand-line toolhttp://edamontology.org/topic_4019BiosciencesWindowsMacLinuxMIThttps://github.com/somenath-combio/mirnaprotpred/Repositoryhttps://mirnaprotpred.biounfold.in/User manual10.3389/fgene.2026.1817432Somenath Duttasomenath@pusan.ac.krhttps://somenath.biounfold.in/https://orcid.org/0000-0002-9580-63863D Cancer Model Development ServicesTo this date, numerous developments, like organoids, in 3D culturing technology, have made creating novel, more physiological human cancer models possible. At Alfa Cytology, we focus on developing 3D cancer models and aim to provide researchers and scientists working in oncology with cutting-edge tools. Our services help clients streamline their drug discovery process and further their knowledge of cancer biology.https://www.alfacytology.com/3d-cancer-models/3d-cancer-model-development-services.html3d-cancer-model-development-servicesbiotools:3d-cancer-model-development-servicesConspectaConspecta 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 reductionName ResolverAn Apache Solr-based dictionary search application based on the synonyms and preferred labels collected by Babel (https://bio.tools/babel).https://github.com/NCATSTranslator/NameResolutionnameresbiotools:nameres1.5.2babelusesNode NormalizerA high-speed frontend for normalizing identifiers using Redis as a backend database. Uses the sets of equivalent identifiers produced by Babel (https://bio.tools/babel).https://github.com/NCATSTranslator/NodeNormalizationnodenormbiotools:nodenorm2.4.1babelusesBabelHand-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 contactSearch OntologiesSearch Ontologies is a tool for the automated extraction of ontology ID codes from web-based ontology repositories using metadata values. It supports the mapping of metadata fields from a structured Excel template to standardized ontology terms by using the BioPortal Search API.https://github.com/foundingGIDE/search_ontologiessearch_ontologiesbiotools:search_ontologieslinkset-automationlinkset-automation is a set of tools to automatically generates CyTargetLinker linksets from different resources, starting with WikiPathways.https://github.com/CyTargetLinker/linkset-automationlinkset-automationbiotools:linkset-automationhttp://edamontology.org/topic_3292Biochemistryhttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_0092Data visualisationPythonShellApache-2.0Emerginghttp://edamontology.org/operation_3431Data depositionhttp://edamontology.org/operation_2428Validationhttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/data_2093Data referencehttp://edamontology.org/format_3752CSVwikipathwaysusescytoscapeusesbridgedbuses10.12688/f1000research.14613.231489175PMC6707396PathBench-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_3591TIFF10.48550/arXiv.2512.17517GlycoDashGlycoDash is an R Shiny dashboard for processing glycomics data obtained from LaCyTools, SweetSuite and Skyline.https://github.com/Center-for-Proteomics-and-Metabolomics/GlycoDashGlycoDashbiotools:GlycoDashv1.11.5-masterhttp://edamontology.org/topic_3292Biochemistryhttp://edamontology.org/topic_0121ProteomicsRMITEmerginghttp://edamontology.org/operation_2428Validationhttp://edamontology.org/operation_0226Annotationhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_3620xlsxhttps://github.com/Center-for-Proteomics-and-Metabolomics/GlycoDash/releases/download/v1.11.5-master/GlycoDash_user_guide_v1.11.5.pdfUser manualskylineuses10.1007/s00216-025-05794-339985669PMC11961463ab1lensBrowser-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 accessdengen-allele-frequency-browserThe DenGen Allele Frequency Browser is a resource of variant allele frequencies and is being made publicly available. The dataset encompasses SNP and indel variant calls in 2,211 individuals from whole genome sequencing of all Danish DenGen participantshttps://allele-frequency-browser.dengen.dk/dengen-allele-frequency-browserbiotools:dengen-allele-frequency-browser1.0RAMENRegional 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 contactFungtionFungtion is a software tool for predicting and visualizing fungal effector proteins using machine-learning models and protein language-model embeddings. It provides effector prediction, similarity-network visualization and relationship-tree analysis for protein sequence inputs.https://github.com/noHup-cc/fungtionfungtionbiotools:fungtionv1.0.0DanteDANTE (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_2572BAMhttps://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_1476PDBhttps://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 formathttps://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_1476PDBhttps://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_3878mdcrdhttps://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_1476PDBhttps://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_1476PDBhttps://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_1476PDBhttps://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/ConsortiumProvider