hgt-siteFinds candidate sites where foreign DNA, such as bacterial or viral DNA, may have been inserted into a host genome. It takes paired-end reads aligned to the host and the per-read output of a taxonomic classifier run on the reads that did not align, and tests each candidate site against the number of chance chimeras that contamination and library preparation would produce at that position, flagging the likely artefacts rather than discarding them. Reads that cross the junction place the insertion point to the base pair. Kraken2, KrakenUniq, Kaiju, Centrifuge, DIAMOND and BLAST tabular output are all accepted, as is any two-column file of read name and taxid. With a GTF or GFF3 annotation it also reports the gene at each site.https://github.com/iraajgangavaram/hgt-sitehgt-sitebiotools:hgt-site0.1.00.1.10.2.00.3.0doi:10.5281/zenodo.23842712doi0.3.0Command-line toolhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3174Metagenomicshttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_3175Structural variationhttp://edamontology.org/topic_3299Evolutionary biologyhttp://edamontology.org/topic_0637TaxonomyMacLinuxPythonMITEmergingFree of chargeOpen accesshttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/operation_3228Structural variation detectionhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_2573SAMhttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_3462CRAMhttp://edamontology.org/data_3028Taxonomyhttp://edamontology.org/format_3475TSV

http://edamontology.org/data_3498Sequence variationshttp://edamontology.org/format_3475TSVhttp://edamontology.org/format_3464JSONhttp://edamontology.org/format_3003BEDhttp://edamontology.org/format_3016VCF

hgt-site run --bam sample.bam --kraken-db kraken2-db --host-taxid 9606 -o sample.hgt-site.tsvhttps://github.com/iraajgangavaram/hgt-siteRepositoryhttps://github.com/iraajgangavaram/hgt-site/issuesIssue trackerhttps://iraajgangavaram.github.io/hgt-site/benchmarks/OtherBenchmarks against LGTSeek, with the scripts and raw resultshttps://github.com/iraajgangavaram/hgt-site/archive/refs/tags/0.3.0.tar.gzSource code0.3.0https://pypi.org/project/hgt-site/Software package0.3.0https://iraajgangavaram.github.io/hgt-site/Generalhttps://iraajgangavaram.github.io/hgt-site/api/API documentationhttps://iraajgangavaram.github.io/hgt-site/citation/Citation instructionsIraaj Gangavaramhttps://orcid.org/0009-0002-4615-2846PersonDeveloperMaintainerETAIN 5G ScientistHow much mobile phone radiation are we exposed to in everyday life? The ETAIN 5G Scientist app shows maps of mobile phone radiation across Europe. It continuously calculates the radiation from cell towers and how strongly your own device transmits during a phone call. The app was developed in the citizen research project ETAIN (Exposure To electromAgnetic fIelds and plaNetary health), which is funded by the EU. ETAIN investigates the effects of mobile phone radiation on human health and on biodiversity. The app is available for Android phones in the Google Play Store. Everyone who uses the app contributes to the research.https://www.etainproject.eu/etain-5g-scientistetain_5g_scientistbiotools:etain_5g_scientist1.9.3https://www.emf-portal.org/uploads/etain_5g_scientist_info_en.pdfGeneralMartin Rööslimartin.roosli@swisstph.chPersonPrimary contactOpen Causal Graph BuilderThis tool guides researchers through building a causal graph by clearly defining causes and consequences of each variable in temporal order, then generating a saturated graph containing all plausible relationships between them. The researcher deliberately removes implausible relationships one-by-one, annotating justifications as they go. This ensures that the absence of a relationship (edge) is a deliberate choice rather than a default, and nudges explicit consideration of time throughout the design and visualisation of the causal graph.https://opencausal.org/build/open_causal_graph_builderbiotools:open_causal_graph_builderopencausalincludedIn10.1136/jech-2026-SSMabstracts.358Hüseyin Küçükalihttps://orcid.org/0000-0003-1669-3107Primary contactSpeciesHubPlatform for managing biodiversity observations, available as a web application and an Android app. Supports data entry with standardised and custom forms, import from spreadsheets, querying, map visualisation, export and team access. Data remains under the control of the owner, who decides what is shared. Public datasets can be published with reduced coordinate precision to protect sensitive locations.https://specieshub.iospecieshubbiotools:specieshubMobile applicationWeb applicationhttp://edamontology.org/topic_3050Biodiversityhttp://edamontology.org/topic_3071Data managementhttp://edamontology.org/topic_0610Ecologyhttp://edamontology.org/topic_0092Data visualisationMacLinuxWindowsMatureFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_0337Visualisationhttps://www.youtube.com/@specieshub-ioOtherhttps://play.google.com/store/apps/details?id=io.specieshubDownloads pageAndroid Apphttps://specieshub.io/supportUser manualhttps://specieshub.io/termsTerms of useHESTA: Human Early Embryogenesis Spatiotemporal Transcriptomic AtlasThe spatial and temporal atlas of gene expression in human embryo at early gestation is critical in understanding embryo development, organogenesis and disease origins. Here, we obtained the spatial-temporal transcriptome from the 77 sagittal sections of 13 human embryos at 12-23 Carnegie stage (CS) by Stereo-seq, established the development trajectory/regulatory profiling of 50 organs, and identified the top organ-specific regulons with the highest score as the potential organ-identity regulators. The atlas refines the key organs/cell types that are vulnerable to virus infection and genetic disorders. We found dynamic changes of imprinting gene expression in specific organs at different stages. Our work, for the first time, revealed the time-lapse and spatial transcriptome dynamics of human embryogenesis after gastrulation.https://db.cngb.org/hesta/hesta_databsebiotools:hesta_databse1.0.0Database portalhttp://edamontology.org/topic_3064Developmental biologyhestaThe spatial and temporal atlas of gene expression in human embryo at early gestation is critical in understanding embryo development, organogenesis and disease origins. Here, we obtained the spatial-temporal transcriptome from the 77 sagittal sections of 13 human embryos at 12-23 Carnegie stage (CS) by Stereo-seq, established the development trajectory/regulatory profiling of 50 organs, and identified the top organ-specific regulons with the highest score as the potential organ-identity regulators. The atlas refines the key organs/cell types that are vulnerable to virus infection and genetic disorders. We found dynamic changes of imprinting gene expression in specific organs at different stages. Our work, for the first time, revealed the time-lapse and spatial transcriptome dynamics of human embryogenesis after gastrulation.https://db.cngb.org/hesta/hestabiotools:hesta1.0.0AgingResearch.NewsAgingResearch.News is a web application for finding and following research on aging and age-related disease. It connects biomedical papers with evidence summaries, clinical trials, research grants and related topics. Readers can search the public site, use topic RSS feeds, or connect an AI assistant through its MCP API. Paper summaries are generated and checked by AI, with links to the underlying research and its limitations. Public reading is free; personalized features and higher API allowances require an account or paid plan.https://agingresearch.newsagingresearch.newsbiotools:agingresearch.newsRRID:SCR_029124rridWeb APIWeb applicationhttp://edamontology.org/topic_3399Geriatric medicinehttp://edamontology.org/topic_3344Biomedical sciencehttp://edamontology.org/topic_3379Preclinical and clinical studieshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_0218Natural language processingProprietaryEmergingFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_0306Text mininghttp://edamontology.org/operation_0305Literature searchSearch new aging research papers, their evidence, clinical trials, grants and drug programs; on the site, through the data API or the MCP server.https://agingresearch.news/contactHelpdeskhttps://agingresearch.news/feed.xmlOtherhttps://agingresearch.news/statusTechnical monitoringhttps://agingresearch.news/api/mcpServiceRemote MCP server (Streamable HTTP)https://github.com/paperfoot/agingresearch-news-mcpSoftware catalogueMCP server listing and client setuphttps://agingresearch.news/developersAPI documentationhttps://agingresearch.news/connectQuick start guidehttps://agingresearch.news/termsTerms of usehttps://agingresearch.news/api/v1/openapi.jsonAPI documentationOpenAPI description of the data APIBoris Djordjevicboris@agingresearch.newsPersonPrimary contactSlideScopeDesktop viewer for scientific and medical images on Windows and macOS, centred on microscopy and whole slide pathology. Opens whole slide scanner formats (Aperio SVS, Hamamatsu NDPI, MIRAX MRXS, Leica SCN, Ventana BIF) alongside acquisition formats (Zeiss CZI, Nikon ND2, Leica LIF, TIFF/OME-TIFF) and DICOM, including CT, MRI and X-ray series, in a single application. Provides pyramid navigation of gigapixel images, metadata inspection, calibrated measurements, annotations, and on-device segmentation and object counting for microscopy images. Medical scans are for viewing and measurement only; not for diagnosis.https://slidescope.science/slidescopebiotools:slidescope1.19.0Desktop applicationhttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_3383Bioimaginghttp://edamontology.org/topic_3384Medical imagingWindowsMacProprietaryMatureCommercialRestricted accesshttps://slidescope.science/en/downloads/Binarieshttps://slidescope.science/en/learn/Generalhttps://slidescope.science/en/how-to-open-czi-files/User manualHow to open ZEISS CZI files, with the free and paid optionshttps://slidescope.science/en/how-to-open-nd2-files/User manualHow to open Nikon ND2 files, with the free and paid optionshttps://slidescope.science/en/how-to-open-svs-files/User manualHow to open Aperio SVS whole-slide images, with the free and paid optionshttps://slidescope.science/en/how-to-open-ndpi-files/User manualHow to open Hamamatsu NDPI whole-slide imageshttps://slidescope.science/en/how-to-open-mrxs-files/User manualHow to open 3DHISTECH MRXS whole-slide imageshttps://www.youtube.com/watch?v=2drQ_Z_1ANETraining materialSlideScope Science 1.9 product tour video (89 s)MEGAM ARG DetectionFree Windows desktop application that detects antimicrobial resistance genes and resistance mutations in bacterial isolate genomes from FASTA assemblies or FASTQ reads. It combines quality control, assembly, taxonomic classification, annotation, MLST typing and several resistance detectors (AMRFinderPlus, ABRicate, RGI with CARD, PointFinder, KMA) in a single workflow that runs locally, without the command line. Research use; not a clinical diagnostic.https://megam-arg-detection.com/en/megam_arg_detectionbiotools:megam_arg_detection2026-11-02WorkflowDesktop applicationhttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3324Infectious diseasehttp://edamontology.org/topic_3305Public health and epidemiologyhttp://edamontology.org/topic_3673Whole genome sequencingWindowsFreewareEmergingFree of chargeOpen accesshttp://edamontology.org/operation_3460Taxonomic classificationhttp://edamontology.org/operation_3218Sequencing quality controlhttp://edamontology.org/operation_3482Antimicrobial resistance predictionhttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/operation_3840Multilocus sequence typinghttp://edamontology.org/operation_0310Sequence assemblyhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_2048Report

FASTQ reads go through quality control and assembly; FASTA assemblies go directly to genome description and resistance detection.https://github.com/rmerah/MEGAMRepositoryPrevious version (v3.2, Docker pipeline, MIT licence).https://megam-arg-detection.com/telechargements/MEGAM-arg-detection.exeBinariesWindows 10/11 x64 installer (377 MB). The application downloads the databases from their official sources and indexes them locally (6.2 GB download).2026-11-02https://megam-arg-detection.com/en/antibiotic-resistance-gene-detection-guide/User manualIllustrated step-by-step guide (Klebsiella pneumoniae HS11286).https://megam-arg-detection.com/en/#faqFAQhttps://megam-arg-detection.com/telechargements/MEGAM-arg-detection.txtRelease notesIn French.https://megam-arg-detection.com/llms.txtGeneralamrfinderplususesabricateusescardusespointfinderusesresfinderusesplasmidfinderusesvfdbuseskmauseskraken2usesprokkausesspadesusesmlstusesfastpusesfastqcusesmultiqcusesquastusesbarrnapusesseqkitusesRachid Merahrachid.merah77@gmail.comhttps://github.com/rmerahPersonDeveloperPrimary contactGossetPharmaceutical intelligence platform that connects drugs, clinical trials, results, patents, regulatory approvals, companies and deals into one knowledge graph updated daily from public sources worldwide, including China. Used for competitive intelligence, landscapes for any target, disease or modality, asset due diligence and trial outcome forecasting (PTRS). Every answer and report links back to its sources. Available on the web and in ChatGPT and Claude through an MCP server and API.https://gosset.aigossetbiotools:gossetWeb APIWeb applicationDatabase portalhttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_3379Preclinical and clinical studieshttp://edamontology.org/topic_0202PharmacologyProprietaryFree of charge (with restrictions)Restricted accesshttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_0306Text mininghttps://gosset.ai/mcp-apiOtherMCP server and APIhttps://docs.gosset.ai/GeneralGosset, Inc.lukasz@gosset.aihttps://gosset.aiProvidersccellfieA Python-based tool to infer metabolic activities from single-cell and spatial transcriptomics data, offering a variety of downstream analyses.https://github.com/earmingol/scCellFiesccellfiebiotools:sccellfie0.6.3Command-line toolhttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_4028Single-cell sequencinghttp://edamontology.org/topic_2259Systems biologyhttp://edamontology.org/topic_3308TranscriptomicsLinuxMacWindowsPythonMITMatureFree of chargeOpen accesshttp://edamontology.org/operation_2495Expression analysishttp://edamontology.org/data_3112Gene expression matrixhttp://edamontology.org/format_3590HDF5

http://edamontology.org/data_3112Gene expression matrixhttp://edamontology.org/format_3590HDF5

https://sccellfie.readthedocs.io/en/latest/API documentation10.1101/2025.05.09.653038PreprintErick Armingolhttps://earmingol.github.io/https://orcid.org/0000-0002-1546-9165RADAR-RamanPython package that decomposes Raman spectra into baseline, cosmic rays, noise and peaks with convolutional neural networks. It includes two pre-trained models (standard and ensemble), a synthetic data generator, training and fine-tuning tools, evaluation metrics, a command-line tool, and readers and writers for the common Raman file formats (SPC, JCAMP-DX, Renishaw WDF, Horiba LabSpec, TriVista, instrument text exports, Excel, Parquet, SQLite, HDF5, MATLAB, JSON, NumPy).https://github.com/bogdanoancea/RADARradar-ramanbiotools:radar-raman0.1.0LibraryCommand-line toolhttp://edamontology.org/topic_3370Analytical chemistryhttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_3306Biophysicshttp://edamontology.org/topic_3572Data quality managementWindowsMacLinuxPythonBSD-3-ClauseEmergingFree of chargeOpen accesshttp://edamontology.org/operation_3435Standardisation and normalisationhttp://edamontology.org/operation_3214Spectral analysishttp://edamontology.org/operation_0335Data formattinghttp://edamontology.org/data_3483Spectrumhttp://edamontology.org/format_3650NetCDFhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_4003NumPy formathttp://edamontology.org/format_3859JCAMP-DXhttp://edamontology.org/format_3620xlsxhttp://edamontology.org/format_3590HDF5http://edamontology.org/format_3475TSVhttp://edamontology.org/format_3626MAThttp://edamontology.org/format_3621SQLite formathttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3464JSON

http://edamontology.org/data_3483Spectrumhttp://edamontology.org/format_3650NetCDFhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/format_4003NumPy formathttp://edamontology.org/format_3859JCAMP-DXhttp://edamontology.org/format_3620xlsxhttp://edamontology.org/format_3590HDF5http://edamontology.org/format_3475TSVhttp://edamontology.org/format_3626MAThttp://edamontology.org/format_3621SQLite formathttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3464JSON

Splits each spectrum into baseline, cosmic rays, noise and peaks; the peaks are the corrected, denoised spectrum.https://github.com/bogdanoancea/RADARRepositoryhttps://github.com/bogdanoancea/RADAR/issuesIssue trackerhttps://pypi.org/project/radar-raman/Software package0.1.0https://doi.org/10.5281/zenodo.23760379Source code0.1.0https://github.com/bogdanoancea/RADAR/blob/main/docs/user_guide.mdUser manualhttps://github.com/bogdanoancea/RADAR/blob/main/docs/cli.mdCommand-line options10.1002/adom.202500736PrimaryBogdan Oanceabogdan.oancea@faa.unibuc.rohttps://unibuc.ro/user/bogdan.oancea/?lang=enhttps://orcid.org/0000-0001-6987-5137PersonDeveloperMaintainerPrimary contactProfessor of Computer Science at the University of Bucharest and Senior Researcher at the National Institute of Research and Development for Biological Sciences, BucharestJoel Sjöberghttps://orcid.org/0000-0002-8572-0431PersonDeveloperNational Institute of Research and Development for Biological Scienceshttps://www.incdsb.ro/en/InstituteProviderIon Petreion.petre@utu.fihttps://users.utu.fi/ionpet/https://orcid.org/0000-0002-5014-5529PersonContributorDeveloperMaintainerProfessor at the University of TurkuNicoleta Simineanicoleta.siminea@incdsb.roPersonContributorDeveloperMaintainerResearcher at the National Institute of Research and Development for Biological SciencesOmigatorTurns a one-sentence research intent into a ranked, evidence-backed shortlist of NCBI GEO datasets. Each candidate series is checked against editable criteria using series text, sample annotations and the linked abstract. Explanations quote the record and quotes are verified.https://omigator.rickinto.placeomigatorbiotools:omigator0.2.0Web applicationCommand-line toolhttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_0203Gene expressionTypeScriptMITEmergingFree of charge (with restrictions)Open accesshttps://github.com/rickintoplace/OmigatorRepositoryhttps://github.com/rickintoplace/Omigator/issuesIssue tracker10.5281/zenodo.190200740.2.0Eirik Heilmanneheilmann@proton.mehttps://rickinto.place/https://orcid.org/0009-0009-5596-736XDeveloperPrimary contactLongPolyASEA framework for allele-specific expression analysis in diploids and polyploids using long-read RNA-seq and phased genome assemblies.https://polyase.readthedocs.io/en/latest/index.htmllongpolyasebiotools:longpolyaseWorkflowhttp://edamontology.org/topic_3308TranscriptomicsOpen accesshttps://github.com/NIB-SI/syntelogfinderRepositorySyntelogfinder: a nextflow pipeline to identify syntenic genes in phased genome assemblies using GENESPACE. Input: phased genome assembly and their annotations in GFF3 format.https://github.com/nadjano/longrnaseqRepositoryA nextflow pipeline for allelic gene and isoform quantification of long-read RNA-seq data, including novel isoform discovery and quality control. Input: long-read RNA-seq data (PacBio or ONT)(2 conditions and replicates) and a phased genome assembly with its annotation in GTF format.https://github.com/NIB-SI/polyaseRepositoryA python package for allele-specific expression analysis using the inputs of the two previous components. Gene and isoform-level ASE analysis, differential isoform usage analysis, and visualization of the results. Input: the outputs of syntelogfinder and longrnaseq.https://github.com/ConesaLab/VALT_Summer_Course/blob/master/practical/day3/allelespecificexpression/notebooks/Jupyter_potato_allele_expression_unrun.ipynbTraining materialhttps://github.com/ConesaLab/VALT_Summer_Course/blob/master/practical/day3/allelespecificexpression/notebooks/Jupyter_potato_allele_expression_unrun.ipynbhttps://polyase.readthedocs.io/en/latest/index.htmlGeneral10.1186/s13007-026-01569-842482259PMC13673704MethodNadja Noltenadja.franziska.nolte@nib.sihttps://orcid.org/0000-0003-3737-2011PersonPrimary contactLiganxLiganx is a free, browser-based molecular docking tool. It docks small molecules into wild-type and mutant protein structures and reports the binding-score difference (delta-delta), making it well suited to drug-resistance and selectivity analysis. No installation required.https://liganx.comliganxbiotools:liganxWeb applicationhttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_3332Computational chemistryNot licensedEmergingFree of chargeOpen accesshttp://edamontology.org/operation_0478Molecular dockinghttp://edamontology.org/operation_3938Virtual screeningSNPlyticsFree macOS application for TaqMan endpoint SNP genotyping. Calls genotypes from two-channel allelic discrimination data with five independent algorithms (ALCHEMY, BCGA, fitPoly, polar thresholds, robust Student-t mixture) and a configurable consensus, with spectral compensation, QC metrics, Hardy-Weinberg and case/control association statistics, multi-plate cohorts, and publication-ready exports including R and Python reproducibility scripts. Reads RDML and tab-delimited endpoint exports. Runs fully offlinehttps://cellxapps.com/snplytics/snplyticsbiotools:snplytics1.0RRID:SCR_029223rridDesktop applicationhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3056Population geneticshttp://edamontology.org/topic_0199Genetic variationMacProprietaryMatureFree of chargeOpen accesshttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_0484SNP detectionhttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/data_3108Experimental measurement

http://edamontology.org/data_0920Genotype/phenotype reporthttp://edamontology.org/format_3752CSV

http://edamontology.org/data_2884Plothttp://edamontology.org/format_3603PNGhttp://edamontology.org/format_3508PDF

Calls genotypes from two-channel endpoint allelic discrimination data with five independent algorithms and a configurable consensus, then computes QC, Hardy-Weinberg and case/control association statistics with exportable figures and reports.https://github.com/oktarguloglu/SNPlytics/issuesIssue trackerhttps://apps.apple.com/app/snplytics/id6803502630Binaries1.0https://github.com/oktarguloglu/SNPlytics/releasesDownloads pagehttps://github.com/oktarguloglu/SNPlytics/releases/latest/download/SNPlytics-1.0.0.dmgBinarieshttps://github.com/oktarguloglu/SNPlytics#readmeGeneralhttps://github.com/oktarguloglu/SNPlytics/blob/main/LICENSETerms of use10.5281/zenodo.23767745OtherMehmet Oktar Gulogluoktar.guloglu@gmail.comhttps://orcid.org/0000-0002-3629-7788PersonDeveloperPrimary contactDrybenchDrybench is a free suite of in-browser research tools for biology and drug development. It covers assay analysis (dose-response and IC50/EC50 fitting, ELISA and protein standard curves, qPCR fold change, plate QC), lab calculations (molarity, dilutions, serial dilutions, A280, buffers), DNA and protein sequence tools (reverse complement, primer Tm, dimer and hairpin checks, protein MW and pI), plasmid maps with restriction digests, small-molecule drug-likeness, protein structure lookup, bioreactor simulation, and clinical-trial and FDA approval data. Each result names its method, data source and limits. The tools run in the web browser, and no account is neededhttps://www.drybench.comdrybenchbiotools:drybenchv1Desktop applicationSuiteBioinformatics portalWeb applicationhttp://edamontology.org/topic_4019BiosciencesEmergingFree of chargeOpen accesshttp://edamontology.org/operation_2403Sequence analysishttps://www.drybench.com/docsTechnical monitoringDocumentationhttps://www.drybench.com/methodsOtherMethods documentationhttps://www.drybench.com/docsGeneralMat Bealemat@drybench.comAF3 InspectorAn open, client-side, zero-install web application designed to dissect, align, and interactively explore the complete ensemble of structural models produced by AlphaFold 3. Preprint: https://www.biorxiv.org/content/10.64898/2026.09.21.753240v1https://pdbms.altervista.org/af3viewer/af3_inspectorbiotools:af3_inspectorhttps://pdbms.altervista.org/af3viewer/Service10.64898/2026.09.21.753240PreprintScratch StudioScratch Studio is a desktop application for Apple Silicon Macs (macOS 11 or later) that analyses scratch (wound-healing) cell-migration assays, from raw images to publication-ready figures and statistics. Wound area is measured with a built-in classical detector or optional Cellpose or SAM 2 segmentation, all run locally. Calibration is read from the scale bar by OCR, or set manually. It reports percent wound closure, closure rate and edge velocity per condition, timepoint and biological replicate, flags blurred, poorly exposed or drifting frames, and picks representative images closest to the group mean. A recommendation engine selects robust tests (Welch t-test and ANOVA, Dunnett comparisons against control, two-way and repeated-measures designs, four-parameter logistic dose–response) with effect sizes and assumption checks. Outputs include charts, a multi-panel figure composer, CSV, Excel and PDF reports, a time-lapse animation, and auto-generated Methods and Results text.https://www.cellxapps.com/scratchstudio/scratch_studiobiotools:scratch_studio1.0.3doi:10.5281/zenodo.23751319doiDesktop applicationhttp://edamontology.org/topic_2229Cell biologyhttp://edamontology.org/topic_3383Bioimaginghttp://edamontology.org/topic_3385Light microscopyhttp://edamontology.org/topic_2269Statistics and probabilityMacPythonPolyForm-Noncommercial-1.0.0EmergingFree of charge (with restrictions)http://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3446Cell migration analysishttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3997MPEG-4http://edamontology.org/format_3592BMPhttp://edamontology.org/format_3591TIFFhttp://edamontology.org/format_3990AVIhttp://edamontology.org/format_3603PNGhttp://edamontology.org/format_3579JPG

http://edamontology.org/data_2884Plothttp://edamontology.org/format_3604SVGhttp://edamontology.org/format_3591TIFFhttp://edamontology.org/format_3603PNGhttp://edamontology.org/format_3508PDFhttp://edamontology.org/format_3579JPG

http://edamontology.org/data_2048Reporthttp://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/format_3620xlsxhttp://edamontology.org/format_3508PDFhttp://edamontology.org/format_3752CSV

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3997MPEG-4http://edamontology.org/format_3467GIF

Input: time-lapse microscopy images (TIFF, PNG, JPEG, BMP) or videos (MP4, AVI, MOV, MKV). Outputs: figures (PNG, JPEG, TIFF, PDF, SVG), results tables and reports (CSV, Excel, PDF), Methods and Results text (plain text, Markdown) and a time-lapse animation (GIF, MP4).https://github.com/oktarguloglu/scratch-studio/issuesIssue trackerhttps://github.com/oktarguloglu/scratch-studio/releases/latestDownloads pageDeveloper-ID signed, Apple-notarized disk image (.dmg) for Apple Silicon Macs.https://github.com/oktarguloglu/scratch-studioGeneralhttps://github.com/oktarguloglu/scratch-studio#downloadInstallation instructionshttps://github.com/oktarguloglu/scratch-studio#how-to-citeCitation instructionshttps://github.com/oktarguloglu/scratch-studio/releasesRelease noteshttps://github.com/oktarguloglu/scratch-studio/blob/main/LICENSETerms of usecellposeusesM. Oktar Gulogluhttps://orcid.org/0000-0002-3629-7788PersonDeveloperMaintainerPrimary contactspatial-continuum-oncologyBiophysical reaction-diffusion and evolutionary game engine resolving the post-ADAURA osimertinib cessation dilemma via microvascular sanctuaries and the Composite Resistance Index (CRI).https://lukecele.github.io/spatial-continuum-oncology/spatial-continuum-oncologybiotools:spatial-continuum-oncology1.0.2Command-line toolWeb applicationhttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_3306Biophysicshttp://edamontology.org/topic_2259Systems biologyhttp://edamontology.org/topic_3308TranscriptomicsLinuxWindowsMacPythonJavaScriptMITMatureFree of chargeOpen accesshttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/data_3108Experimental measurementhttp://edamontology.org/format_3475TSVhttp://edamontology.org/format_3752CSV

http://edamontology.org/data_2048Reporthttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_3603PNGhttp://edamontology.org/format_3508PDF

Simulates multiscale spatiotemporal drug distribution, perivascular sanctuaries, and subclonal evolutionary dynamics in resected lung adenocarcinoma.spatial-continuum --helphttps://github.com/Lukecele/spatial-continuum-oncologyRepositoryPrimary source code and development repositoryhttps://doi.org/10.5281/zenodo.23754999Software cataloguePermanent CERN Zenodo archive releasehttps://github.com/Lukecele/spatial-continuum-oncology/issuesIssue trackerIssue reporting and bug trackinghttps://pypi.org/project/spatial-continuum/Software packageOfficial PyPI distribution wheel and sdist1.0.2https://github.com/Lukecele/spatial-continuum-oncology/archive/refs/tags/v1.0.2.zipSource codeSource code ZIP bundle1.0.2https://github.com/Lukecele/spatial-continuum-oncology#readmeGeneralMain architectural documentation and user guidehttps://github.com/Lukecele/spatial-continuum-oncology/blob/main/CITATION.cffCitation instructionsCitation File Format10.21203/rs.3.rs-11530312/v1PreprintFlagship theoretical and clinical study in review with Nature PortfolioLuca Celebranohttps://github.com/Lukecelehttps://orcid.org/0009-0007-0931-355505290cv24PersonDeveloperPrimary contactMD Candidate, Department of Clinical Medicine and Surgery, Università degli Studi di Napoli Federico IIUniversità degli Studi di Napoli Federico IIhttp://www.unina.it05290cv24InstituteProviderHost institutionspatial-continuumBiophysical reaction-diffusion and evolutionary game engine resolving the post-ADAURA osimertinib cessation dilemma via microvascular sanctuaries and the Composite Resistance Index (CRI).https://lukecele.github.io/spatial-continuum-oncology/spatial-continuumbiotools:spatial-continuum1.0.2Web applicationCommand-line toolhttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_3306Biophysicshttp://edamontology.org/topic_2259Systems biologyPythonJavaScriptMIThttp://edamontology.org/operation_2426Modelling and simulationhttps://github.com/Lukecele/spatial-continuum-oncologyRepositoryhttps://doi.org/10.5281/zenodo.23754999Software cataloguehttps://pypi.org/project/spatial-continuum/Software package1.0.210.21203/rs.3.rs-11530312/v1PreprintLuca Celebranohttps://orcid.org/0009-0007-0931-3555PersonDeveloperPrimary contactColonyCounterQuantifies colony-formation (clonogenic) assays from flatbed scans of stained multi-well plates. It locates each well, segments and counts colonies, measures colony size and staining intensity, and runs the comparative statistics, producing a report.https://github.com/SpencerFrangou/ColonyCountercolonycounterbiotools:colonycounterCommand-line toolhttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_2229Cell biologyLinuxMacWindowsPythonMITEmergingFree of chargehttp://edamontology.org/operation_3443Image analysishttp://edamontology.org/operation_2238Statistical calculationhttps://github.com/SpencerFrangou/ColonyCounterRepositoryGitHub repositoryhttps://github.com/SpencerFrangou/ColonyCounterUser manualRepository README10.5281/zenodo.23780010PrimarySpencer W. Frangouhttps://orcid.org/0009-0008-1125-4053PersonDeveloperXenoPanelConfiguration-driven toolkit for targeted transcriptomic panel data. It removes cross-species (host) contamination in xenograft samples, standardizes and normalizes gene-expression measurements, runs differential expression, and supports decomposition and network and pathway analyses.https://spencerfrangou.github.io/XenoPanel/xenopanelbiotools:xenopanelLibraryCommand-line toolhttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_3170RNA-SeqLinuxWindowsMacRPythonMITEmergingFree of chargehttp://edamontology.org/operation_3187Sequence contamination filteringhttp://edamontology.org/operation_3435Standardisation and normalisationhttp://edamontology.org/operation_3223Differential gene expression profilinghttps://github.com/SpencerFrangou/XenoPanelRepositoryGitHub repositoryhttps://spencerfrangou.github.io/XenoPanel/User manualProject website10.5281/zenodo.23768221PrimarySpencer W. Frangouhttps://orcid.org/0009-0008-1125-4053PersonDeveloperSplicRSplicR is building the next generation of biotech software, making CRISPR screening faster, simpler, and more accessible to researchers.https://www.splicr.org/splicrbiotools:splicrspaCRspaCR links pooled CRISPR-Cas9 perturbations to single-cell spatial phenotypes in high-content microscopy images. It segments cells, nuclei, pathogens and organelles with Cellpose, measures morphology, intensity, texture and colocalization features into a SQLite project, trains image and measurement classifiers, maps sequencing reads to wells and gRNAs, and estimates per-guide and per-gene effects by regression.https://einarolafsson.github.io/spacr/spacrbiotools:spacr1.5.1.6doi:10.5281/zenodo.21343316doiDesktop applicationLibraryCommand-line toolhttp://edamontology.org/topic_3383Bioimaginghttp://edamontology.org/topic_3385Light microscopyhttp://edamontology.org/topic_2229Cell biologyhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_0085Functional genomicshttp://edamontology.org/topic_3474Machine learningWindowsMacLinuxPythonBSD-3-ClauseEmergingFree of chargeOpen accesshttp://edamontology.org/operation_3937Feature extractionhttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_3443Image analysishttp://edamontology.org/data_3424Raw imagehttp://edamontology.org/format_3727OME-TIFFhttp://edamontology.org/format_3591TIFFhttp://edamontology.org/format_3603PNG

http://edamontology.org/data_2968Imagehttp://edamontology.org/format_3591TIFFhttp://edamontology.org/format_3603PNG

http://edamontology.org/data_2082Matrixhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3621SQLite format

Mask and Measure modules: Cellpose segmentation of cells, nuclei, pathogens and organelles, followed by morphology, intensity, texture, spatial and colocalization measurement of every object into a SQLite project, with object crops.spacr-run mask --settings settings.csv ; spacr-run measure --settings settings.csvhttp://edamontology.org/operation_3553Image annotationhttp://edamontology.org/operation_2990Classificationhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3591TIFFhttp://edamontology.org/format_3603PNG

http://edamontology.org/data_1772Scorehttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3621SQLite format

Annotate and Classify modules: keyboard-driven labelling of object crops with active-learning queues, then training of image or measurement-based classifiers, with held-out performance recorded alongside each checkpoint.spacr-run classify --settings settings.csvhttp://edamontology.org/operation_3933Demultiplexinghttp://edamontology.org/operation_3196Genotypinghttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1930FASTQ

http://edamontology.org/data_2082Matrixhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3621SQLite format

Map Barcodes module: assigns sequencing reads to plate wells and to gRNA barcodes, and reports per-well guide abundance with collision and coverage QC.spacr-run map_barcodes --settings settings.csvhttp://edamontology.org/operation_3659Regression analysishttp://edamontology.org/operation_3658Statistical inferencehttp://edamontology.org/data_2082Matrixhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3621SQLite format

http://edamontology.org/data_0920Genotype/phenotype reporthttp://edamontology.org/format_3752CSV

Regression module: estimates guide, gene, condition and control effects with model families suited to continuous, fractional and count responses, and returns a ranked gene-level hit list.spacr-run regression --settings settings.csvhttp://edamontology.org/operation_3935Dimensionality reductionhttp://edamontology.org/operation_3432Clusteringhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/data_2082Matrixhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3621SQLite format

http://edamontology.org/data_2884Plothttp://edamontology.org/format_3603PNG

UMAP, gating, graph-building and QC dashboard tools for exploring single-object embeddings and per-plate quality.https://github.com/EinarOlafsson/spacrRepositorySource code repository.https://github.com/EinarOlafsson/spacr/issuesIssue trackerBug reports and feature requests.https://pypi.org/project/spacr/Software catalogueReleased package on PyPI.https://anaconda.org/conda-forge/spacrSoftware catalogueconda-forge package.https://pypi.org/project/spacr/Software packagepip install "spacr[qt]"1.5.0.9https://anaconda.org/conda-forge/spacrSoftware packageconda install conda-forge::spacrhttps://github.com/EinarOlafsson/spacrSource codeGit repository; the main branch carries the latest release.https://github.com/EinarOlafsson/spacr/releases/latestDownloads pageSelf-contained desktop installers for Linux, macOS and Windows.https://einarolafsson.github.io/spacr/GeneralProject documentation site.https://einarolafsson.github.io/spacr/api/spacr/index.htmlAPI documentationGenerated Python API reference.https://einarolafsson.github.io/spacr/tutorials/Training materialInteractive walkthroughs of the core workflow.https://github.com/EinarOlafsson/spacr/blob/main/docs/source/installer_guide.rstInstallation instructionsInstallers, extras, update, uninstall and troubleshooting.https://github.com/EinarOlafsson/spacr/blob/main/CITATION.cffCitation instructionsMachine-readable citation metadata.https://github.com/EinarOlafsson/spacr/blob/main/CONTRIBUTING.mdContributions policyhttps://github.com/EinarOlafsson/spacr/blob/main/CODE_OF_CONDUCT.mdCode of conduct10.64898/2026.07.08.737057PrimaryA pooled image-based CRISPR screen identifies EAF1 as a T. gondii modulator of ESCRT subversion. bioRxiv, 2026.10.1016/j.celrep.2025.11569440349346UsageIRE1a promotes phagosomal calcium flux to enhance macrophage fungicidal activity. Cell Reports, 2025.10.1128/msphere.01011-2440172222UsageMetabolic adaptability and nutrient scavenging in Toxoplasma gondii. mSphere, 2025.10.64898/2026.07.20.739547UsageToxoplasma GRA8 engages the host ESCRT accessory protein ALG-2. bioRxiv, 2026.10.5281/zenodo.21343316OtherArchived software releases, concept DOI for all versions.Einar Birnir Olafssonolafsson@med.umich.comhttps://orcid.org/0000-0002-3388-061XPersonPrimary contactDeveloperMaintainerLead developer and maintainer.Christophe-Sebastien Arnoldhttps://orcid.org/0000-0002-2392-5837PersonContributorJacob A. Kellermeierhttps://orcid.org/0000-0001-9211-7406PersonContributorPatrick A. Rimplehttps://orcid.org/0009-0000-6834-8343PersonContributorHargobinder Kaurhttps://orcid.org/0000-0002-8275-2091PersonContributorYifan Wanghttps://orcid.org/0000-0001-9451-0041PersonContributorJonathan Z. Sextonhttps://orcid.org/0000-0002-9244-5888PersonContributorStaffan Svardhttps://orcid.org/0000-0002-7392-1746PersonContributorName is 'Staffan Svard' here; the CITATION.cff spelling is 'Svard' with a-diaeresis.Vern B. Carruthershttps://orcid.org/0000-0001-6859-8895PersonContributorMatthew J. O'Mearahttps://orcid.org/0000-0002-3128-5331PersonContributorSigBridgeRIdentifies phenotype-associated cell subpopulations by integrating phenotypic data (e.g., survival, drug sensitivity), bulk gene expression, and single-cell RNA-seq (scRNA-seq) profiles. It employs multiple algorithms to reliably connect cellular features with clinical or functional phenotypes, offering a unified pipeline for multi-modal analysis that uncovers biologically and clinically relevant cell states in heterogeneous datasets.https://github.com/WangLabCSU/SigBridgeRsigbridgerbiotools:sigbridger3.8.5http://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_3308TranscriptomicsWindowsLinuxMacRGPL-3.0MatureFree of chargeOpen accesshttps://github.com/WangLabCSU/SigBridgeR/issuesIssue trackerhttps://github.com/WangLabCSU/SigBridgeRRepositoryhttps://github.com/WangLabCSU/SigBridgeR/archive/refs/tags/v3.8.5.zipSource code3.8.5https://wanglabcsu.github.io/SigBridgeR/Quick start guideEvidenceEvidence is a web application developed by Helena Bioinformatics for publishing and exploring versioned scientific study records. It connects cohort-level results with methods, completed sensitivity analyses, source files, code and citations. Interactive controls explore released results and documented analytical decisions, with links to the pinned scientific source. The application does not compute new scientific results in the browser and does not provide patient-specific interpretation or clinical decision support.https://evidence.helena.bio/helena-evidencebiotools:helena-evidenceWeb applicationhttp://edamontology.org/topic_4010Open sciencehttps://evidence.helena.bio/methodsGeneralPublication method, versioned sources, completed sensitivity analyses and source provenance.Helena Bioinformaticscontact@helena.biohttps://www.helena.bio/DeveloperBioinformatics software company in Sofia, Bulgaria. Developer and provider of Evidence.UndertoneUndertone is a web application developed by Helena Bioinformatics for interpreting whole-study GWAS summary statistics. It identifies and ranks associated loci and brings fine-mapping, candidate variants and genes, regulatory evidence, tissue or cell context, and mechanism hypotheses into traceable analysis workspaces and reports. Fine-mapping and downstream evidence depend on compatible inputs and reference data. Outputs support research and testable biological hypotheses; association evidence does not establish causality or clinical utility.https://undertone.helena.bio/undertonebiotools:undertoneWeb applicationhttp://edamontology.org/topic_3517GWAS studyHelena Bioinformaticscontact@helena.biohttps://www.helena.bio/DeveloperBioinformatics software company in Sofia, Bulgaria. Developer and provider of Undertone.TalindrewTalindrew is a browser-based molecular biology workbench with its own MCP server. Edit DNA on circular and linear plasmid maps; simulate restriction, Gibson, Golden Gate, Gateway, TOPO/TA and In-Fusion cloning; plan whole strategies on an OpenCloning-compatible workspace (pydna engine, OpenCloning JSON in and out); design and score PCR primers; verify clones against AB1/SCF/ZTR Sanger traces; align up to 200 sequences; simulate digests and agarose gels; design CRISPR guides; translate, find ORFs and optimise codons; predict protein structures; screen ligands with the FoldRx fold-pocket-dock-ADMET pipeline; and record it all in an electronic lab notebook. The remote MCP server (https://mcp.talindrew.com/mcp) gives Claude, ChatGPT, Codex, Cursor and other AI assistants 90 of these tools. Opens SnapGene .dna, GenBank, FASTA, EMBL and ApE files. Free plan; nothing to install.https://www.talindrew.comtalindrewbiotools:talindrewWeb applicationWorkbenchWeb APIhttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_3912Genetic engineeringhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3519PCR experimenthttp://edamontology.org/topic_3895Synthetic biologyhttp://edamontology.org/topic_0632Probes and primershttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_0607Laboratory information managementhttp://edamontology.org/topic_3068Literature and languageWindowsLinuxMacProprietaryEmergingFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_0253Sequence feature detectionhttp://edamontology.org/operation_0361Sequence annotationhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_0231Sequence editinghttp://edamontology.org/operation_0578Plasmid map drawinghttp://edamontology.org/data_2887Nucleic acid sequence recordhttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_1286Plasmid maphttp://edamontology.org/format_3508PDFhttp://edamontology.org/format_3604SVGhttp://edamontology.org/format_3603PNG

http://edamontology.org/data_2887Nucleic acid sequence recordhttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/format_1929FASTA

Sequence editor and plasmid maps: circular, linear and base-level views; cut, paste and reverse-complement with annotations that follow the edit; automatic detection of 60 common features (markers, origins, promoters, tags). Also opens SnapGene .dna and ApE files.http://edamontology.org/operation_0431Restriction site recognitionhttp://edamontology.org/operation_0365Restriction digesthttp://edamontology.org/data_2887Nucleic acid sequence recordhttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_1239Restriction digest

Restriction analysis over 600+ enzymes in eleven sets (commercial, NEB, Thermo, unique cutters, Type IIS, Golden Gate), with Dam, Dcm and EcoKI methylation sensitivity, then a digest and agarose gel simulation with six ladders.http://edamontology.org/operation_3095Nucleic acid designhttp://edamontology.org/operation_0365Restriction digesthttp://edamontology.org/operation_0308PCR primer designhttp://edamontology.org/data_2887Nucleic acid sequence recordhttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_2887Nucleic acid sequence recordhttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/format_1929FASTA

In-silico cloning: restriction-ligation, Gibson, Golden Gate, Gateway BP/LR, TOPO/TA, In-Fusion, HiFi, PCR, homologous recombination and CRISPR steps on one node-graph workspace. Reads and writes OpenCloning cloning-strategy JSON and runs reactions on the pydna engine, so a file opens in either tool. Kit templates (MoClo YTK and others) included.http://edamontology.org/operation_2419Primer and probe designhttp://edamontology.org/operation_0455Nucleic acid thermodynamic property calculationhttp://edamontology.org/operation_0308PCR primer designhttp://edamontology.org/data_2887Nucleic acid sequence recordhttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_1240PCR primershttp://edamontology.org/format_1929FASTA

Primer design over any selected region: ranked pairs scored on Tm (nearest-neighbour, Wallace, salt-adjusted), GC, 3' clamp, hairpins, self- and cross-dimers and binding sites; mutagenesis and cloning-overhang primers; amplicon prediction across the origin of circular templates.http://edamontology.org/operation_0491Pairwise sequence alignmenthttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_0924Sequence tracehttp://edamontology.org/format_3000AB1http://edamontology.org/format_3018ZTRhttp://edamontology.org/format_1632SCFhttp://edamontology.org/data_2887Nucleic acid sequence recordhttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0863Sequence alignment

Clone verification: align Sanger sequencing traces to the expected construct and show mismatches with the chromatogram.http://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newick

Multiple sequence alignment of DNA, RNA or protein: up to 200 sequences of up to 30 kb, with consensus, conservation track, identity heat map and UPGMA tree.http://edamontology.org/operation_3095Nucleic acid designhttp://edamontology.org/data_2887Nucleic acid sequence recordhttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1929FASTA

CRISPR guide RNA design: find and rank guides in a selected region, ready to add as a CRISPR step in the cloning workspace.http://edamontology.org/operation_0286Codon usage analysishttp://edamontology.org/operation_0250Protein property calculationhttp://edamontology.org/operation_2510DNA back-translationhttp://edamontology.org/operation_0436Coding region predictionhttp://edamontology.org/operation_0371DNA translationhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1929FASTA

Translation and proteins: six-frame translation and ORF finding (circular-aware), reverse translation, codon optimisation with CAI, and protein properties (molecular weight, pI, extinction coefficients, GRAVY, instability).http://edamontology.org/operation_0474Protein structure predictionhttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_1477mmCIF

Protein structure: search AlphaFold DB, predict structures with ESMFold, and view them in 3D coloured by pLDDT (prediction on paid plans).http://edamontology.org/operation_3938Virtual screeninghttp://edamontology.org/operation_4009Small molecule designhttp://edamontology.org/operation_2575Binding site predictionhttp://edamontology.org/operation_0482Protein-ligand dockinghttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2301SMILES stringhttp://edamontology.org/format_1196SMILES

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

FoldRx drug discovery pipeline, built as a node graph: fold the target, find pockets, dock and rank ligands, ADMET filters (Lipinski, PAINS, hERG, Ames, Caco-2), pose checks, selectivity and analog design (paid plans).http://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_0305Literature searchhttp://edamontology.org/data_2044Sequence

http://edamontology.org/data_0971Article

http://edamontology.org/data_2887Nucleic acid sequence recordhttp://edamontology.org/format_1936GenBank format

Literature and repositories: search PubMed, Europe PMC and NCBI Gene, and import sequences from Addgene, NCBI, Benchling, SnapGene, iGEM and Euroscarf into the workspace.https://app.talindrew.comServiceThe web app. Sign in with Google; the Free plan includes the cloning suite and the lab notebook.https://mcp.talindrew.com/mcpServiceRemote MCP server (Streamable HTTP, OAuth): 90 molecular biology tools for Claude, ChatGPT, Codex, Cursor, VS Code and other MCP clients.https://github.com/Arnab28122000/talindrew-mcpRepositoryConnection details and setup instructions for the MCP server.https://registry.modelcontextprotocol.io/v0/servers?search=com.talindrew/mcpSoftware catalogueOfficial MCP Registry entry com.talindrew/mcp.https://www.youtube.com/@talindrewSocial mediaVideo walkthroughs.https://www.talindrew.com/featuresGeneralEvery capability, one line each.https://www.talindrew.com/guidesUser manualHow-to guides for cloning, primers, CRISPR, alignment and drug discovery.https://www.talindrew.com/mcpInstallation instructionsAPI documentationConnecting the MCP server to 23 AI apps, and the full tool list.https://www.talindrew.com/videosTraining materialNarrated walkthroughs with chapters and transcripts.https://www.talindrew.com/changelogRelease notesDated release notes; RSS at /changelog/rss.xml.https://www.talindrew.com/termsTerms of usehttps://www.talindrew.com/privacyOtherPrivacy policy.https://www.talindrew.com/guides/mcp-servers-for-molecular-biologyUser manualComparison of MCP servers for molecular biology (Talindrew, BioMCP, gget-mcp, Addgene MCP and others).https://www.talindrew.com/guides/claude-for-molecular-cloningQuick start guideUsing Claude with the Talindrew MCP server for molecular cloning.opencloningusespydnausesprimer3usesbiopythonusesTalindrewtalindrew@gmail.comhttps://www.talindrew.comProjectProviderDeveloperPrimary contactParetoMolFree browser-based web application for multi-objective Pareto analysis of drug-like molecules. Computes physicochemical properties with RDKit.js (WebAssembly, client-side), identifies Pareto-optimal subsets, and provides interactive analysis views. Optional ADMET predictions via ADMET-AI (Chemprop D-MPNN).https://paretomol.comparetomolbiotools:paretomol0.22.0Web applicationhttp://edamontology.org/topic_2258Cheminformaticshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_3343Compound libraries and screeninghttp://edamontology.org/topic_2840Toxicologyhttp://edamontology.org/topic_3375Drug metabolismWindowsMacLinuxJavaScriptMITFree of chargeOpen accesshttp://edamontology.org/operation_2425Optimisation and refinementhttp://edamontology.org/operation_3438Calculationhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/data_2087Molecular propertyhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_1196SMILEShttp://edamontology.org/format_3814SDF

http://edamontology.org/data_2087Molecular propertyhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3814SDF

https://github.com/IlkhamFY/paretomolRepositoryhttps://github.com/IlkhamFY/paretomol/issuesIssue tracker10.1039/d6dd00366dPrimaryIlkham YabbarovPersonDeveloperPrimary contactRodrigo A. Vargas-HernándezPersonContributorpyLocusZoompyLocusZoom is an open-source Python library for visualizing genome-wide association study (GWAS) results. It creates LocusZoom-style regional association plots with linkage disequilibrium (LD) coloring, gene and exon tracks, and recombination overlays. Additional plots include Manhattan, QQ, Miami, eQTL, fine-mapping credible sets, PheWAS, forest plots, LD heatmaps and colocalization comparisons. Matplotlib provides static figures; Plotly and Bokeh provide interactive views. The library accepts pandas DataFrames and includes loaders for PLINK, GEMMA, REGENIE, BOLT-LMM, SAIGE, GTEx, SuSiE and FINEMAP outputs. It supports canine and feline reference data, automatic Ensembl gene annotations, and custom reference data for other species. LD can be supplied or calculated with PLINK. Requires Python 3.11 or later and is released under GPL-3.0-or-later.https://github.com/michael-denyer/pyLocusZoompylocuszoombiotools:pylocuszoom5.4.0doi:10.5281/zenodo.22665975doiLibraryhttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_3055Quantitative geneticshttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_0622GenomicsPythonGPL-3.0-or-laterEmergingFree of chargehttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/data_0920Genotype/phenotype report

http://edamontology.org/data_2884Plothttp://edamontology.org/format_3604SVGhttp://edamontology.org/format_3508PDFhttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_3603PNG

Visualizes GWAS summary statistics, eQTL associations, fine-mapping results and study effect estimates. Regional plots can include gene annotations, recombination rates and supplied or PLINK-calculated LD. Returns native Matplotlib, Plotly or Bokeh figures for display and export; available export formats depend on the backend.https://github.com/michael-denyer/pyLocusZoomRepositoryhttps://github.com/michael-denyer/pyLocusZoom/issuesIssue trackerhttps://doi.org/10.5281/zenodo.22665975OtherZenodo concept DOI for citing pyLocusZoom software releases.https://pypi.org/project/pylocuszoom/Software packagehttps://anaconda.org/bioconda/pylocuszoomSoftware packageBioconda package; its available version may differ from the current PyPI release.https://github.com/michael-denyer/pyLocusZoom/releasesDownloads pagehttps://github.com/michael-denyer/pyLocusZoomSource codehttps://github.com/michael-denyer/pyLocusZoom/blob/main/docs/GETTING-STARTED.mdInstallation instructionsQuick start guidehttps://github.com/michael-denyer/pyLocusZoom/blob/main/docs/USER_GUIDE.mdUser manualAPI documentationhttps://github.com/michael-denyer/pyLocusZoom/blob/main/docs/CONFIGURATION.mdGeneralSpecies, reference data and plotting configuration.https://github.com/michael-denyer/pyLocusZoom/blob/main/examples/getting_started.ipynbTraining materialhttps://github.com/michael-denyer/pyLocusZoom/blob/main/CITATION.cffCitation instructionshttps://github.com/michael-denyer/pyLocusZoom/blob/main/CHANGELOG.mdRelease notesMichael Denyerhttps://github.com/michael-denyerhttps://orcid.org/0000-0001-9667-5683PersonDeveloperMaintainerPrimary contactDRS-Transcript-PredictionPredict transcripts based on a finding candidate start/stop sites, and filter alternative transcripts that could make use of various start/stop combinations.https://github.com/Dunning-Hotopp-Lab/Direct_RNA_Sequencingdrs-transcript-predictionbiotools:drs-transcript-prediction1.0.5Command-line toolhttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_3512Gene transcriptsPythonAGPL-3.0http://edamontology.org/operation_3258Transcriptome assemblyhttps://anaconda.org/bioconda/drs-transcript-predictionSoftware package10.1128/mbio.02359-2439287442PMC11481537Julie C Dunning Hotoppjdhotopp@som.umaryland.eduhttps://orcid.org/0000-0003-3862-986XSynBio StudioOpen-source integrated development environment (IDE) for synthetic biology: design genetic circuits, simulate them, and work with biological parts in one desktop app. Includes a web demo and a Python engine.https://github.com/jorgegn29/Synbio-studiosynbio_studiobiotools:synbio_studioDesktop applicationWeb applicationhttp://edamontology.org/topic_3895Synthetic biologyWindowsJavaScriptPythonAGPL-3.0https://github.com/jorgegn29/Synbio-studioRepositorySource code repositoryhttps://jorgegn29.github.io/Synbio-studio/OtherOnline web demo of SynBio Studiohttps://huggingface.co/spaces/jorgegn29/synbio-studioServiceWeb demo on Hugging Face Spaceshttps://huggingface.co/spaces/jorgegn29/synbio-studio-engineServiceSimulation engine and MCP server10.5281/zenodo.23436206Jorge Guillem NajarroPersonDeveloperHIDE-DeconvHIDE-Deconv is a framework for characterizing cellular remodeling from bulk RNA-seq data using hierarchical cell-type deconvolution across multiple levels of cellular resolution. It provides an integrated workflow for single-cell reference preprocessing, estimation of cellular compositions, and downstream analysis of deconvolution results, including visualization, clustering, differential composition, and survival analysis.https://github.com/dvoelkl/HIDE-deconvhide-deconvbiotools:hide-deconv0.4.3LibraryCommand-line toolhttp://edamontology.org/topic_3307Computational biologyhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3308TranscriptomicsWindowsMacLinuxPythonMITEmergingFree of chargeOpen accesshttp://edamontology.org/operation_3935Dimensionality reductionhttp://edamontology.org/data_3917Count matrixhttp://edamontology.org/format_3752CSVhttp://edamontology.org/data_3917Count matrixhttp://edamontology.org/format_3590HDF5

http://edamontology.org/data_2082Matrix

Run the HIDE-Deconv guided deconvolution workflow.`hide-deconv run`http://edamontology.org/operation_2238Statistical calculation

http://edamontology.org/data_2048Report

Perform statistical tests on the cellular compositions, to find differences between different cohorts.`hide-deconv analyze diff`http://edamontology.org/operation_2238Statistical calculation

http://edamontology.org/data_2968Image

http://edamontology.org/data_2048Report

Perform statistical tests between two cohorts and visualize the differences at different cell type annotation layers.´hide-deconv analyze hdiff`http://edamontology.org/operation_3432Clustering

http://edamontology.org/data_2968Image

http://edamontology.org/data_2082Matrix

Run unsupervised clustering using greedy modular communities on the deconvolved cell-type proportions.`hide-deconv analyze cluster`http://edamontology.org/operation_3432Clustering

http://edamontology.org/data_2968Image

http://edamontology.org/data_2082Matrix

Run k-mean clustering on the deconvolved cell type composition.`hide-deconv analyze kmean`http://edamontology.org/operation_0337Visualisation

http://edamontology.org/data_2968Image

Create a PCA plot of the deconvolved cell type composition and label the data by meta information provided by a sample sheet`hide-deconv analyze pca`http://edamontology.org/operation_0337Visualisationhttp://edamontology.org/data_3917Count matrixhttp://edamontology.org/format_3590HDF5Get an overview of observation, variables and unstructured data inside a h5ad anndata file.`hide-deconv anndata inspect`http://edamontology.org/operation_0226Annotationhttp://edamontology.org/data_3917Count matrixhttp://edamontology.org/format_3590HDF5

http://edamontology.org/data_3917Count matrixhttp://edamontology.org/format_3590HDF5

Creates a temporary csv table, that can be used to merge cell types together to a more coarse grained cell type annotation. The annotation is stored in a new observation column and the resulting anndata h5ad file is saved to the disk.`hide-deconv anndata add-annotation`http://edamontology.org/operation_3695Data filteringhttp://edamontology.org/data_3917Count matrixhttp://edamontology.org/format_3590HDF5

http://edamontology.org/data_3917Count matrixhttp://edamontology.org/format_3590HDF5

Subsets the single cell anndata h5ad file to a subset of values inside an observation column and stores it to the disk.`hide-deconv anndata subset`https://github.com/dvoelkl/HIDE-deconvRepositoryhttps://github.com/dvoelkl/HIDE-deconv/issuesIssue trackerhttps://zenodo.org/records/22028522Source codeVersion used in the preprint.0.1.0https://zenodo.org/records/22730480Source code0.4.0https://zenodo.org/records/23705607Source code0.4.3https://github.com/dvoelkl/HIDE-deconv/blob/main/docs/Userguide.mdUser manualhttps://dvoelkl.github.io/HIDE-deconv/API documentation10.64898/2026.08.24.746754Preprint0.1.0Dennis Voelkldennis.k.volkl@uib.nohttps://orcid.org/0009-0001-9550-8434PersonDeveloperFranziska GörtlerFranziska.Gortler@uib.nohttps://orcid.org/0000-0003-2015-5766PersonPrimary contactgeneSetSimplifyRgeneSetSimplifyR is a tool that simplifies lists of gene sets based on semantic similarity of gene ontology terms, clustering overlapping gene sets and giving each cluster an informative two-word label.https://github.com/IsoformAnalysisGroup/geneSetSimplifyRgenesetsimplifyrbiotools:genesetsimplifyrhttp://edamontology.org/topic_0089Ontology and terminologyhttp://edamontology.org/topic_0091BioinformaticsWindowsMacLinuxRGPL-3.0Emerginghttp://edamontology.org/operation_3459Functional clusteringhttp://edamontology.org/data_0842Identifierhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_3753Over-representation datahttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_3754GO-term enrichment datahttp://edamontology.org/format_2330Textual format

http://edamontology.org/operation_0337Visualisationhttp://edamontology.org/data_0842Identifierhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_3753Over-representation datahttp://edamontology.org/format_2330Textual format

http://edamontology.org/data_2884Plothttp://edamontology.org/format_2333Binary format

https://isoformanalysisgroup.github.io/geneSetSimplifyR/Installation instructionsUser manualCPB Gene Expression AtlasThe CPB Gene Expression Atlas is a web-based resource providing gene expression data for the Colorado potato beetle (Leptinotarsa decemlineata), facilitating research on insecticide resistance, insect physiology, and related areas.https://cpb-atlas.uni-mainz.de/cpbbiotools:cpbhttp://edamontology.org/topic_3500Zoologyhttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/operation_0525Genome assemblyhttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3766Weighted correlation network analysishttps://cpb-atlas.uni-mainz.de/resourcesOther10.1038/S41597-025-04607-739971983PMC11840028Shuqing Xushuqing.xu@uni-mainz.dehttps://orcid.org/0000-0001-7010-4604PersonmetagRootmetagRoot is a database of protein families associated with plant root microbiomes, integrating metagenomic and metatranscriptomic data to provide comprehensive annotations and structural context.https://pavlopoulos-lab.org/metagroot/metagrootbiotools:metagroothttp://edamontology.org/topic_3697Microbial ecologyhttp://edamontology.org/topic_0780Plant biologyhttp://edamontology.org/topic_0623Gene and protein familieshttp://edamontology.org/topic_3810Agricultural sciencehttp://edamontology.org/topic_3941Metatranscriptomicshttp://edamontology.org/operation_3460Taxonomic classificationhttps://www.metagroot.orgOther10.1101/2025.05.22.653656Georgios A. PavlopoulosPersonLIGPLOTProgram which plots schematic diagrams of protein-ligand interactions.http://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/ligplotbiotools:ligplotDesktop applicationhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_2814Protein structure analysisLinuxWindowsMachttp://edamontology.org/operation_0482Protein-ligand dockinghttp://www.mybiosoftware.com/ligplot-4-5-3-ligplot-1-3-plot-schematic-diagrams-protein-ligand-interactions.htmlSoftware cataloguehttp://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/manual/User manualhttp://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/faq.htmlGeneral10.1093/protein/8.2.127763088210.1021/ci200227u21919503Roman Laskowskiroman@ebi.ac.ukhttp://www.ebi.ac.uk/~roman/PersonPrimary contactABS-ScanPerforms alanine scanning mutagenesis for a given protein-ligand complex.http://proline.biochem.iisc.ernet.in/abscan/abs-scanbiotools:abs-scanWeb servicehttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_0128Protein interactionsLinuxWindowsMacPHPhttp://edamontology.org/operation_0239Sequence motif recognitionhttp://edamontology.org/operation_2423Prediction and recognitionhttp://www.mybiosoftware.com/abs-scan-webserver-for-insilico-binding-site-alanine-scanning-mutagenesis.htmlSoftware cataloguehttp://proline.biochem.iisc.ernet.in/abscan/index.phpGeneral10.12688/f1000research.5165.225685322PMC4319546Nagasuma Chandranchandra@biochem.iisc.ernet.inhttp://proline.physics.iisc.ernet.in/chandralab/PersonPrimary contactBiospliceAn analytical tool for generating downstream sequences following RNA splicing analysis, including CDS, protein sequences, and visualization of variant positions.https://www.spliceview.cn/BioSpliceBiosplicebiotools:Biosplice1.0.0Web applicationhttp://edamontology.org/topic_3320RNA splicingLinuxPythonMITFree of chargeOpen accesshttp://edamontology.org/operation_2499Splicing analysishttp://edamontology.org/data_2526Text data

http://edamontology.org/data_2977Nucleic acid sequence

Directory containing the rMATS analysis output files: SE.MATS.JC.txt, A3SS.MATS.JC.txt, A5SS.MATS.JC.txt, RI.MATS.JC.txt, MXE.MATS.JC.txt (missing event types are skipped)python main.py \ -r <rmats-output-dir> \ -g <genome.fa> \ -t <annotation.gtf> \ -o ./results \ --job-id myjob \ --fdr 0.05 --psi 0.2 --minjc 15https://www.spliceview.cn/BioSpliceServicehttps://github.com/rennmeng/BioSpliceSource code1.0.0https://www.spliceview.cn/BioSpliceQuick start guidePlant DataDiscoveryThe purpose of this web portal is to facilitate the discoverability of public data on plant biology managed by different laboratories across the world. The web portal indexes and makes findable any kind of plant data. Plant DataDiscovery is an implementation of DataDiscovery.https://urgi.versailles.inrae.fr/data-discovery/Plant_DataDiscoverybiotools:Plant_DataDiscoveryWeb APIWeb applicationWeb serviceDatabase portalhttp://edamontology.org/topic_0780Plant biologyhttp://edamontology.org/topic_0610Ecologyhttp://edamontology.org/topic_3071Biological databaseshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3810Agricultural scienceBSD-3-Clauseelixir-fr-sdp-2019MatureFree of chargeOpen accessToolsDataInteroperabilityFrancehttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_3625Relation extractionhttp://edamontology.org/operation_0227Indexinghttp://edamontology.org/operation_3908Information retrievalhttp://edamontology.org/data_0968Keywordhttp://edamontology.org/data_2353Ontology data

http://edamontology.org/data_2080Database search results

http://edamontology.org/data_2093Data reference

http://edamontology.org/data_0842Identifier

https://urgi.versailles.inrae.frOtherURGI websitehttps://urgi.versailles.inrae.fr/data-discovery/aboutGeneralhttps://urgi.versailles.inrae.fr/data-discovery/joinContributions policyhttps://urgi.versailles.inrae.fr/data-discovery/legalTerms of usehttps://urgi.versailles.inrae.fr/data-discovery/helpUser manualgnpisusesDataDiscoveryuses10.1186/s13059-018-1491-4PrimaryAlaux M, Rogers J, Letellier T, Flores R, Alfama F, Pommier C, Mohellibi N, Durand S, Kimmel E, Michotey C, Guerche C, Loaec M, Lainé M, Steinbach D, Choulet F, Rimbert H, Leroy P, Guilhot N, Salse J, Feuillet C, International Wheat Genome Sequencing Consortium, Paux E, Eversole K, Adam-Blondon A-F, Quesneville H (2018) Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data. Genome Biology, 19:11110.1038/hortres.2016.56Adam-Blondon, A.-F., Alaux, M., Pommier, C., Cantu, D., Cheng, Z.-M., Cramer, G. R., Davies, C., Delrot, S., Deluc, L., di Gaspero, G., Grimplet, J., Fennell, A., Londo, J. P., Kersey, P., Mattivi, F., Naithani, S., Neveu, P., Nikolski, M., Pezzotti, M., Reisch, B. I., Topfer, R., Vivier, M., Ware, D., Quesneville, H. (2016). Towards an open grapevine information system. Horticulture Research, 3, 8 p.Support serviceurgi-support@inrae.frPrimary contactSupportRepetDBRepeats intermine databasehttp://urgi.versailles.inra.fr/repetdbRepetDBbiotools:RepetDB1Web applicationWeb serviceDatabase portalhttp://edamontology.org/topic_3071Data managementhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0121ProteomicsLinuxMacRRubyJavaPythonJavaScriptPerlLGPL-2.1MatureFree of chargehttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_2436Gene-set enrichment analysishttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/data_1255Sequence featureshttp://edamontology.org/data_2353Ontology data

http://edamontology.org/data_3753Over-representation data

http://edamontology.org/data_3786Query script

http://edamontology.org/data_1255Sequence features

https://registry.intermine.orgSoftware cataloguehttp://intermine.orgOtherhttp://intermine.readthedocs.org/en/latest/web-services/API documentationhttps://flymine.readthedocs.io/en/latest/User manual10.1093/bioinformatics/bts57723023984PMC3516146OtherxcmsFramework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.https://bioconductor.org/packages/xcmsxcmsbiotools:xcms4.10.1LibraryWeb applicationCommand-line toolhttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_3172MetabolomicsLinuxWindowsMacRGPL-2.0-or-laterGalaxy ToolsBioConductorBiocondaRforMassSpectrometryMatureOpen accessMetabolomicsCzech RepublicFranceGermanyhttp://edamontology.org/operation_3215Peak detectionhttp://edamontology.org/operation_2428Validationhttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/operation_3694Mass spectrum visualisationhttp://edamontology.org/operation_3628Chromatographic alignmenthttp://edamontology.org/operation_3634Label-free quantificationhttp://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3654mzXMLhttp://edamontology.org/format_3244mzMLhttp://edamontology.org/format_3650NetCDFhttp://edamontology.org/data_0943Mass spectrumhttp://edamontology.org/format_3654mzXMLhttp://edamontology.org/format_3244mzMLhttp://edamontology.org/format_3650NetCDF

http://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3248mzQuantMLhttp://edamontology.org/format_3650NetCDF

http://edamontology.org/operation_3203Chromatogram visualisationhttp://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3244mzML

http://edamontology.org/data_2884Plothttp://edamontology.org/format_3547Image format

https://github.com/sneumann/xcmsRepositoryLink to the repository hosting the R code.https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/3.12.0+galaxy1Galaxy servicehttp://metlin.scripps.edu/download/Mirrorhttps://github.com/sneumann/xcmsSource codehttps://bioconductor.org/packages/xcmsUser manualcamerausedByramclustrusedByworkflow4metabolomicsusedBy10.1021/acs.analchem.5c04338Carl BruniusPersonContributorChristopher ConleyPersonDeveloperColin A. SmithPersonDeveloperJohannes RainerPersonDeveloperMichael WittingPersonContributorPablo VangeenderhuysenPersonContributorPaul BentonPersonDeveloperPhilippine LouailPersonDeveloperRalf TautenhahnPersonDeveloperSteffen NeumannPersonDeveloperMaintainerWilliam KumlerPersonDeveloperPSIPREDThe PSIPRED Protein Analysis Workbench unites many available analysis tools into a single web based framework. An excellent tool for prediction of secondary structure, with access to GenTHREADER for protein fold recognition and MEMSAT-2 transmembrane topology prediction.http://bioinf.cs.ucl.ac.uk/psipred/psipredbiotools:psipredRRID:SCR_018546rridWeb applicationhttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_0736Protein folds and structural domainshttp://edamontology.org/topic_3542Protein secondary structurehttp://edamontology.org/topic_0130Protein folding, stability and designhttp://edamontology.org/topic_2814Protein structure analysisLinuxWindowsMachttp://edamontology.org/operation_0469Protein secondary structure prediction (turns)http://edamontology.org/operation_0303Protein fold recognitionhttp://edamontology.org/operation_0267Protein secondary structure predictionhttp://bioinf.cs.ucl.ac.uk/index.php?id=779General10.1093/bioinformatics/16.4.4041086904110.1006/jmbi.1999.30911049386810.1093/nar/gkt38123748958PMC3692098psipred teampsipred@cs.ucl.ac.ukPersonPrimary contactARYANA-BSARYANA-BS is a software tool for context-aware alignment of bisulfite sequencing reads. It improves alignment accuracy by integrating DNA methylation patterns and genomic context, outperforming existing methods like BSMAP and Bismark.https://github.com/hnikaein/aryanaaryana-bsbiotools:aryana-bshttp://edamontology.org/topic_3674Methylated DNA immunoprecipitationhttp://edamontology.org/topic_3295Epigeneticshttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/operation_0495Local alignmenthttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/operation_3211Genome indexinghttp://edamontology.org/operation_3186Bisulfite mapping10.1186/S12859-025-06182-540691759PMC12281798Hassan Nikaeinnikaein@ce.sharif.eduPersonAli Sharifi-Zarchisharifi@sharif.eduPersongnomADGenome Aggregation Database (gnomAD) - browser that aggregates exome and whole-genome sequencing data from a wide variety of large-scale sequencing projects. It enables search of genetic variation information by gene, variant or region.http://gnomad.broadinstitute.org/gnomadbiotools:gnomadRRID:SCR_014964rridWeb applicationDatabase portalhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3077Data acquisitionhttp://edamontology.org/topic_3366Data integration and warehousinghttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3325Rare diseasesLinuxWindowsMacODbL-1.0RD-connectRare DiseaseMatureFree of chargeOpen accesshttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_3436Aggregationhttp://edamontology.org/operation_3197Genetic variation analysishttps://github.com/macarthur-lab/gnomadjs/issuesIssue trackerhttp://gnomad.broadinstitute.org/faqGeneral10.1038/nature1905727535533PMC5018207Primaryexomeconsortium@gmail.comConsortiumPrimary contactSuperPredThe SuperPred web server compares the structural fingerprint of an input molecule to a database of drugs connected to their drug targets and affected pathways. As the biological effect is well predictable, if the structural similarity is sufficient, the web-server allows prognoses about the medical indication area of novel compounds and to find new leads for known targets. Such information can be useful in drug classification and target prediction.http://bioinformatics.charite.de/superpredsuperpredbiotools:superpredWeb applicationhttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_0209Medicinal chemistryhttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_3336Drug discoveryhttp://edamontology.org/topic_3375Drug metabolismLinuxWindowsMachttp://edamontology.org/operation_2489Protein subcellular localisation predictionhttp://edamontology.org/operation_0360Structural similarity searchhttp://edamontology.org/operation_2436Gene-set enrichment analysishttp://prediction.charite.de/index.php?site=faqGeneral10.1093/nar/gkn30718499712PMC2447784Janette Nickeljanette.nickel@charite.dePersonPrimary contactBjoern-Oliver GohlkeBjoern-Oliver.Gohlke@charite.dePersonPrimary contactPriyanka BanerjeePriyanka.Banerjee@charite.dePersonPrimary contactJevgeni EhremanJevgeni.Ehreman@charite.dePersonPrimary contactMathias Dunkemathias.dunkel@charite.dePersonPrimary contactRheaRhea is a comprehensive and non-redundant resource of expert-curated chemical and transport reactions of biological interest developed by the Swiss-Prot group at SIB Swiss Institute of Bioinformatics. Rhea can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analysis. Rhea describes enzyme-catalyzed reactions covering the IUBMB Enzyme Nomenclature list as well as additional reactions, including spontaneously occurring reactions. Rhea is built on ChEBI (Chemical Entities of Biological Interest) ontology of small molecules to describe its reaction participants. Since December 2018, Rhea is the standard for enzyme annotation in UniProt.https://www.rhea-db.org/rheabiotools:rheaDatabase portalhttp://edamontology.org/topic_0821Enzymeshttp://edamontology.org/topic_3314Chemistryhttp://edamontology.org/topic_0602Molecular interactions, pathways and networksLinuxWindowsMacCC-BY-NC-4.0DataSwitzerlandhttps://www.rhea-db.org/downloadDownloads pagehttps://www.rhea-db.org/documentationGeneralchebiusesuniprotkbusedBymetabolightsusedByreactomeusedBy10.1093/nar/gky87630272209PMC6324061PrimarySIB Swiss Institute of BioinformaticsInstituteContact Formhttp://www.rhea-db.org/feedbackPersonPrimary contactOMAProject that aims to identify orthologs among publicly available, complete genomes. With many hundreds of genomes analyzed to date, it is one of the largest projects of its kind.http://omabrowser.org/oma/home/omabiotools:omaDesktop applicationWeb applicationDatabase portalhttp://edamontology.org/topic_3299Evolutionary biologyhttp://edamontology.org/topic_0797Comparative genomicsMacLinuxWindowsDataSwitzerlandhttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_3671Texthttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/data_0842Identifierorthology prediction and paralogy OMA grouphttps://omabrowser.org/oma/about/General10.1093/nar/gku115825399418PMC4383958Primary10.1093/nar/gkad102037962356PMC10767875Primary10.1093/nar/gkaa100733174605PMC7779010Primary10.1093/nar/gkx101929106550PMC5753216PrimarySIBInstituteProvidercontact@omabrowser.orgPersonPrimary contactChristophe DessimozChristophe.Dessimoz@unil.chPersonPrimary contactBgeeDBA package for the annotation and gene expression data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, mapped to genes by expression patterns.https://bioconductor.org/packages/BgeeDB/bgeedbbiotools:bgeedbCommand-line toolLibraryhttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_0089Ontology and terminologyhttp://edamontology.org/topic_0102MappingLinuxWindowsMacRGPL-3.0BioConductorSwitzerlandhttp://edamontology.org/operation_2422Data retrievalhttps://github.com/BgeeDB/BgeeDB_RSource codehttps://bioconductor.org/packages/release/bioc/html/BgeeDB.htmlUser manual10.12688/f1000research.9973.1PrimaryAndrea Komljenovicandreakomljenovic@gmail.comPersonPrimary contactFrederic Bastianbgee@sib.swisshttp://orcid.org/0000-0002-9415-5104PersonPrimary contactJulien Wollbretthttp://orcid.org/0000-0002-3099-3117Julien Rouxhttp://orcid.org/0000-0002-4192-5099