ab1lensBrowser-based viewer for Sanger sequencing chromatograms in AB1/ABIF and SCF format, and for the .srd raw files of the Nanofor-05 capillary sequencer, converted to ABIF as they open. Shows raw and analysed traces, base calls (called or edited), per-base quality and the full ABIF directory, and puts two reads side by side with their tag tables aligned. A read aligns against a pasted or loaded reference, which reports identity, mismatches, indels and the ends that did not align, and flips the strand when the read is on the other one. End trimming (modified Mott or sliding window) has draggable handles, motif search is IUPAC-aware and finds primers, and QC metrics copy out as CSV. Drag on a trace to select a base range, then copy it as FASTA, zoom to it or export just that region. Exports the read as FASTA, FASTQ, .qual or ABIF and the chromatogram as a high-resolution PNG. Open files are kept as local sessions. Runs entirely in the browser — files are never uploaded.https://fishka.bio/ab1lensab1lensbiotools:ab1lensDesktop applicationWeb applicationhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0092Data visualisationWindowsLinuxMacTypeScriptFreewarefishka.bioMatureFree of chargeOpen accesshttp://edamontology.org/operation_3203Chromatogram visualisationhttp://edamontology.org/operation_0363Reverse complementhttp://edamontology.org/operation_0239Sequence motif recognitionhttp://edamontology.org/operation_3192Sequence trimminghttp://edamontology.org/operation_0233Sequence conversionhttp://edamontology.org/operation_3218Sequencing quality controlhttp://edamontology.org/data_0924Sequence tracehttp://edamontology.org/format_3000AB1http://edamontology.org/format_1632SCFhttp://edamontology.org/operation_0491Pairwise sequence alignmenthttp://edamontology.org/data_0924Sequence tracehttp://edamontology.org/format_3000AB1http://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_1929FASTAhttps://fishka.bioSoftware cataloguefishka.bio — the tool collection ab1lens belongs tohttps://fishka.bio/downloadDownloads pageOffline build — the same application as a self-contained archive, runs from local files with no serverhttps://fishka.bio/ab1lens/showcaseTraining materialShowcase gallery — an annotated screenshot per task, from quality control to aligning a read against a reference10.5281/zenodo.21444547Other2026.07.19Software deposit (concept DOI — resolves to the latest version) covering the fishka.bio tools, including ab1lens.Fishka Bioswim@fishka.biohttps://fishka.bioProjectPrimary contactDeveloperMaintainerreadhitBrowser-based viewer that maps sequencing reads onto one short reference — an amplicon, gene or plasmid. Reads open as Sanger AB1/ABIF, SCF, FASTA, FASTQ or a SAM somebody else already mapped (gzipped files are unpacked in place); the reference as FASTA, GenBank or a read. Both read orientations are tried automatically. The pileup reports per-position depth, where reads disagree with the target, and the consensus — phred-weighted for capillary reads, which keep their chromatogram under the letters. An optional protein lane translates target and consensus side by side. Reads are placed by minimap2 compiled to WebAssembly, or by the built-in aligner. One read or the whole alignment saves as FASTA. Runs entirely in the browser — files are never uploaded.https://fishka.bio/readhitreadhitbiotools:readhitWeb applicationhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_0199Genetic variationWindowsMacLinuxTypeScriptFreewarefishka.bioEmergingFree of chargeOpen accesshttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/operation_0491Pairwise sequence alignmenthttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_2573SAMhttp://edamontology.org/data_0924Sequence tracehttp://edamontology.org/format_3000AB1http://edamontology.org/format_1632SCFhttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_3203Chromatogram visualisationhttp://edamontology.org/operation_0371DNA translationhttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_2573SAMhttps://fishka.bioSoftware cataloguefishka.bio — the tool collection readhit belongs tohttps://fishka.bio/readhit/showcaseTraining materialShowcase gallery — an annotated screenshot per task, from a handful of Sanger reads to an NGS pileup opened from a SAMFishka Bioswim@fishka.biohttps://fishka.bioProjectPrimary contactDeveloperMaintainergbatlasBrowser-based viewer for GenBank and GenPept records — .gb, .gbk, .gbff, .gp and plain GenBank text. Renders an interactive linear and circular feature map, including circular plasmid maps, alongside the annotated source text and the nucleotide/protein sequence.
Translates CDS features using the record's own genetic code and translation qualifiers, flags where the stored /translation disagrees with a plain translation, and adds optional computed layers: ORF prediction and restriction-site mapping. Drag a range in the sequence band to select it, then copy that stretch — either strand, as DNA or as protein, plain or FASTA. Filters features by type, handles multi-record files, and keeps open records as local sessions, so a closed tab can be picked up where it was left. Runs entirely in the browser — files are never uploaded.https://fishka.bio/gbatlasgbatlasbiotools:gbatlasDesktop applicationWeb applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_3511Nucleic acid sites, features and motifsWindowsLinuxMacTypeScriptFreewarefishka.bioMatureFree of chargeOpen accesshttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/operation_0436Coding region predictionhttp://edamontology.org/operation_0371DNA translationhttp://edamontology.org/operation_0431Restriction site recognitionhttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/format_1937genpepthttps://fishka.bioSoftware cataloguefishka.bio — the tool collection gbatlas belongs tohttps://fishka.bio/downloadDownloads pageOffline build — the same application as a self-contained archive, runs from local files with no serverhttps://fishka.bio/gbatlas/showcaseTraining materialShowcase gallery — an annotated screenshot per task, from the circular plasmid map to CDS translation and restriction sites10.5281/zenodo.21444547Other2026.07.19Software deposit (concept DOI — resolves to the latest version) covering the fishka.bio tools, including gbatlas.Fishka Bioswim@fishka.biohttps://fishka.bioProjectPrimary contactDeveloperMaintainerpickletBrowser-based tool to open almost any file that carries sequence — FASTA, FASTQ, GenBank, EMBL, Swiss-Prot, AB1/ABIF, SCF, Clustal, Stockholm, PHYLIP, NEXUS, MSF, PIR, MEGA, GFF3, SAM, BAM, GFA, PDB and ACE — see every sequence inside, pick the ones you want, and save them as FASTA. The format is detected from the file content, not from the extension, so unlabelled or misnamed files still open, and gzip-compressed files are unpacked in place. Records can be filtered by length, name, GC or sequence type, reverse-complemented, transcribed DNA↔RNA or translated to protein, deduplicated and reordered before saving. Runs entirely in the browser — files are never uploaded.https://fishka.bio/pickletpickletbiotools:pickletDesktop applicationWeb applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3071Data managementWindowsLinuxMacTypeScriptFreewarefishka.bioMatureFree of chargeOpen accesshttp://edamontology.org/operation_2121Sequence file editinghttp://edamontology.org/operation_0371DNA translationhttp://edamontology.org/operation_0233Sequence conversionhttp://edamontology.org/operation_0372DNA transcriptionhttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/data_0849Sequence recordhttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1975GFF3http://edamontology.org/format_1930FASTQhttp://edamontology.org/format_3001ACEhttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1991megahttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_3976GFA 2http://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1632SCFhttp://edamontology.org/format_3975GFA 1http://edamontology.org/format_1961Stockholm formathttp://edamontology.org/format_3000AB1http://edamontology.org/format_2573SAMhttp://edamontology.org/format_1912Nexus formathttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_1963UniProtKB formathttp://edamontology.org/format_1947GCG MSFhttp://edamontology.org/format_1936GenBank formathttps://fishka.bioSoftware cataloguefishka.bio — the tool collection picklet belongs tohttps://fishka.bio/downloadDownloads pageOffline build — the same application as a self-contained archive, runs from local files with no serverhttps://fishka.bio/picklet/showcaseTraining materialShowcase gallery — an annotated screenshot per task, from opening an unlabelled file to filtering, translating and saving the picked records10.5281/zenodo.21444547Other2026.07.19Software deposit (concept DOI — resolves to the latest version) covering the fishka.bio tools, including picklet.Fishka Bioswim@fishka.biohttps://fishka.bioProjectPrimary contactDeveloperMaintainerCognitionBioChemA structural pharmacology workbench for cognition-related CNS targets, built so that a displayed number must trace to a computation. Runs Boltz-2 locally for structure prediction, validates chemistry with RDKit, enforces a provenance record on every value, and reports eight studies pre-registered under content hashes before any data was seen. Its headline result is negative: designed peptides did not separate from composition-matched shuffles of their own amino acids.https://github.com/hopejsh/CognitionBioChemcognitionbiochembiotools:cognitionbiochem1.0.0doi:10.5281/zenodo.22032684doiconcept DOI, resolves to the latest releasedoi:10.5281/zenodo.22032685doi1.0.0RRID:SCR_028851rridWeb applicationCommand-line toolhttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_3336Drug discoveryMacLinuxPythonJavaScriptApache-2.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0474Protein structure predictionhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTABoltz-2 v2.2.1 runs locally; every predicted structure is retained under content-addressed custody with its confidence files.http://edamontology.org/operation_2428Validationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1477mmCIFBackbone geometry, per-residue pLDDT and interface PAE are read from the model's own file; a value that was never computed renders as a label.http://edamontology.org/operation_2480Structure analysishttp://edamontology.org/data_2301SMILES stringhttp://edamontology.org/format_1196SMILESRDKit validation: parsing, molecular formula, InChIKey and stereochemistry completeness. A SMILES that fails to parse is shown as unverified.https://github.com/hopejsh/CognitionBioChemRepositoryhttps://github.com/hopejsh/CognitionBioChem/issuesIssue trackerhttps://github.com/hopejsh/CognitionBioChem/archive/refs/tags/v1.0.0.tar.gzSource code1.0.0https://github.com/hopejsh/CognitionBioChem#readmeGeneralhttps://github.com/hopejsh/CognitionBioChem/blob/main/docs/REGISTRATION.mdCitation instructionshttps://github.com/hopejsh/CognitionBioChem/blob/main/NOTICETerms of useThe `license` field above is Apache-2.0, which covers this project's code, but the repository is not single-licensed. It redistributes third-party scientific data that keeps its own terms: CC BY 4.0 (UniProt, AlphaFold DB), CC BY-SA 3.0 (ChEMBL-derived files -- SHARE-ALIKE, so reuse carries an obligation onward), CC0 1.0 (RCSB depositions) and MIT (Boltz-2 model outputs). NOTICE lists which files fall under which.Seung Ho Jungseung.jung@gmail.comhttps://orcid.org/0000-0001-7914-5306PersonDeveloperMaintainerGelyzeGelyze is a web-based image analysis tool for agarose gel electrophoresis of nucleic acids. A user uploads a gel image, confirms the proposed lane positions and the ladder baseline, and a deterministic algorithm then estimates fragment size from ladder calibration and quantifies relative band intensity by densitometry. Measurement and interpretation are kept separate: the numbers come from the algorithm, and an assistive AI layer explains the resulting pattern in plain language without producing any of the values. For research use only.https://lab-ww.bioinsight.jpgelyzebiotools:gelyzeWeb applicationhttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_3047Molecular biologyProprietaryEmergingFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_3443Image analysishttps://lab-ww.bioinsight.jp/helpUser manualhttps://lab-ww.bioinsight.jp/faqFAQhttps://lab-ww.bioinsight.jp/termsTerms of useBioInsight Co., Ltd.contact@bioinsight.co.jphttps://bioinsight.co.jpInstituteProviderPrimary contactPhonaLabPhonaLab is a browser-based platform for acoustic analysis of voice recordings, aimed at speech-language pathologists, voice clinicians, and researchers. It computes validated multiparametric acoustic indices — including the Acoustic Voice Quality Index (AVQI), Acoustic Breathiness Index (ABI), smoothed cepstral peak prominence (CPPS), and glottal-to-noise excitation ratio (GNE) — from sustained-vowel and connected-speech recordings, using Praat algorithms via the Parselmouth interface. Audio is processed in memory and not stored. Interface available in English, Brazilian Portuguese, and Spanish.https://www.phonalab.com/phonalabbiotools:phonalabRRID:SCR_028845rridDOI:10.5281/zenodo.21987370doiWeb applicationhttp://edamontology.org/topic_3303Medicinehttp://edamontology.org/topic_3063Medical informaticshttp://edamontology.org/topic_0092Data visualisationPythonJavaScriptProprietaryEmergingFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/operation_0337Visualisationhttps://www.instagram.com/phonalab.voice/Social mediahttps://doi.org/10.1016/j.jvoice.2026.04.009Citation instructionsPeer-reviewed publication describing algorithm verification and concurrent validity of the platform's acoustic voice quality indices.https://www.phonalab.com/guidesTraining materialExplanatory guides on acoustic voice measures (CPPS, GNE, MPT/DSI) and clinical workflows.https://www.phonalab.com/termsTerms of useAudio is processed in memory and is not stored on the server.https://www.phonalab.com/faqFAQ10.1016/j.jvoice.2026.04.00942049572Primary10.1016/j.jvoice.2026.07.05142603770MethodJorge Carlos Lucerolucero@unb.brhttps://lucerojc.github.io/https://orcid.org/0000-0003-0597-3808PersonPrimary contactDeveloperProfessor of Computer Science at University of Brasília (Brazil)PhonaLab Inova Simplessupport@phonalab.comhttps://www.phonalab/comInstituteProviderMembrane Visual QCOpen-source PyMOL plugin for membrane-aware review of predicted, designed and experimental protein structures. Membrane Visual QC provides planar membrane-relative geometry, residue core/interface classification, hydropathy and ligand-context review, solvent-accessibility context, PDBTM/OPM orientation-source checks, and reproducible batch reporting. It is designed as a review assistant rather than a biological structure validator.https://github.com/TrPavel/membrane-visual-qcmembrane_visual_qcbiotools:membrane_visual_qc1.0.0Desktop applicationPlug-inCommand-line toolhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_3292Biochemistryhttp://edamontology.org/topic_0081Structure analysisWindowsPythonMITEmergingFree of chargeOpen accesshttps://github.com/TrPavel/membrane-visual-qcRepositorySource code and project repository.https://github.com/TrPavel/membrane-visual-qc/issuesIssue trackerBug reports, feature requests and user feedback.https://github.com/TrPavel/membrane-visual-qc/releases/download/v1.0.0/MembraneVisualQC-1.0.0.zipSoftware packageStable PyMOL Plugin Manager package.1.0.0https://github.com/TrPavel/membrane-visual-qc/blob/main/docs/index.mdGeneralhttps://github.com/TrPavel/membrane-visual-qc/blob/main/docs/quick_start.mdQuick start guidehttps://github.com/TrPavel/membrane-visual-qc/blob/main/docs/tutorial.mdUser manualhttps://youtu.be/lowQey_D610Training materialv1.0 video walkthrough.Pavel Trofimchiktrofimchikpavel@icloud.comhttps://github.com/TrPavelhttps://orcid.org/0009-0007-6030-6019PersonPrimary contactDeveloperMaintainerPathBench-MILPathBench-MIL is a comprehensive, flexible benchmarking/AutoML framework for multiple instance learning in histopathology. PathBench-MIL is expected to be deprecated and replaced by PathForge.https://github.com/Sbrussee/PathBench-MILPathBench-MILbiotools:PathBench-MILhttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_3474Machine learningLinuxShellPythonGPL-3.0LegacyFree of chargehttp://edamontology.org/operation_2425Optimisation and refinementhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3659Regression analysishttp://edamontology.org/operation_2990Classificationhttp://edamontology.org/data_2093Data referencehttp://edamontology.org/format_3752CSVhttp://edamontology.org/data_2968Imagehttp://edamontology.org/format_3591TIFFpathforgehasNewVersion10.48550/arXiv.2512.17517PathForgePathForge is a modular benchmarking framework for multiple instance learning in computational pathology. It supports whole slide image feature extraction, HDF5 artifact generation, tile overviews, benchmarking, pipeline optimization, classification, regression, survival and retrieval tasks, and support for model inference and visualization.https://github.com/Sbrussee/PathForgepathforgebiotools:pathforgeCommand-line toolhttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_3474Machine learningLinuxShellPythonMITMatureFree of chargehttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3659Regression analysishttp://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_3591TIFFhttps://github.com/Sbrussee/PathForgeRepositoryhttps://pathforge.readthedocs.io/en/latest/Otherhttps://pathforge.readthedocs.io/en/latest/GeneralQuick start guideUser manualPathBench-MILisNewVersionOf10.48550/arXiv.2512.17517PreprintPublication describes predecessor, PathBench-MILMailsDaddy MBOX to PST ConverterMailsDaddy MBOX to PST Converter is designed to move single or multiple MBOX file to Outlook PST, EML, MSG, HTML etc.https://www.mailsdaddy.com/mbox-to-pst-converter/mailsdaddy_mbox_to_pst_converterbiotools:mailsdaddy_mbox_to_pst_converter8.1Desktop applicationhttp://edamontology.org/topic_3071Data managementWindowsC++OtherCommercialhttp://edamontology.org/operation_4042Data management planningconvert data from MBOX-based email client to Outlook and others.https://www.mailsdaddy.com/thunderbird-to-outlook-converter/ServiceThunderbbird to Outlook Converterhttps://www.mailsdaddy.com/dl/mbox-to-pst-converter.zipSoftware package8.1https://www.mailsdaddy.com/installation/mbox-to-pst-converter.pdfInstallation instructions10.5281/zenodo.215330788.1Somit Vishwakarmavishwakarmasomit205@gmail.comhttps://orcid.org/0000-0002-9579-0601FT-ITC AnalysisFT-ITC Analysis is free, open-source desktop software for processing, fitting, and analysing isothermal titration calorimetry (ITC) data. It imports raw data from MicroCal, TA Instruments/NanoAnalyze, and PEAQ ITC project files, as well as integrated heat data and FT-ITC project files. The software supports baseline correction, injection integration, interaction-model fitting, global analysis, uncertainty estimation, advanced thermodynamic analyses, and publication-figure export on macOS, Windows, and Linux.https://ft-itc.orgft-itc-analysisbiotools:ft-itc-analysisDesktop applicationhttp://edamontology.org/topic_3306Biophysicshttp://edamontology.org/topic_3314ChemistryWindowsMacLinuxC#MITEmergingFree of chargeOpen accesshttps://ft-itc.org/app-desktopDownloads pagehttps://github.com/FrederikTheisen/FT-ITC-AnalysisSource codehttps://github.com/FrederikTheisen/FT-ITC-Analysis/wikiUser manualFrederik Theisenapplication@ft-itc.orghttps://orcid.org/0000-0002-3412-4242PersonDeveloperCUDA-Ising-OsteoA GPU-accelerated Ising/QUBO optimisation pipeline for osteoporosis gene-target discovery. It performs expression-based feature selection and GWAS-seeded STRING network-module detection with a batched GPU parallel-tempering sampler (PyTorch/CUDA, with a NumPy CPU fallback), and includes a cross-cohort replication protocol and orthogonal validation of candidate genes.https://github.com/Oscarlee9203/cuda-ising-osteocuda-ising-osteobiotools:cuda-ising-osteo1.0.0spoQCspoQC is a modular framework for multimodal quality control (QC) of imaging-based spatially resolved transcriptomics (SRT). It independently evaluates cell segmentation, imaging, and transcript data to identify high-quality regions (HQRs) across entire tissue sections. In addition, spoQC uses Markov random fields (MRFs) to incorporate spatial dependencies and generate spatially refined QC masks.https://github.com/heylf/spoQCspoqcbiotools:spoqc0.0.1Command-line toolPythonMITEmergingFree of chargeOpen accesshttps://pypi.org/project/spoqc/Software packagepip install0.0.1https://quay.io/repository/heylf/spoqcContainer filedocker/singularity container0.0.1https://spoqc.readthedocs.io/en/latest/User manualComplete documentation of spoQCFlorian Heylflorian.heyl@dkfz-heidelberg.dehttps://orcid.org/0000-0002-3651-5685Ezgi Senhttps://orcid.org/0009-0005-0816-2076Niklas Müller-Bötticherhttps://orcid.org/0000-0001-5103-7282par2-circadianFits second-order autoregressive AR(2) models to gene expression time series and reports the eigenvalue modulus |lambda|, a single statistic quantifying temporal persistence: how strongly a gene's recent past constrains its next value. Ranks genes into a clock/target/background hierarchy and reports correlation length, half-life and root type (real or complex) per gene.https://github.com/mickwh2764/par2discoverypar2-circadianbiotools:par2-circadian1.1.7doi:10.5281/zenodo.21963192doi1.1.7Command-line toolLibraryhttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_3315MathematicsLinuxMacWindowsPythonOtherEmergingFree of chargeOpen accesshttp://edamontology.org/operation_0314Gene expression profilinghttp://edamontology.org/operation_3659Regression analysishttp://edamontology.org/operation_3565RNA-seq time series data analysishttp://edamontology.org/operation_3664Statistical modellinghttp://edamontology.org/data_3112Gene expression matrixhttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3475TSVInput is a matrix with genes as rows and evenly spaced timepoints as columns. Output is one row per gene giving the AR(2) coefficients, |lambda|, root type, correlation length and half-life, plus a hierarchy summary.par2 expression.csv -o results.csvhttps://github.com/mickwh2764/par2discoveryRepositorySource repositoryhttps://github.com/mickwh2764/par2discovery/issuesIssue trackerBug reports and feature requestshttps://par2discovery.comOtherPAR(2) Discovery Engine: interactive analyses built on this packagehttps://github.com/mickwh2764/par2-reproducibilityOtherReproducibility repository: analysis code, dataset accessions and expected resultshttps://scicrunch.org/resolver/RRID:SCR_028837OtherRRID:SCR_028837 (SciCrunch Registry)https://pypi.org/project/par2-circadian/Software packagepip install par2-circadian1.1.7https://github.com/mickwh2764/par2discoverySource codeGit repository1.1.7https://github.com/mickwh2764/par2discovery#readmeGeneralInstallation, Python API and command-line usagehttps://github.com/mickwh2764/par2discovery/blob/main/CITATION.cffCitation instructionsCITATION.cff, schema 1.2.0https://github.com/mickwh2764/par2discovery/blob/main/LICENSETerms of usePolyForm Noncommercial 1.0.0: free for research and other noncommercial use; commercial use requires a separate licence. bio.tools has no SPDX entry for PolyForm, hence license: Other.10.21203/rs.3.rs-9283100/v1PrimaryMethodMethod preprint describing the AR(2) eigenvalue modulus and the clock/target/background hierarchy.10.5281/zenodo.21963192OtherArchived software, concept DOI resolving to the latest release.Michael Whitesidemickwh@msn.comhttps://par2discovery.comhttps://orcid.org/0009-0000-0643-5791PersonDeveloperMaintainerPrimary contactAuthor and maintainerPan.bioPan.bio is a cloud genomics platform for pipeline execution, exploratory analysis, and clinical variant interpretation. Workflows runs validated Nextflow and nf-core pipelines including Sarek, rnaseq, scrnaseq, mag, ampliseq, chipseq and atacseq without local installation. Notebooks provides Python and R sessions with a preinstalled bioinformatics stack, importing public data from GEO, SRA and IPG by accession and reading Workflows outputs directly. VAIC applies ACMG/AMP variant classification with gene-specific rule sets from CanVIG-UK and ClinGen ENIGMA, with automated evidence criteria implemented for BRCA1 and BRCA2. Cohorts provides federated analysis of patient data within a Trusted Research Environment.https://pan.biopan_biobiotools:pan_bio1.0WorkflowWeb serviceWeb applicationhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3577Personalised medicinehttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_3676Exome sequencinghttp://edamontology.org/topic_3170RNA-SeqLinuxMacWindowsPythonRProprietaryMatureCommercialRestricted accesshttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_1930FASTQWorkflows: cloud execution of validated nf-core and Nextflow pipelines including Sarek for germline and somatic variant calling.http://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/operation_3226Variant prioritisationhttp://edamontology.org/data_3498Sequence variationshttp://edamontology.org/format_3016VCFhttp://edamontology.org/format_2330Textual formatVAIC: ACMG/AMP classification with gene-specific rules from CanVIG-UK and ClinGen ENIGMA. Automated evidence criteria are implemented for BRCA1 and BRCA2. Evidence is aggregated from ClinVar, CanVar, gnomAD v4.1, BayesDel, REVEL and SpliceAI. Accepts HGVS notation, variant lists and VCF on GRCh38 or GRCh37. Outputs include clinical reports plus FHIR and HL7 for EMR integration. Every criterion applied is shown with its strength and contribution. The final classification decision rests with the clinical user.http://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/data_2091Accessionhttp://edamontology.org/format_2330Textual formatNotebooks: Python and R analysis sessions with pandas, numpy, matplotlib, ggplot2, samtools and bedtools preinstalled. Imports datasets from GEO, SRA and IPG by accession and reads Workflows outputs without re-upload. The bioMind Notebook Agent generates analysis code from plain-language descriptions for the user to inspect and run.https://pan.bio/company/contact/HelpdeskContact and demo requestsPan.biohttps://pan.bioInstituteProviderDeveloperNEXCISIONExact, validated excision of coordinate-defined genomic regions from transposed NEXUS matrices.https://github.com/RhysWhite/nexcisionnexcisionbiotools:nexcision0.1.1doi:10.5281/zenodo.21936049doi0.1.1Command-line toolhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_3293PhylogeneticsLinuxMacWindowsPythonMITEmergingFree of chargehttp://edamontology.org/operation_3081Sequence alignment editinghttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1949nexus-seqhttp://edamontology.org/data_1017Sequence rangeRemove coordinate-labelled NEXUS matrix rows overlapping user-defined 1-based inclusive genomic regions.nexcise NEXUS REGIONS [options]https://github.com/RhysWhite/nexcisionRepositorySource code and development repository.https://github.com/RhysWhite/nexcision/issuesIssue trackerBug reports and feature requests.https://github.com/RhysWhite/nexcision-benchmarkingRepositoryIndependent validation, adversarial testing, and scalability benchmarking materials.https://github.com/RhysWhite/nexcision/releases/tag/v0.1.1Source codeTagged NEXCISION v0.1.1 source release.0.1.1https://pypi.org/project/nexcision/0.1.1/Software packagePython package for installation with pip.0.1.1https://anaconda.org/bioconda/nexcisionSoftware packageBioconda package for Conda-based environments.0.1.1https://nexcision.readthedocs.io/GeneralHosted NEXCISION documentation.https://nexcision.readthedocs.io/en/latest/installation/Installation instructionsInstallation via PyPI, Bioconda, or tagged GitHub releases.https://nexcision.readthedocs.io/en/latest/workflow-integration/User manualWorkflow integration, provenance reporting, validation policies, and Snakemake examples.10.64898/2026.07.26.740842PreprintPrimary NEXCISION methods and validation preprint.Rhys Whiterhys.white@phfscience.nzhttps://www.phfscience.nz/staff-profiles/rhys-white/https://orcid.org/0000-0001-6620-758XPersonPrimary contactDeveloperMaintainerBRANCHSNVBRANCHSNV reports strict clade-exclusive nucleotide markers separately from single-nucleotide substitutions reconstructed on a selected edge of a rooted phylogenetic tree, while retaining ambiguity across equally parsimonious ancestral-state reconstructions.https://branchsnv.readthedocs.io/en/latest/branchsnvbiotools:branchsnv0.1.0doi:10.5281/zenodo.21919038doi0.1.0Command-line toolhttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_0194Phylogenomicshttp://edamontology.org/topic_0622GenomicsLinuxMacWindowsPythonMITEmergingFree of chargehttp://edamontology.org/operation_0324Phylogenetic analysishttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1912Nexus formathttp://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newickInterrogates one selected branch of a rooted phylogeny, reporting strict clade-exclusive nucleotide markers separately from substitutions reconstructed on the focal edge under equal-cost parsimony.branchsnv find \
--alignment alignment.nex \
--tree tree.nwk \
--outgroup-file outgroup_tips.txt \
--clade-tips clade_tips.txt \
--mode both \
--output branch_snvs.tsv \
--members-output branch_members.txt \
--report branchsnv_report.jsonhttps://github.com/RhysWhite/branchsnvRepositoryhttps://github.com/RhysWhite/branchsnv/issuesIssue trackerhttps://github.com/RhysWhite/branchsnv-validationOtherhttps://pypi.org/project/branchsnv/Software packagehttps://github.com/RhysWhite/branchsnv/releasesDownloads pagehttps://branchsnv.readthedocs.io/en/latest/FAQhttps://branchsnv.readthedocs.io/en/latest/Citation instructionsP2RankNovel machine learning-based method for prediction of ligand binding sites from protein structure.http://siret.ms.mff.cuni.cz/p2rankp2rankbiotools:p2rankDesktop applicationhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_2258Cheminformaticshttp://edamontology.org/topic_1317Structural biologyhttp://edamontology.org/topic_0128Protein interactionsLinuxWindowsMacJavaGroovyMITELIXIR-CZCzech Republichttp://edamontology.org/operation_2575Protein binding site predictionhttp://siret.ms.mff.cuni.cz/p2rankGeneral10.1186/s13321-018-0285-830109435PMC6091426David Hokszahoksza@ksi.mff.cuni.czPersonPrimary contactASAPASAP (Assemble Species by Automatic Partitioning) is a method to build species partitions from single locus sequence alignments.
ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity.https://bioinfo.mnhn.fr/abi/public/asapasap-assemblebiotools:asap-assembleWeb applicationDesktop applicationhttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_0637Taxonomyhttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/operation_3478Phylogenetic reconstructionhttp://edamontology.org/operation_3200DNA barcodinghttp://edamontology.org/operation_0310Sequence assemblyhttp://edamontology.org/operation_3359Splittinghttps://bioinfo.mnhn.fr/abi/public/asap/help_asap.htmlGeneralhttps://bioinfo.mnhn.fr/abi/public/asap/FAQ_asap.htmlFAQ10.1111/1755-0998.1328133058550Nicolas Puillandrepuillandre@mnhn.frPersonFolkloreDeterministic, rule-based variant interpretation platform for clinical genetics laboratories. Automates ACMG/AMP 2015 classification using a Bayesian point-based framework (Tavtigian et al. 2018) with BayesDel ClinGen SVI-calibrated thresholds (Pejaver et al. 2022). Integrates 8 reference databases (gnomAD v4.1, ClinVar, dbNSFP 4.9c, SpliceAI, gnomAD Constraint, HPO, ClinGen, Ensembl VEP). Analyzes nuclear and mtDNA variants, structural and copy-number variants (SV/CNV), with trio/family and cohort analysis. Supports HPO-based phenotype matching, biomedical literature mining across 2M+ PubMed publications, and structured clinical report generation. AI assists in evidence synthesis but does not make classification decisions. EU-hosted on dedicated infrastructure in Helsinki, Finland (GDPR-compliant).https://folklore.helena.bioHelixInsightbiotools:HelixInsight3.39.1RRID:SCR_028669rrid3.39.1Web APIWeb applicationhttp://edamontology.org/topic_3574Human geneticshttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3325Rare diseaseshttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3063Medical informaticsLinuxPythonProprietaryMatureCommercialRestricted accesshttp://edamontology.org/operation_3225Variant classificationhttp://edamontology.org/data_3498Sequence variationshttp://edamontology.org/format_3016VCFhttp://edamontology.org/operation_3197Genetic variation analysishttp://edamontology.org/operation_0305Literature searchhttp://edamontology.org/operation_0362Genome annotationhttps://github.com/helena-bioinformatics/folklore-mcpRepositoryPublic Apache-2.0 MCP protocol adapter source; the Folklore SaaS platform and clinical interpretation backend remain proprietary.https://api.helena.bio/folklore/v1/mcpServicePublic remote endpoint for Folklore Clinical Variant Interpretation MCP version 1.2.2.https://registry.modelcontextprotocol.io/v0.1/servers?search=io.github.helena-bioinformatics%2Ffolklore&version=latestSoftware catalogueOfficial MCP Registry entry: io.github.helena-bioinformatics/folklore.https://folklore.helena.bio/integrationsOtherOfficial Folklore integrations and MCP client connection page.https://api.helena.bio/folklore/v1/healthTechnical monitoringPublic health and discovery metadata endpoint for the Folklore MCP service.https://github.com/helena-bioinformatics/folklore-mcpSource codeApache-2.0 standalone MCP protocol adapter. Excludes proprietary clinical interpretation logic, private data, credentials and operational infrastructure.1.2.2https://folklore.helena.bio/docsGeneralComplete production documentation covering every threshold, database version, and classification rule. Intended for clinical geneticists, laboratory directors, accreditation auditors, and bioinformaticians.https://folklore.helena.bio/how-it-worksGeneralSeven-stage analysis pipeline (quality control, annotation, classification, phenotype matching, literature, screening, interpretation) transforming a raw VCF into a clinician-ready report, each stage producing traceable, auditable output.https://folklore.helena.bio/methodologyGeneralACMG/AMP 2015 classification methodology (Richards et al. 2015) via Bayesian point-based system (Tavtigian et al. 2018), BayesDel ClinGen SVI-calibrated thresholds (Pejaver et al. 2022), and SpliceAI aligned to ClinGen SVI 2023 (Walker et al. 2023). Optional ClinGen VCEP overlay for ~50-60 genes. Strictly evidence-based, no ML determines pathogenicity.https://folklore.helena.bio/methodology/mtdnaGeneralMitochondrial DNA variant classification under the ClinGen Mitochondrial Disease Working Group (MMDWG) 2020 specification (McCormick et al. 2020). Operates as an independent module from the nuclear ACMG/AMP pipeline; every variant carries an explicit framework provenance label. Strength tiers follow ClinGen mtDNA VCEP v1.0.0.https://folklore.helena.bio/methodology/family-analysisGeneralInheritance-aware evidence from trio (proband + both parents), duo, and proband-plus-sibling analyses. Implements ClinGen SVI 2018 de novo PS2/PM6 (PMID 29543229), Jarvik & Browning 2016 LOD segregation framework (PMID 27236918), and ClinGen SVI 2021 PP1 strength bands. Augments the existing ACMG/AMP classification without re-calling variants.https://folklore.helena.bio/methodology/svGeneralStructural and copy-number variant evaluation under the Riggs 2020 joint ACMG/ClinGen technical standard. Documents the point-based loss and gain metrics, dosage-sensitivity evidence, and five-tier classification, with reference data and documented limitations.https://folklore.helena.bio/screening-methodologyGeneralPrioritizes classified variants for clinical review. After ACMG classification determines what each variant is, screening determines which to review first based on patient-specific clinical relevance. Evaluates seven independent dimensions, applies clinical profile boosts, and produces a four-tier priority ranking with transparent, visible score components.https://folklore.helena.bio/docs/folklore-connectorAPI documentationCanonical connector guide for Folklore Clinical Variant Interpretation MCP (io.github.helena-bioinformatics/folklore), version 1.2.2.https://github.com/helena-bioinformatics/folklore-mcp#readmeGeneralPublic Apache-2.0 MCP protocol adapter README. The Folklore SaaS platform and clinical interpretation backend remain proprietary.https://github.com/helena-bioinformatics/folklore-mcp/blob/main/CHANGELOG.mdRelease notesRelease history for the public Folklore MCP protocol adapter.10.5281/zenodo.21105027Preprint1.0Methodological framework for real-world performance studies of the platform's variant classification, demonstrated on three internal validation cohorts.10.5281/zenodo.21189571Preprint1.0A Deterministic Classification Core with an Agentic Interpretation Layer: An Architecture for Auditable, Human-Gated Clinical Variant Analysis10.5281/zenodo.21763096PreprintRobustness and cross-cohort concordance of developmental regulons in endometrial carcinoma. Authors: Draga Toncheva, Vasil Sgurev and Vladimir Mitev.10.5281/zenodo.21922952Other1.2.2Archived public Apache-2.0 Folklore MCP adapter release. All-version DOI: 10.5281/zenodo.21922951.Helena Bioinformaticscontact@helena.biohttps://helena.bioInstituteDeveloperPeptide Reconstitution CalculatorA transparent, unit-aware calculator for the mathematical relationship between peptide mass, target concentration and solution volume. It normalizes mg, micrograms, mL and microlitres, shows the formula and includes a reference syringe visualization. Research-use-only software: it does not select a solvent, validate a laboratory method, calculate a dose or provide administration guidance.https://peptidomexico.com.mx/calculadora/peptide_reconstitution_calculatorbiotools:peptide_reconstitution_calculator0.1.0Web applicationhttp://edamontology.org/topic_3314ChemistryMITEmergingFree of chargeOpen accesshttp://edamontology.org/operation_3438Calculationhttps://github.com/PeptidoMexico/peptidomexico-open-scienceRepositorySource repository, package code, demo, fixtures and reproducible test vectors.https://github.com/PeptidoMexico/peptidomexico-open-science/issuesIssue trackerPublic issue tracker for reproducibility questions and bug reports.https://github.com/PeptidoMexico/peptidomexico-open-science/archive/refs/heads/main.zipSource codeSource archive for the unit-aware calculation package, demo and reproducible fixtures.0.1.0https://github.com/PeptidoMexico/peptidomexico-open-science#readmeGeneralREADME with installation, formula, assumptions, test vectors and research-use-only scope.Peptido México Open Sciencehola@peptidomexico.com.mxhttps://github.com/PeptidoMexico/peptidomexico-open-sciencepeptide-qcpeptide-qc analyzes a standard peptide sequence and returns residue composition, elemental formula, average and monoisotopic mass, approximate charge and pI, and Kyte-Doolittle hydropathy. It is a deterministic command-line tool and JavaScript library for research software tests and teaching. It does not identify unknown samples, certify purity, model unusual chemistry or provide clinical interpretation.https://peptidomexico.com.mx/calculadora/peptide-qcbiotools:peptide-qc0.1.0Command-line toolLibraryhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0080Sequence analysisWindowsMacLinuxJavaScriptMIThttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/data_2976Protein sequenceOutputs deterministic sequence composition and approximate physicochemical properties for standard residues.npx peptide-qc analyze --sequence ACDEFGHIK --ph 7 --jsonhttps://github.com/PeptidoMexico/peptidomexico-open-scienceRepositoryhttps://github.com/PeptidoMexico/peptidomexico-open-science/issuesIssue trackerhttps://www.npmjs.com/package/peptide-qcSoftware package0.1.0https://github.com/PeptidoMexico/peptidomexico-open-scienceSource code0.1.0https://peptidomexico-open-science.readthedocs.io/en/latest/peptide-qc/User manualQuick start guidehttps://github.com/PeptidoMexico/peptidomexico-open-science/blob/main/CITATION.cffCitation instructionsPéptido Méxicohola@peptidomexico.com.mxhttps://peptidomexico.com.mx/DeveloperMaintainerProvideredfcoreedfcore is a zero-dependency TypeScript library for reading EDF, EDF+, BDF, and BDF+ physiological recordings in browser and Node.js applications. It provides programmatic access to biosignal samples, channel metadata, per-channel sampling rates, physical units, annotations, and discontinuous recording timelines.https://edfcore.vercel.app/edfcorebiotools:edfcoreLibraryhttp://edamontology.org/topic_3304Neurobiologyhttp://edamontology.org/topic_0605Informaticshttp://edamontology.org/topic_3316Computer scienceLinuxWindowsMacJavaScriptTypeScriptMITEmergingFree of chargeOpen accesshttps://github.com/tayal-sarthak/edfcoreRepositoryhttps://www.npmjs.com/package/edfcoreServicehttps://www.npmjs.com/package/edfcoreSoftware packagehttps://edfcore.vercel.app/API documentationSarthak Tayalsarthaktayal2@gmail.comhttps://github.com/tayal-sarthakMTBC Gene AtlasContinuously updated functional re-annotation of the Mycobacterium tuberculosis complex gene set, anchored on the MTBC0 ancestral genome rather than on a single strain. Serves one record per gene combining Pfam domains, ESMFold structures with Foldseek search, protein language-model features, orthology, curated knowledge, protein association networks and intra-species selection inferred from 145209 sequenced genomes, with dated sources and a graded confidence level for every field. Intended as a successor to Mycobrowser, which is no longer maintained.https://mtbc.gclab.frmtbc_gene_atlasbiotools:mtbc_gene_atlas1Web applicationDatabase portalWeb APIhttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_0085Functional genomicshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_0736Protein folds and structural domainsLinuxWindowsMacPythonCC-BY-4.0Mycobacterium tuberculosis complexMatureFree of chargeOpen accesshttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/data_1026Gene symbolhttp://edamontology.org/data_2295Gene IDQuery by H37Rv locus tag (Rv1908c) or gene name (katG); every field carries its provenance and confidence.http://edamontology.org/operation_0331Variant effect predictionhttp://edamontology.org/operation_0303Protein fold recognitionStructure-based leads for genes with no domain assignment, and population-scale selection signal per gene.https://github.com/cguyeux/mtbc-gene-atlasRepositorySource code repository, one script per evidence layer (MIT license).https://doi.org/10.5281/zenodo.20815246Downloads pageZenodo concept DOI: resolves to the latest archived release (per-gene records, consolidated layers, reproducibility bundle).https://mtbc.gclab.fr/api/v1API specificationVersioned read-only REST API over the served records.https://mtbc.gclab.fr/aboutGeneralScope, evidence layers, citation and coordinate-system conventions.10.5281/zenodo.20815246OtherArchived data and code releases (concept DOI). Replace or complement with the article DOI once the manuscript is accepted, keeping this entry so the data release stays citable on its own.Christophe Guyeuxguyeux@gmail.comhttps://orcid.org/0000-0003-0195-4378PersonDeveloperMaintainerPrimary contactFEMTO-ST Institute (CNRS UMR 6174), Universite Marie et Louis Pasteur, Besancon, France.FEMTO-ST Institute, CNRS UMR 6174https://www.femto-st.frInstituteProviderComputaseLocal Python sequence utilities for nucleotide composition, DNA and RNA reverse complements, NCBI genetic-code translation, six-frame candidate ORF enumeration, and IUPAC motif searches. Computase accepts raw nucleotide strings or one FASTA record and returns structured, bounded results with explicit scientific conventions.https://github.com/madhusudan-kulkarni/computasecomputasebiotools:computase0.1.1Libraryhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0077Nucleic acidsMacWindowsLinuxPythonMITEmergingFree of chargehttp://edamontology.org/operation_0236Sequence composition calculationhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/format_1929FASTAReports composition, ambiguity-preserving GC bounds, and concrete-base GC skew.http://edamontology.org/operation_0363Reverse complementhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/format_1929FASTAPreserves the DNA or RNA alphabet and supports IUPAC ambiguity symbols.http://edamontology.org/operation_0371DNA translationhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/format_1929FASTATranslates complete DNA or RNA codons with a selected NCBI genetic-code table.http://edamontology.org/operation_0253Sequence feature detectionhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/format_1929FASTAEnumerates sequence-defined candidate ORFs in six frames; it does not predict genes.http://edamontology.org/operation_0239Sequence motif recognitionhttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1964plain text format (unformatted)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1353Sequence motifhttp://edamontology.org/format_1964plain text format (unformatted)Finds overlapping IUPAC motif matches on the forward, reverse, or both strands.https://github.com/madhusudan-kulkarni/computaseRepositoryhttps://github.com/madhusudan-kulkarni/computase/issuesIssue trackerhttps://pypi.org/project/computase/Software package0.1.1https://github.com/madhusudan-kulkarni/computase/archive/refs/tags/v0.1.1.tar.gzSource code0.1.1https://github.com/madhusudan-kulkarni/computase#readmeGeneralInstallation instructionsQuick start guideCitation instructionshttps://github.com/madhusudan-kulkarni/computase/blob/main/CHANGELOG.mdRelease notesMadhusudan Kulkarnihttps://github.com/madhusudan-kulkarni/computasehttps://orcid.org/0009-0004-0270-9731PersonDeveloperMaintainerPrimary contactConspectaConspecta 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 you and one collaborator, every workspace included. Paid plans open it to the whole lab and add additional storage, AI object detection, external integrations via API, and bring-your-own AI assistant integration.https://conspecta.bioconspectabiotools:conspectaRRID:SCR_028623rridWeb applicationhttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_3385Light microscopyhttp://edamontology.org/topic_3934Cytometryhttp://edamontology.org/topic_3047Molecular biologyLinuxMacWindowsProprietaryEmergingFree of charge (with restrictions)Open access (with restrictions)http://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/operation_3443Image analysishttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3935Dimensionality reductionhttps://conspecta.bio/guide/User manualnnUNetnnU-Net is a self-configuring method for deep learning-based biomedical image segmentation, developed by the Applied Computer Vision Lab (ACVL) of Helmholtz Imaging and the Division of Medical Image Computing at the German Cancer Research Center (DKFZ). It is designed to automatically adapt to a given dataset, analyzing the provided training cases to configure a matching U-Net-based segmentation pipeline without requiring expertise from the user.
The tool provides pretrained models for
Pancreas and Pancreas tumor segmentation, Colon cancer primaries segmentation, Abdominal organ segmentation, Liver and liver tumor segmentation, Kidney and kidney tumor segmentation, Brain Tumor segmentation and Hippocampus (MR data) segmentationhttps://github.com/MIC-DKFZ/nnUNet/tree/nnunetv1nnunetbiotools:nnunet1.0Command-line toolLinuxPythonApache-2.0EUCAIMMaturehttp://edamontology.org/operation_3553Image annotationhttp://edamontology.org/data_3424Raw imagehttp://edamontology.org/format_3548DICOM formatRun nnUnet pretrained on Task007_Pancreas targeting are pancras and pancreas tumordocker run --rm -v /host/dataset/study_001/:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output --gpus all nnunet-pancreas-tumourhttp://edamontology.org/operation_3553Image annotationhttp://edamontology.org/data_3424Raw imagehttp://edamontology.org/format_3548DICOM formatRun nnUnet model pretrained on Task029_LiTS targeting are liver and liver tumordocker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output --gpus all nnunet-liver-tumourhttp://edamontology.org/operation_3553Image annotationhttp://edamontology.org/data_3424Raw imagehttp://edamontology.org/format_3548DICOM formatRun nnUnet pretrained on Task004_Hippocampus MRI data targeting posterior and anterior parts of the hippocampusdocker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output --gpus all nnunet-hippocampus-segmentationhttp://edamontology.org/operation_3553Image annotationhttp://edamontology.org/data_3424Raw imagehttp://edamontology.org/format_3548DICOM formatRun nnUnet pretrained on Task010_Colon targeting are colon cancer primaries.docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output --gpus all nnunet-colon-cancerhttp://edamontology.org/operation_3553Image annotationhttp://edamontology.org/data_3424Raw imagehttp://edamontology.org/format_3548DICOM formatRun nnUnet pretrained on Task169_BrainTumorPET targeting are brain tumordocker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output --gpus all nnunet-brain-tumour-pethttp://edamontology.org/operation_3553Image annotationhttp://edamontology.org/data_3424Raw imagehttp://edamontology.org/format_3548DICOM formatRun nnUNet model pretrained on Task017_AbdominalOrganSegmentation targeting thirteen different abdominal organsdocker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output --gpus all nnunet-abdominal-organ-segmentationhttp://edamontology.org/operation_3553Image annotationhttp://edamontology.org/data_3424Raw imagehttp://edamontology.org/format_3548DICOM formatRun nnUNet model pretrained on Task135_KiTS2021 targeting are kidney, tumor and cyst.docker run --rm -v /host/dataset/study_001:/home/eucaim/nnUNet_input -v /host/data_out:/home/eucaim/nnUNet_output --gpus all nnunet-kidney-tumourhttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/nnunet-hippocampus-segmentation/artifacts-tabSoftware cataloguehttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/nnunet-kidney-tumour/artifacts-tabSoftware cataloguehttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/nnunet-abdominal-organ-segmentation/artifacts-tabSoftware cataloguehttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/nnunet-colon-cancer/artifacts-tabSoftware cataloguehttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/nnunet-brain-tumour-pet/artifacts-tabSoftware cataloguehttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/nnunet-liver-tumour/artifacts-tabSoftware cataloguehttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/nnunet-pancreas-tumour/artifacts-tabSoftware cataloguehttps://github.com/MIC-DKFZ/nnUNet/tree/nnunetv1GeneralGitHub Readmehttps://github.com/MIC-DKFZ/nnunet-eucaim-docker/User manualDocker containers and other relevant instructions10.1038/s41592-020-01008-zMethodDKFZ Heidelbergr.floca@Dkfz-Heidelberg.dehttps://www.dkfz.de/InstituteProviderContributorMaintainerGroup Lead and Board Member, Medical Image Computing department, DKFZ HeidelbergPharmaGistPharmaGist is a web server for detecting pharmacophores or the spatial arrangement of features that enables a molecule to interact with a specific target receptor. Users input a set of structures of molecules that bind with the receptor for outputs of candidate pharmacophores that can be used in rational drug design.http://bioinfo3d.cs.tau.ac.il/PharmaGistpharmagistbiotools:pharmagistWeb applicationhttp://edamontology.org/topic_0209Medicinal chemistryhttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0130Protein folding, stability and designhttp://edamontology.org/topic_0082Structure predictionLinuxWindowsMachttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_0482Protein-ligand dockinghttp://bioinfo3d.cs.tau.ac.il/pharma/help.htmlGeneral10.1093/nar/gkn18718424800PMC2447755PharmaGist Administratorppdock@tau.ac.ilPersonPrimary contactSlideScopeDesktop viewer for microscopy and whole slide pathology images on Windows and macOS. Opens whole slide scanner formats (Aperio SVS, Hamamatsu NDPI, MIRAX MRXS, Leica SCN, Ventana BIF) alongside acquisition formats (Zeiss CZI, Nikon ND2, DICOM, TIFF/OME-TIFF) in a single application, providing pyramid navigation of gigapixel images, metadata inspection, calibrated measurements, annotations, and on-device segmentation and object counting.https://slidescope.science/slidescopebiotools:slidescope1.8.6Desktop applicationhttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_3383Bioimaginghttp://edamontology.org/topic_3384Medical imagingWindowsMacProprietaryMatureCommercialRestricted accesshttps://slidescope.science/en/downloads/Binarieshttps://slidescope.science/en/learn/GeneralBaktaRapid & standardized annotation of bacterial genomes, MAGs & plasmidshttps://github.com/oschwengers/baktabaktabiotools:baktav1.12.1Command-line toolWeb applicationhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0091BioinformaticsLinuxMacPythonGPL-3.0MatureFree of chargeOpen accessToolsGermanyhttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/data_0925Sequence assemblyhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2914Sequence features metadatahttp://edamontology.org/format_3475TSVhttp://edamontology.org/data_2012Sequence coordinateshttp://edamontology.org/format_1975GFF3http://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1364Hidden Markov modelhttp://edamontology.org/format_3329HMMER3bakta --db <db-path> --prefix <prefix> --output <output-path> genome.fastahttps://github.com/oschwengers/baktaRepositoryhttps://github.com/oschwengers/bakta/issuesIssue trackerhttps://bioconda.github.io/recipes/bakta/README.htmlOtherhttps://bakta.computational.bioServicehttps://zenodo.org/records/14916843OtherMandatory annotation databasev6.0https://github.com/oschwengers/bakta/blob/main/README.mdGeneralhttps://github.com/oschwengers/bakta/blob/main/CONTRIBUTION.mdContributions policyhttps://github.com/oschwengers/bakta/blob/main/CODE_OF_CONDUCT.mdCode of conducthttps://bakta.readthedocs.io/User manualdiamonduseshmmer3usesinfernalusestrnascan-seusesblastusesaragornusespilercruses10.1099/mgen.0.00068534739369PMC8743544Primary1.110.1093/nar/gkaf33540271661PMC12230652PrimaryOliver Schwengersoliver.schwengers@cb.jlug.dehttps://github.com/oschwengershttps://orcid.org/0000-0003-4216-2721PersonPrimary contactDeveloperMaintainerJustus Liebig University Giessenhttps://www.uni-giessen.deInstituteProviderVIEWpolyProvides a graphical user interface to integrate, visualize and explore results from linkage and quantitative trait loci analysis, together with genomic information for autopolyploid species. The app is meant for interactive use and allows users to optionally upload different sources of information, including gene annotation and alignment files, enabling the exploitation and search for candidate genes in a genome browser. In its current version, 'VIEWpoly' supports inputs from 'MAPpoly', 'polymapR', 'diaQTL', 'QTLpoly', 'polyqtlR', 'GWASpoly', and 'HIDECAN' packages.https://github.com/Breeding-Insight/viewpolyviewpolybiotools:viewpoly1.0.3Bioinformatics portalhttp://edamontology.org/topic_3053GeneticsLinuxWindowsMacAGPL-3.0MatureOpen accesshttp://edamontology.org/operation_3197Genetic variation analysisDisplay Shiny Interfacerun_app()onemapAnalysis of molecular marker data from model and non-model systems. For the later, it allows statistical analysis by simultaneously estimating linkage and linkage phases (genetic map construction) according to Wu and colleagues (2002) <doi:10.1006/tpbi.2002.1577>. All analysis are based on multi-point approaches using hidden Markov models.https://github.com/Cristianetaniguti/onemaponemapbiotools:onemap3.2.6QploidyProvides functions for estimating ploidy levels and detecting aneuploidy in individuals using allele intensities or allele count data from high-throughput genotyping platforms, including single nucleotide polymorphism (SNP) arrays and sequencing-based technologies. Implements method described in Taniguti et al. (2025) <doi:10.1002/tpg2.70044> an extended version of the 'PennCNV' signal standardization method by Wang et al. (2007) <doi:10.1101/gr.6861907> for higher ploidy levels. Computes B-allele frequencies (BAF), z-scores, and identifies copy number variation patterns.https://github.com/Cristianetaniguti/Qploidyqploidybiotools:qploidy1.5.4BIOSZENBIOSZEN is an open-source R package and modular Shiny application for reproducible analysis and visualization of experimental biological data from Excel or CSV files. It supports statistical testing, control-based normalization, replicate-aware quality control, and customizable scientific plots.
Its microbial growth-curve module analyzes optical-density time series and automatically extracts quantitative growth parameters, including maximum specific growth rate (µMax), doubling time, lag time, maximum optical density (ODmax), time to maximum growth, area under the curve (AUC), and initial optical density (OD0).
Results can be exported as processed datasets, statistical summaries, analysis metadata, scientific graphics, and editable PowerPoint figures.https://github.com/bioszen/BIOSZENbioszenbiotools:bioszen2.1.1Desktop applicationWeb applicationhttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_3301MicrobiologyWindowsMacRGPL-3.0Free of chargeOpen accesshttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/operation_0337VisualisationStatistical analysis, control-based normalization, replicate-aware quality control, and customizable visualization of experimental biological data from Excel or CSV files.http://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/operation_2945Data analysishttp://edamontology.org/operation_0337VisualisationAnalysis and visualization of microbial optical-density time series, including extraction of uMax, max_percap_time, doubling time, lag time, ODmax, max_time, AUC, OD0, and related growth parameters.https://github.com/bioszen/BIOSZENRepositorySource code, example files, documentation, and development history.https://github.com/bioszen/BIOSZEN/issuesIssue trackerBug reports, installation problems, and feature suggestions.https://bioszen-test.share.connect.posit.cloudServiceLimited online demonstration of the BIOSZEN Shiny application.https://zenodo.org/records/18217210Downloads pageArchived release files and permanent software record.2.1.1https://bioszen.r-universe.dev/BIOSZENSoftware packageInstallable R package for BIOSZEN 2.1.1, including access to the Shiny application.2.1.1https://github.com/bioszen/BIOSZEN#readmeGeneralUser manualQuick start guidehttps://github.com/bioszen/BIOSZEN/blob/main/inst/app/www/MANUAL_EN.mdUser manualComplete BIOSZEN user manual in English.https://github.com/bioszen/BIOSZEN#citationCitation instructions10.5281/zenodo.18217210Primaryall versions10.5281/zenodo.18217522Primary1.0.0Benjamín Szenfeldbioszenf@gmail.comhttps://orcid.org/0009-0003-4702-4149PersonDeveloperMaintainerPrimary contactGenome of Slovakia - Population variant browserThe Genome of Slovakia Population Browser is an interactive tool for exploring genetic variation in the Slovak population, based on whole-genome sequencing data from >1000 individuals. It enables users to search genomic variants, examine their allele frequencies and distribution within the cohort, and compare population-specific observations with international reference datasets. The browser supports research, clinical variant interpretation, and the identification of variants that may be common, rare, or potentially specific to the Slovak population.https://gos.cusp.uniba.sk/genome_of_slovakia_-_population_variant_browserbiotools:genome_of_slovakia_-_population_variant_browserDatabase portalWeb applicationhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_0092Data visualisationhttp://edamontology.org/topic_3366Data integration and warehousinghttp://edamontology.org/topic_3056Population geneticsAndroidWindowsiOSMacLinuxMatureFree of chargeOpen access (with restrictions)Toolshttp://edamontology.org/operation_3197Genetic variation analysishttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_3436AggregationMarcel Kucharíkmarcel.kucharik@uniba.skhttps://orcid.org/0000-0002-5373-8282PersonMaintainerDeveloperTomáš Szemestomas.szemes@uniba.skhttps://orcid.org/0000-0002-0900-2534PersonJaroslav Budišjaroslav.budis@uniba.skhttps://orcid.org/0000-0002-8667-6655PersonJán Radvánszkyjan.radvanzsky@uniba.skhttps://orcid.org/0000-0001-9657-1198PersonProviderIngrid Lojováingrid.lojova@uniba.skhttps://orcid.org/0000-0001-7659-0850PersonProviderBCFtoolsBCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.http://www.htslib.org/bcftoolsbiotools:bcftools1.01.11.21.31.3.11.41.4.11.51.61.71.81.91.101.10.11.10.21.111.121.131.141.151.15.11.161.171.181.191.201.211.21.11.221.22.11.231.23.11.24Command-line toolSuitehttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_2885DNA polymorphismhttp://edamontology.org/topic_3517GWAS studyhttp://edamontology.org/topic_3516Genotyping experimentWindowsMacLinuxCMITBCFtoolsMatureFree of chargeOpen accesshttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/operation_3227Variant callinghttp://edamontology.org/data_3498Sequence variationshttp://edamontology.org/format_3016VCFhttp://edamontology.org/format_3020BCFMultiple data munging operations.https://github.com/samtools/bcftoolsRepositoryhttp://www.htslib.org/support/#listsMailing listhttps://github.com/samtools/bcftools/issuesIssue trackerhttp://www.htslib.org/download/Downloads pagehttp://www.htslib.org/doc/bcftools.htmlGeneralhttp://www.htslib.org/workflow/#mapping_to_variantOtherA workflow for BCFtools.htslibuses10.1093/bioinformatics/btp35219505943PMC2723002PrimaryThe Sequence Alignment/Map format and SAMtools.10.1093/gigascience/giab00833590861PMC7931819PrimaryTwelve years of SAMtools and BCFtools.Wellcome Sanger Institutesamtools@sanger.ac.ukhttps://www.sanger.ac.uk/InstituteProviderSamtools Help mailing listhttps://lists.sourceforge.net/lists/listinfo/samtools-helpProjectSupportSAMtoolsSAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.http://www.htslib.org/samtoolsbiotools:samtools1.01.11.21.31.3.11.41.4.11.51.61.71.81.91.101.111.121.131.141.151.15.11.161.16.11.171.181.191.19.11.19.21.201.211.21.11.221.22.11.22.21.231.23.11.24Command-line toolSuitehttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_3325Rare diseasesWindowsMacLinuxCMITAnimal and Crop GenomicsRare DiseaseSAMtoolsMatureFree of chargeOpen accesshttp://edamontology.org/operation_0335Data formattinghttp://edamontology.org/operation_3695Data filteringhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_0227Indexinghttp://edamontology.org/operation_1812Data parsinghttp://edamontology.org/operation_3096Data editinghttp://edamontology.org/operation_3802Data sortinghttp://edamontology.org/data_0924Sequence tracehttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_2573SAMhttp://edamontology.org/format_3462CRAMhttps://github.com/samtools/samtoolsRepositoryhttp://www.htslib.org/support/#listsMailing listhttps://github.com/samtools/samtools/issuesIssue trackerhttp://www.htslib.org/download/Downloads pagehttp://www.htslib.org/doc/#howtosOtherHowTos for samtoolshttp://www.htslib.org/doc/#manual-pagesUser manualhttp://www.htslib.org/download/Installation instructionshtslibuses10.1093/bioinformatics/btp35219505943PMC2723002PrimaryThe Sequence Alignment/Map format and SAMtools.10.1093/gigascience/giab00833590861PMC7931819PrimaryTwelve years of SAMtools and BCFtools.10.1093/bioinformatics/btr50921903627PMC3198575Richard Durbinrd@sanger.ac.ukPersonContributorWellcome Sanger Institutesamtools@sanger.ac.ukhttps://www.sanger.ac.uk/InstituteProviderPrimary contactSamtools Help mailing listhttps://lists.sourceforge.net/lists/listinfo/samtools-helpProjectSupportHTSlibThe main purpose of HTSlib is to provide access to genomic information files, both alignment data (SAM, BAM, and CRAM formats) and variant data (VCF and BCF formats). The library also provides interfaces to access and index genome reference data in FASTA format and tab-delimited files with genomic coordinates. It is utilized and incorporated into both SAMtools and BCFtools.http://www.htslib.org/htslibbiotools:htslib1.01.11.21.2.11.31.3.11.3.21.41.4.11.51.61.71.81.91.101.10.11.10.21.111.121.131.141.151.15.11.161.171.181.191.201.21.11.221.22.11.22.21.231.23.11.24Libraryhttp://edamontology.org/topic_3071Data managementWindowsLinuxMacCMITAnimal and Crop GenomicsMatureFree of chargeOpen accesshttp://edamontology.org/operation_2409Data handlinghttp://edamontology.org/data_0924Sequence tracehttp://edamontology.org/format_3462CRAMhttp://edamontology.org/format_2572BAMhttp://edamontology.org/format_2573SAMhttp://edamontology.org/format_1930FASTQhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3498Sequence variationshttp://edamontology.org/format_3020BCFhttp://edamontology.org/format_3016VCFhttps://github.com/samtools/htslibRepositoryhttp://www.htslib.org/support/#listsMailing listhttps://github.com/samtools/htslib/issuesIssue trackerhttp://www.htslib.org/download/Downloads pagehttp://www.htslib.org/doc/#manual-pagesUser manualsamtoolsusedBybcftoolsusedBy10.1093/gigascience/giab00733594436PMC7931820PrimaryHTSlib: C library for reading/writing high-throughput sequencing data.Wellcome Sanger Institutesamtools@sanger.ac.ukhttps://www.sanger.ac.uk/InstituteProviderPrimary contactSamtools Help mailing listhttps://lists.sourceforge.net/lists/listinfo/samtools-helpProjectSupportSamen Meten Data PortalIn the dataportal citizen science data and official measurement networks share their data. We combine and visualize the data. Citizen scientists can compare their data with other sensor data and official data. We provide a correction for relative humidity based on the official data and we give an estimate of the quality of the data, the “plausibility”.https://samenmeten.rivm.nl/samen_meten_data_portalbiotools:samen_meten_data_portalsamenmeten@rivm.nlSamen Meten Knowledge PortalThe (Dutch) knowledge portal focuses on the exchange of information. Technological developments enable anyone to measure for example air quality or noise with increasing accuracy. But when are measurements meaningful? how do you perform measurements in the best possible way? and who else is developing new methods? To answer these questions, the knowledge portal offers an overview of the materials, sensors and devices that are available for environmental measurements. We also provide information about citizen science projects and the sharing and use of data.https://www.samenmeten.nl/samen_meten_knowledge_portalbiotools:samen_meten_knowledge_portalsamenmeten@rivm.nlProSeqGOProSeqGO predicts Gene Ontology (GO) terms for protein sequences using ESM2 embeddings and a trained 1-Dimensional Convolutional Neural Network multi-label classifier. By integrating recent advances in protein language models, ProSeqGO facilitates large-scale, automated functional annotation directly from sequence input, empowering researchers to infer protein function, explore biological mechanisms, and accelerate discovery in genomics and proteomics.https://proseqgo.com/proseqgobiotools:proseqgov1.0.0Web serviceCommand-line toolBashSQLPythonMITFree of chargeOpen accesshttp://edamontology.org/operation_1777Protein function predictionhttp://edamontology.org/data_2976Protein sequencePredicts the probability of Gene Ontology (GO) term membership for an input protein sequence using ESM2 embeddings and 1D CNNhttps://github.com/BehRoooz/proseqgoRepositoryhttps://github.com/BehRoooz/proseqgo/releasesSource codepdb2printConverts Protein Data Bank structures into 3D-printable models. Each polymer chain is meshed separately and written as a named object in a single 3MF file, so a multi-material printer can assign one filament per chain. Protein chains can be rendered as a solvent-excluded surface, a cartoon, or a backbone tube; nucleic acids as a tube-and-rung form with the strands of a duplex welded at every base pair. Press-fit magnet pockets are optionally placed at chain interfaces, so a complex comes apart where its subunits actually meet. All meshes are checked for watertightness before export.https://pdb2print.orgpdb2printbiotools:pdb2print1.2.0Web applicationLibraryhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0097Nucleic acid structure analysisLinuxWindowsMacPythonJavaScriptMITEmergingFree of chargeOpen accesshttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_1477mmCIFhttp://edamontology.org/data_1459Nucleic acid structurehttp://edamontology.org/format_1476PDBhttp://edamontology.org/format_1477mmCIFOutput is a 3MF file containing one named, separately coloured mesh object per polymer chain, ready for a multi-material slicer. 3MF is not yet represented in EDAM, so no output format term is given.https://github.com/davidtheadmin/pdb2printRepositoryhttps://github.com/davidtheadmin/pdb2print/issuesIssue trackerhttps://github.com/davidtheadmin/pdb2printSource codehttps://github.com/davidtheadmin/pdb2printGeneralhttps://github.com/davidtheadmin/pdb2print/blob/main/CITATION.cffCitation instructions10.5281/zenodo.21599702PrimaryDavid Häckesdavid@haeckes.dehttps://orcid.org/0000-0002-2177-5206PersonDeveloperPrimary contactFAIR EVA for EUCAIMFAIR EVA: Evaluator, Validator & Advisor has been developed to check the FAIRness level of digital objects from different repositories or data portals. It requires the object identifier (preferably persistent and unique identifier) and the repository to check. It also provides a generic and agnostic way to check digital objects.
This software started to be developed within IFCA-Advanced-Computing receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 857647.https://github.com/IFCA-Advanced-Computing/FAIR_evafair_eva_4_eucaimbiotools:fair_eva_4_eucaimEUCAIM_plugin_0.3EUCAIM_plugin_0.3.1EUCAIM_plugin_0.4.0EUCAIM_0.4.2v0.6.1Plug-inWeb serviceCommand-line toolhttp://edamontology.org/topic_4012FAIR dataLinuxPythonApache-2.0EUCAIMMatureFree of chargeOpen accesshttp://edamontology.org/operation_2428Validationhttp://edamontology.org/operation_0336Format validationhttp://edamontology.org/data_1048Database IDfair-eva-cli batch -p eucaim_legacyhttps://github.com/IFCA-Advanced-Computing/FAIR_evaRepositoryRepository for FAIR EVA, without the EUCAIM specific pluginhttps://gitlab.ifca.es/eucaim/fair_eucaimRepositoryRepository for FAIR-EVA for eucaim plugin. Currently not public.https://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/fair_eucaim/artifacts-tabSoftware cataloguehttps://harbor.eucaim.cancerimage.eu/harbor/projects/4/repositories/fair_eucaim_web/artifacts-tabSoftware cataloguehttps://github.com/IFCA-Advanced-Computing/FAIR_eva/blob/main/docs/index.mdGeneralDocumentation for the main package, EUCAIM plugin specific documentation not included.https://gitlabpages.ifca.es/fair-eva-guide-608baa/User manualWiki page with FAIR EVA for EUCAIM specific instructions.10.1038/s41597-023-02652-8Fernando Aguilarhttps://orcid.org/0000-0001-9462-4831PersonDeveloperMaintainerDocumentorCreator and devloper of the main package FAIR EVA.
This software started to be developed within IFCA-Advanced-Computing receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 857647.David Rodríguezhttps://orcid.org/0000-0002-9160-5106PersonDeveloperPrimary contactDeveloper of the EUCAIM plugin.Inés Victoriahttps://orcid.org/0009-0003-7950-3937PersonDeveloperDeveloper of the EUCAIM plugin.PySMACKSPython computational framework for analysis of single-molecule FRET datahttps://github.com/molcretb/PySMACKSpysmacksbiotools:pysmacks1.0.0RRID:SCR_028788rridLibraryhttp://edamontology.org/topic_3306Biophysicshttp://edamontology.org/topic_3383BioimagingLinuxWindowsPythonMITEmergingFree of chargeOpen accesshttp://edamontology.org/operation_3443Image analysisRun the GUI of PySMACKSPySMACKS_GUIhttps://github.com/molcretb/PySMACKSRepositoryhttps://github.com/molcretb/PySMACKS/issuesIssue trackerhttps://molcretb.github.io/PySMACKS/OtherDocumentationhttps://pypi.org/project/PySMACKS/Software package1.0.0b2https://molcretb.github.io/PySMACKSUser manualGeneralInstallation instructionsBastien Molcrettebastien.molcrette@unibas.chhttps://schmid.chemie.unibas.ch/en/https://orcid.org/0000-0002-5995-5376PersonPrimary contactDeveloperDocumentorMaintainerContributorfull-stack developer of PySMACKSSonja Schmidsonja.schmid@unibas.chhttps://schmid.chemie.unibas.ch/en/https://orcid.org/0000-0002-3710-5602PersonSupportTeam leader at the University of Basel, in which PySMACKS is developedFlaskTrackFlaskTrack is an AI-powered laboratory operations platform combining electronic laboratory notebook, laboratory information management, workflow execution, inventory management, molecular biology, and compliance capabilities. Researchers can create version-controlled protocols and workflows, execute guided procedures, track samples and batches, manage reagents, tools, plasmids, DNA sequences, primers, and assemblies, and preserve traceability through audit trails, approvals, and electronic signatures. AI-assisted features convert research papers, SOPs, and laboratory documentation into structured workflows for human review and approval. FlaskTrack supports role-based access, data exports, APIs, validation documentation, and workflows designed to assist laboratories working toward FDA 21 CFR Part 11 requirements. It is intended for academic, biotechnology, pharmaceutical, CRO, tissue culture, synthetic biology, microbiology, and other life science laboratories.https://flasktrack.comflasktrackbiotools:flasktrackhttps://docs.flasktrack.comUser manualAPI documentationUser documentation for the day to day usage of the FlaskTrack lab operating platformbiotools-linterA rule-based checker for the bio.tools database.https://biotools-linter.biodata.ceitec.cz/biotools-linterbiotools:biotools-linterWeb serviceWeb APICommand-line toolhttp://edamontology.org/topic_3572Data quality managementLinuxMacWindowsOtherPythonMITEmergingFree of chargeOpen accesshttp://edamontology.org/operation_0336Format validation--linthttps://github.com/3top1a/biotools-linterRepositoryhttps://biotools-linter.biodata.ceitec.cz/dash/Technical monitoringhttps://github.com/3top1a/biotools-linterSource codehttps://biotools-linter.biodata.ceitec.cz/docsGeneralhttps://biotools-linter.biodata.ceitec.cz/api/documentation/API documentation10.1093/nar/gkag42042363751PMC13355044PrimaryFilip Rusz251814@mail.muni.czhttps://orcid.org/0009-0002-0046-9725PersonDeveloperJCatTool that can adjust the codon usage of an input sequence to the selected organism. Useful for improving the expression of foreign genes in hosts with different codon usage.http://www.jcat.de/jcatbiotools:jcatWeb applicationhttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_3500ZoologyLinuxWindowsMachttp://edamontology.org/operation_2962Codon usage bias calculationhttp://edamontology.org/operation_0285Codon usage table comparisonhttp://edamontology.org/operation_0286Codon usage analysishttp://edamontology.org/operation_0284Codon usage table generationhttp://edamontology.org/operation_2964Codon usage fraction calculationhttp://www.jcat.de/Introduction.jspGeneral10.1093/nar/gki37615980527PMC1160137Andreas Groteandreas.grote@tu-bs.dePersonPrimary contactProtein Degrader Discovery and ScreeningCreative Biogene offers an end-to-end solution for protein degrader development, integrating advanced computational screening, experimental validation, and optimization strategies to accelerate your drug discovery process.https://www.creative-biogene.com/protein_degraderbiotools:protein_degraderedf2csvedf2csv is a local command-line tool for converting EDF, EDF+, BDF, and BDF+ physiological recordings into CSV and JSON files. It exports signal values, channel information, annotations, and recording metadata while preserving original sampling rates, physical units, and discontinuities.https://edf2csv.vercel.app/edf2csvbiotools:edf2csvCommand-line toolhttp://edamontology.org/topic_4019Bioscienceshttp://edamontology.org/topic_3168SequencingLinuxMacWindowsTypeScriptMITEmergingFree of chargeOpen accesshttp://edamontology.org/operation_3434Conversion