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OpenProteo is the open-source Rust stack for proteomics raw-file access. It reads Thermo, Bruker, and Waters acquisitions through a single API (via the sibling OpenTFRaw, OpenTimsTDF, and OpenWRaw readers), converts them to PSI-MS mzML 1.1.0 with a canonical writer, and provides a zero-copy read_arrow() API (enabled by default) that loads directly into Polars or Pandas via PyArrow. No vendor SDKs, no Windows-only DLLs, no binary blobs in the release pipeline. Includes a one-shot vendor2mzml CLI.

OpenWRaw is a standalone, cross-platform reader for Waters MassLynx .raw acquisition directories, implemented in pure Rust with no dependency on vendor DLLs. Python bindings built on PyO3 expose functions, scans, and ion-mobility data as native Python objects from Waters QTof and SYNAPT instrument families, ready to be assembled into a Pandas or Polars DataFrame.

OpenTFRaw is a standalone, cross-platform reader for Thermo Fisher Scientific .raw mass-spectrometry files, implemented in pure Rust with no dependency on vendor DLLs or .NET. Python bindings built on PyO3 return NumPy arrays for spectral data, straightforward to load into Pandas or Polars. Covers format versions 8 through 66 (LCQ Classic through Orbitrap Astral and modern TSQ instruments), supporting both centroid and profile spectra.

Biomedical Model Context Protocol (MCP) server unifying literature search across PubMed/Europe PMC, entity pivoting across genes/variants/drugs/diseases/pathways/proteins, local study analytics, and Claude Code/Codex integration for agentic biomedical research (531+ stars, MIT License, 2025-2026)

Open-source, local-first desktop AI research workbench for scientific computing with Python/R, MCP bioinformatics tools, SSH/WSL/GPU runtimes, and OpenAI/Anthropic models (857+ stars, 2026)

Rust implementations of algorithms and data structures useful for bioinformatics.

Given a set of KEGG orthology group identifiers, identify the KEGG modules whose definition is satisfied

xgt is a command-line tool for programmatic access to the GTDB REST API. It provides four subcommands: search (genome queries with pagination), genome (cards, metadata, taxonomic history), taxon (lineage and genome set retrieval), and diff (per-rank taxonomic comparison between any two GTDB releases). All subcommands support batch input, JSON/CSV/TSV output, file splitting, and automatic retry. Implemented in Rust as a self-contained binary with no runtime dependencies.

OpenTimsTDF is a standalone, cross-platform reader for Bruker timsTOF .tdf and .tdf_bin acquisition files, implemented in pure Rust with no dependency on vendor SDKs. Python bindings built on PyO3 expose frame, scan, and peak data as native Python objects, providing ion-mobility-aware access that can be assembled into a Pandas or Polars DataFrame.

seqlib is a type-safe Rust library for working with DNA and RNA sequences.

DANTE is a software tool for genotyping and characterizing tandem repeats (TRs) from both second- and third-generation sequencing data. It supports the analysis of short-read massively parallel sequencing (sr-MPS) and long-read massively parallel sequencing (lr-MPS), enabling accurate repeat characterization across a wide range of loci. A key feature of DANTE is its ability to determine genotypes at nucleotide resolution, including the characterization and phasing of complex repeat motifs. For sr-MPS data, the tool determines allele size and sequence composition of alleles for which spanning reads are generated. In addition, it identifies alleles that exceed the sequencing read length by estimating their presence from partial read evidence and supports the visualisation of the sequence composition of partial reads. For lr-MPS data, where complete repeat regions are typically sequenced, DANTE determines the allele size and sequence composition of identified alleles.

Fast FASTQ filtering by matching reads against one or more regex patterns.

DICOM workbench - tag editor, anonymizer, MPR viewer