Find open-source science resources

Open Babel is a chemical toolbox designed to speak the many languages of chemical data.

Molecular Biology Tools is a free browser-based collection of molecular biology utilities for routine sequence analysis, primer design, Sanger sequencing primer planning, cloning setup, and wet-lab calculations. The site includes tools for PCR primer design, Sanger primer design and primer walking, primer binding checks, restriction site analysis, reverse complement generation, ORF and protein translation, codon optimization, ligation calculations, molarity calculations, dilution calculations, and multi-solute solution recipe preparation. The tools run in the browser and are intended for quick experimental planning, without requiring logins or uploading sequences to the server.

Comprehensive set of programs for phylogenetic analyses; available for PC and Mac; source code available for easy compiling in UNIX.

FlavoTyper is a bioinformatics tool that performs in silico serotyping of Flavobacterium psychrophilum genome assemblies.

MONAI Label is an intelligent open source image labeling and learning tool that enables users to create annotated datasets and build AI annotation models for clinical evaluation. MONAI Label enables application developers to build labeling apps in a serverless way, where custom labeling apps are exposed as a service through the MONAI Label Server.

The ProteinsPlus web server aims to support life scientists in working with protein structures. Protein structures are the key to understanding protein function. They are an important resource in many biotechnological application areas from pharmaceutical research to biocatalysis. ProteinsPlus focuses on protein-ligand interactions. The server provides support for the initial steps of dealing with protein structures, namely structure search, quality assessment, and preprocessing. JAMDA enables users to perform an on-the-fly molecular docking of up to five molecules. The poses can then be visualized in 2D (PoseView, PoseEdit). Furthermore, advanced options, such as protein pocket detection (DoGSite), prediction of water molecule positions (WarPP), protein structure ensemble generation (SIENA), prediction of metal coordination (METALizer), the analysis of solvent channels in protein crystals (LifeSoaks), or the categorization of protein-protein-interfaces (HyPPI) are supported.

SeqBench is a browser-based toolkit for DNA, RNA and protein sequence analysis: primer design, restriction digest and cloning simulation, CRISPR guide design, codon optimization, pairwise alignment and plasmid annotation. Supports batch FASTA processing and multi-tool workflow pipelines, and every tool is also exposed as a REST API and MCP server for scripted or agent-driven use. All computation runs client-side in the browser, so input sequences are never uploaded to a server.

regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.

RxDock is a fast and versatile open-source docking program that can be used to dock small molecules against proteins and nucleic acids. It is designed for high-throughput virtual screening (HTVS) campaigns and binding mode prediction studies.

Bin Chicken - recovery of low abundance and taxonomically targeted metagenome assembled genomes (MAGs) through strategic coassembly

Community Terrestrial Systems Model (includes the Community Land Model of CESM)

Thoa is a cloud bioinformatics platform. Write your Nextflow or Snakemake pipeline, point it at your data, and Thoa handles the rest: provisioning VMs (up to 12TB RAM), resolving dependencies, managing execution. No cloud expertise needed. Every job captures its full context:data, software versions, environment, machine specs, as a reproducibility artifact. Share it with a colleague and they can view or re-run the analysis without an account. Key features: AI debugger that fixes environment and dependency issues in real time. Pipeline tracking with per-step telemetry. if step 47 of 200 fails, re-run from there, not from scratch. One-click data sharing without registration. AI-assisted workflow creation from plain English. Free tier available. Starter $35/mo, Pro $109/mo, Team $480/mo. Zero-egress storage. Based in Zug, Switzerland. thoa.io​​​​​​​​​​​​​​​​

URGI (Unit Resources Genomics-Info) is a bioinformatics facility who support various research activities on plants of agronomic and forestry interest for INRAE. The platform has federated with 3 other INRAE ​​bioinformatics platforms to form the BioinfOmics research infrastructure. It is part of the French Institute of Bioinformatics which is the French node of the European infrastructure ELIXIR . URGI is part of the Saclay Plant Science network and of the Graduate School Biosphera . URGI is labeled by GIS IBiSA and is ISO-9001 certified.

Comparative genomics-driven translational research tool.

Multi-agent system for drug-discovery gene target validation. LangGraph agents over an MCP data layer (~26 data sources, ~44 tools) score evidence across six independent lenses (genetics, biology, safety, clinical, commercial, regulatory) into a provenanced dossier. Configurable local/cloud LLM routing with full Langfuse/OTEL traceability.

metagWGS is a workflow dedicated to the analysis of metagenomic data. It allows assembly, taxonomic annotation, and functional annotation of predicted genes. Since release 2.3, binning step with the possibility of cross-alignment is included. It has been developed in collaboration with several CATI BIOS4biol agents. Funded by Antiselfish Project (Labex Ecofect), ExpoMicoPig project (France Futur elevage) and SeqOccIn project (CPER - Occitanie Toulouse / FEDER), ATB_Biofilm funded by PNREST Anses, France genomique (ANR-10-INBS-09-08) and Resalab Ouest.

Browser-based tool for viewing, comparing, and inspecting Sanger sequencing ab1 / ABIF chromatogram files. Files are processed locally in the browser.

Conspecta is a browser-based research platform that brings microscopy image analysis, flow cytometry, molecular biology, sample tracking, and publication-ready figures into one connected workspace. It replaces the patchwork of disconnected tools most labs assemble, so a lab's data, samples, and results stay linked from experiment to figure with full traceability. Built for imaging-heavy and flow-heavy biology labs, new PIs, and early-stage biotech. Research-focused, not regulated or clinical. Free for individuals. Paid team plans add shared workspaces.

xnattools is a python package with a set of modules for performing various operations on data stored in XNAT servers. The main purpose is to provide one standardized platform for running operations on XNAT servers. The package currently contains four tools that use this platform: dicom to nifty conversion, thumbnail generation from dicom, DICOM header data collection, in bulk downloading of a project.

BioCalculator is a mobile toolkit for biology and laboratory calculations. It consolidates calculators and preparation guides for molecular biology, microbiology, virology, stock solutions, buffers, dilutions, unit conversions, and TCID50 endpoint dilution workflows for students and lab professionals.

Python package for biodatafuse project.

AmsterdamUMCdb is a database of de-identified health data related to tens of thousands of intensive care unit admissions, including demographics, vital signs, laboratory tests and medications.

austraits is an R package for accessing the AusTraits Plant database and working with traits.build databases