Finding the right open source scientific software for a research problem is harder than it should be. The number of tools has exploded over the last few years, well beyond biotech, and they sit scattered across separate indices and GitHub lists that change constantly. There is rarely an easy way to tell which tools are still maintained and which have been abandoned.
We started an internal tracker so we could always build on the latest tools. That tracker became Open Science Index.
It is now live, with 6,720 resources indexed at the time of writing and updated daily: a single cross-domain directory of open source scientific software, AI models, datasets, and research resources spanning every scientific field. You can search it, filter it, and submit your own tools.
The open science ecosystem is fragmented
Thousands of valuable tools exist across biology, chemistry, physics, materials science, and earth science. Finding the right one usually means jumping between dozens of separate registries, outdated awesome lists, and domain-specific sites that rarely connect to one another.
Open source AI models tend to live on Hugging Face, organized by machine learning task rather than by scientific application. A model that predicts protein structure and a model that classifies microscopy images are filed under “image segmentation” and “token classification,” which tells a biologist almost nothing. Traditional bioinformatics tools sit in places like bio.tools or lie scattered across GitHub. Databases live somewhere else again.
The result is that researchers spend hours hunting for, evaluating, and comparing tools that should be discoverable in a single search.
What you can search
Open Science Index is organized by scientific application rather than by software category, so you can start from the problem instead of the tech stack:
- Bioinformatics tools: sequence analysis, variant annotation, single-cell and gene expression analysis, genome assembly
- Open source AI models: biological foundation models, protein structure prediction, protein design, medical image analysis
- Scientific and biological databases: genomics, proteomics, microbiome, chemical, and biomedical databases
- Drug discovery tools: screening libraries, molecular generation, docking, cheminformatics
- Computational biology and lab software: flow cytometry analysis, microscopy analysis, simulation and modeling
A researcher should be able to describe what they are trying to do, whether that is folding a protein, generating a new molecule, analyzing a single-cell dataset, or simulating a climate feedback loop, and immediately see every credible open source option in one place, with enough information to choose between them.
Every entry shows whether the tool is actually alive
This is the part that separates a directory from a link dump. Every entry carries consistent, comparable signals:
- GitHub stars alongside commit recency
- Citations
- Downloads and installs
- Container pulls
- Latest release
- Open issues
- An inferred maintenance status
Abandoned projects are flagged rather than buried. The difference between a repository with five thousand stars and no commits in two years and one with five hundred stars and a steady release rhythm becomes obvious at a glance. Star counts alone have quietly misled a lot of research groups into building on dead code.
Where the data comes from
All of this rests on steady, ongoing ingestion from the registries and platforms we build on: bio.tools, Bioconductor, Bioregistry, Hugging Face, BIOS, and others.
Open Science Index does not try to replace any of them. It connects their efforts, links back to the original sources, and makes everything searchable across scientific domains that individual registries were never built to cover.
Frequently asked questions
Is Open Science Index free? Yes. It indexes free and open source scientific software, and the index itself is free to search.
What counts as an open source scientific tool here? Software, AI models, datasets, and databases with an open license that are used in scientific research. That includes bioinformatics tools, computational chemistry packages, open source microscopy software, and biological foundation models.
How do you know if a tool is still maintained? We infer maintenance status from commit recency, release cadence, and open issue activity, and show those signals on every entry so you can judge for yourself rather than trusting a single label.
Can I find alternatives to a specific tool? Yes. Because entries are grouped by scientific application rather than by ML task or language, you can compare open source options side by side for the same problem, such as protein structure prediction or variant annotation.
How often is the index updated? Daily.
How do I add my tool? Submit it here. We review submissions and pull in metadata from the source repository automatically.
Start searching
Open Science Index is live. Search and filter across every scientific domain, submit a tool, and send us feedback by email or on X.
