Motivation
BioChef democratizes access to bioinformatics tools, bridging biologists, healthcare professionals, and computational tools by running C-based genomic utilities directly in the browser via WebAssembly.
The case for BioChef
Most genomic tools require local installs and trust in opaque container images. BioChef closes that gap with a signed, browser-native pipeline.
The problem
Most bioinformatics tools require local installs, native toolchains, and trust in opaque container images. End users like clinicians, students, and reviewers can't easily inspect or run them, and reproducibility suffers.
The solution
A YAML recipe declares the tool. biochef-hub validates, builds (WASM via
Emscripten/biowasm), tests, generates SBOM + SLSA, signs with cosign, and publishes a
signed bundle to registry.biochef.app. The static BioChef web app then
loads it by digest and runs it client-side. No servers, no uploads.
In practice
See how BioChef helps different teams solve real problems.
Researchers
Run signed tools for FASTA/FASTQ manipulation, format conversion, and statistics with reproducible parameters.
Privacy
The whole BioChef app is a static page. Tools are compiled to WebAssembly and execute on your sequence inside the browser tab.
Workflow authors
Drag tools into a DAG, configure parameters, and re-run live as you iterate. Save and reload recipes in one click.
Side by side
A quick comparison of how each task changes when tools live in a signed registry and run as WebAssembly.
| Aspect | Traditional toolchain | With BioChef |
|---|---|---|
| Tool provenance | Opaque containers, ad-hoc signing | Signed recipes → Hub → Registry with SBOM and SLSA |
| Getting started | Install toolchain, build from source, manage dependencies | Open the BioChef app in a browser tab |
| Data handling | Upload sequences to a server you have to trust | WASM execution keeps every byte inside the browser tab |
| Iterating on a workflow | Edit shell script, re-run, hope for reproducibility | DAG editor with live re-execution; recipes are signed and replayable |
| Sharing a result | Send a tarball plus a README | Share the recipe. Anyone can re-run it from the registry |
Tool provenance
Traditional
Opaque containers, ad-hoc signing
With BioChef
Getting started
Traditional
Install toolchain, build from source, manage dependencies
With BioChef
Data handling
Traditional
Upload sequences to a server you have to trust
With BioChef
Iterating on a workflow
Traditional
Edit shell script, re-run, hope for reproducibility
With BioChef
Sharing a result
Traditional
Send a tarball plus a README
With BioChef