Publications, talks, and milestones from the BioChef project. Follow along as the browser-native, signed bioinformatics platform grows.
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Peer-reviewed publications, conference talks, and project milestones, most recent at the top.
Training· home.biochef.app · Workflows
14 hands-on tutorials, all in the browser
Fourteen step-by-step tutorials teach genomics with BioChef workflows, from first steps with DNA sequences to read QC, mapping and coverage, variants, viral consensus and amplicon sequencing, gene prediction, genome assembly and comparison, and phylogenetics. Each takes 15 to 30 minutes and comes with its data, the finished workflow and an exercise with its solution. Every result was checked in the app against a known answer. Nothing to install, and the data stays on your computer. Browse them by workflow type, community or subject.
Milestone· Trinity College Dublin · ELIXIR Federated Human Data Community Meeting
BioChef among the ELIXIR Human Data projects for 2027–28
At the ELIXIR Federated Human Data Community Meeting in Dublin, BioChef was presented as one of the projects of the HDTR 2027–28 programme, in the federated data analysis line: a hybrid workflow platform for privacy-preserving federated analysis that separates workflow design from secure execution, with an agent deployed in secure environments and links to GA4GH connectors and LS-AAI.
Release· biochef-hub · biochef-recipes
12 BioChef tools now also build natively
A recipe can now declare a native build script next to its WebAssembly one. biochef-hub builds both and records the build tools’ versions and the script’s SHA-256. Twelve of the 31 recipes ship native builds today: fastp, FastTree, gffread, GTO, ksw2, LASTZ, minimap2, MUSCLE, Prodigal, samblaster, samtools and seqtk. These are the builds the BioChef agent, in development, will run next to the data.
Since August, the app checks the signature on the tool catalogue with a public key built into the app, loads each tool by its immutable digest, and verifies the SHA-256 of its bundle, JavaScript and WebAssembly before running it. A tool that fails a check cannot be added to a workflow. The app now also checks the registry’s reply against the expected digest before reading it.
BioData.pt | ELIXIR Portugal wrote about the BioChef paper: an open catalogue of bioinformatics tools compiled to WebAssembly, run from a drag-and-drop editor in the browser, with the data kept on the user’s machine. The piece points to what this means for the FEGA and GDI communities, which work with sensitive genomic data, and to how each tool is declared as a recipe, then built, tested, signed and published with its software bill of materials and SLSA provenance.
Jorge Silva presented BioChef at the ELIXIR human Copy Number Variation (hCNV) Community face-to-face meeting, discussing use-case workflows, benchmarking, and how a browser-native, signed toolchain can serve the wider ELIXIR human data communities.
Milestone· University of Aveiro · MSc in Informatics Engineering
João Andrade defends his MSc thesis on BioChef
BioChef lead developer João Andrade defended his MSc dissertation, “Uma plataforma web client-side baseada em plug-ins para execução híbrida de workflows” (a client-side, plug-in-based web platform for hybrid workflow execution) — the architecture behind BioChef. Supervised by José Luís Oliveira and Jorge Miguel Silva (IEETA, University of Aveiro).
BioChef presented at the BioData.pt | ELIXIR-PT Technical Meeting 2026
Jorge Silva and João Andrade (IEETA, University of Aveiro) introduced BioChef in a two-hour session at the 7th annual BioData.pt | ELIXIR-PT Technical Meeting, which gathered 31 participants. The 2026 edition put AI and machine learning at the heart of the agenda, with hands-on work on Deucalion, the Portuguese national supercomputer.
Publication· BMC Bioinformatics 27:103 · Open access · CC-BY 4.0Featured
BioChef published in BMC Bioinformatics
The peer-reviewed paper describing BioChef — a client-side, WebAssembly-based workflow builder for genomic data analysis — is out in BMC Bioinformatics. Rosa, J., Andrade, J., Silva, J. M., & Oliveira, J. L. (2026). Biochef: a client-side WebAssembly-based workflow builder for genomic data analysis. BMC Bioinformatics 27, 103.
The first public write-up of BioChef went online as a Research Square preprint ahead of peer review — the client-side, WebAssembly-based approach to running genomic workflows entirely in the browser.