Open Arsenal

From Sequence to Solution

BioFoundry is an open-source computational biology platform designed to unify primer design, genome validation, and CRISPR-aware experimental planning into a single, streamlined workflow. Built with a modular and extensible architecture, it allows researchers to move efficiently from raw DNA sequence input to fully validated experimental designs. By combining traditional bioinformatics methods with modern development practices, BioFoundry provides a transparent and reproducible foundation for genetic research.

At its core, BioFoundry includes a powerful primer design engine that handles forward and reverse primer generation, thermodynamic optimization, and structural analysis such as hairpins and dimers. This is paired with a genome-aware validation layer that integrates tools for off-target detection and specificity analysis across entire genomes. These capabilities help ensure that designed primers are not only efficient but also highly reliable in real-world laboratory conditions.

A key differentiator of BioFoundry is its integrated CRISPR module, which enables coordinated design of primers alongside guide RNAs. This allows researchers to plan validation strategies for gene editing experiments, including knockout, knock-in, and base editing workflows. By aligning primer placement with CRISPR cut sites and accounting for off-target risks, BioFoundry supports more accurate and efficient verification of genetic edits.

In addition to its core scientific functionality, BioFoundry is built for modern research environments. It offers API and CLI access for automation, visualization tools for interpreting results, and a project-based workflow system for organizing experiments. The platform is fully open source under the AGPL-3.0+ license, encouraging collaboration, transparency, and community-driven innovation. With planned advancements such as AI-assisted experiment planning and simulation tools, BioFoundry aims to evolve into a comprehensive computational biology platform that truly delivers on its vision: from sequence to solution.