PyRosetta Bootcamp

User, PyRosetta

PyRosetta Bootcamp is a week-long, immersive experience, targeted to new Rosetta Community members seeking to become more proficient users through Rosetta's python interface. It has been offered online and in-person.

PyRosetta & ML Intro Bootcamp 2025

Course Description & Solicitation for Participation This week-long bootcamp is targeted to new protein designers just getting started in the field and aiming to develop foundational knowledge and skills to use well-established tools.

The learning progression of this bootcamp is broken into two sections. Section I includes: (1) Rosetta protein biophysics basics/conceptual fundamentals; (2) PyRosetta structure and syntax (Pose, Score Function, Movers); (3) modeling protocols in PyRosetta (Minimization, Packing and Relaxing); (4) Introduction to Rosetta Community and coding conventions. Section II includes: (1) ML Protein modeling algorithm architecture, training/testing basics, (2) survey of ML-based modeling options; (3) review of ML-based protein design and protein generation algorithms (e.g ProteinMPNN and RFDiffusion).

By the end of this workshop, participants will be able to select and apply appropriate PyRosetta and/or ML-based methods for their projects and troubleshoot common errors. Additionally participants will learn about the Rosetta Commons and the resources and opportunities the community provides, and make new connections with Commons members from outside their own research group.

While comprehensive expertise with Rosetta is not achievable in a weeklong program, participants should expect to develop a strong conceptual foundation of the tools and an awareness of the resources and means to expand upon their skills as their projects progress. They will join a network of enthusiastic scientists developing and employing best-in-class tools to tackle human-centered challenges in food, health, and energy.

If this sounds like the right fit for you (or your student), wonderful! Please consider applying to participate here (link TBD). Your responses will be reviewed by the instructor, coordinator, and TA team for alignment with need (i.e. early in grad career, limited lot of lab support, limited protein design experience), preparation (i.e. Python experience) and bootcamp fit (i.e. ready for a rigorous, intensive week).

Details: When: mid-January Where: University of California, Davis Instructor: Deniz Akpinaroglu (deniz.Akpinaroglu@ucsf.edu) TAs: TBD Deniz and Marissa will propose TAs