OMSF Project News - October 2024
Here are the October 2024 updates from OMSF projects! This month brings new faces, exciting progress on key initiatives, and some major industry recognitions.
New Faces at the Org!
We are thrilled to welcome Alyssa Travitz and Josh Horton, two new research software engineers at Open Free Energy, as well as Ryan Renslow, the project director of an exciting new project we’ll share more about in the weeks to come!
OpenFold
OpenFold is excited to announce the addition of Bristol-Myers Squibb, Novo Nordisk, Exscientia, Abiologics, Visterra, and Lambda Labs to the ever-growing OpenFold community. Welcome aboard! For more information, contact Mallory Tollefson.
Open Force Field
Interchange 0.4 is in the release candidate phase and will hit the main channel soon. This includes some behavior and API changes, and an update of the OpenFF ecosystem to Pydantic 2 - use the script below to try out the changes early!
mamba create -n interchange_04 -c conda-forge/label/openff-interchange_rc -c conda-forge openff-interchangeWork on the Protein Force Field continues, and Open Force Field is hoping to expand support to both proteins and small molecules soon.
Meanwhile, the team is deploying 1000-2000 simultaneous cores to process QC datasets, preparing for the next generation of charge models. Also, the team is moving forward with exciting changes to NAGL1, including a neural network to assign charges.
Are you interested in adding your own thing? Check out Anything Goes for some fun proofs-of-concept or, submit your own changes. We’ll merge any even slightly relevant PR - Go crazy!
Open Free Energy
Datryllic has been contracted by the OpenFE Project to take on product ownership of the gufe library as well as provide staff training for the next 8 months. Their expertise as long time contributors to OpenFE and the wider OMSF ecosystem is welcomed!
OpenFE v1.1 is now out. This includes:
- Enhanced system solvation option, e.g. dodecahedron and octahedron boxes. Internal tests have demonstrated upwards of 1.6x speed improvements by switching to dodecahedron boxes
- Reduced results JSON files (from ~ 120 MB to ~ 4 MB)
- A variety of small bug fixes which should not affect simulation outcomes
- A full changelog can be seen here: https://docs.openfree.energy/en/stable/CHANGELOG.html#v1-1-0
Alchemiscale v0.5.1 is now out with support for the latest changes in the OpenFE ecosystem. We also want to announce the migration of the Alchemiscale platform to the OpenFE github organization.
OpenFE, in collaboration with OpenFF (many thanks to Matt Thompson), has successfully completed initial proof of concept work towards supporting non-OpenMM molecular dynamics engines (i.e. GROMACS). More work towards this is expected in the coming year.
Open Rosetta
It’s been an incredible time for Open Rosetta and Rosetta Commons, with David Baker awarded this year's Nobel Prize! Congratulations to the Baker lab and the entire Rosetta Commons community!
The European Rosetta Con is fully booked with 340 participants. If you’re interested in following up with upcoming workshops or interviews, we encourage you to get in touch!
With their recent POSE Phase II award, the team is hard at work fulfilling the grant requirements. Keep on the lookout for opportunities to join the Open Rosetta team in the near future.
BPDMC
BPDMC has secured its first financial contributors! If you are in the Boston metro and want to see the latest and greatest in the protein modeling space, BPDMC has meetings every month, and they are happy to have you. They've got pizza!
Ecosystem Infrastructure at OMSF (Eco-Infra)
The internal software team at OMSF continues to make strides with new playbooks and GitHub Actions Runners now in use by OpenFE and OpenFF. We’re excited to see the momentum build!
That wraps up our October update! Be sure to subscribe with us for more exciting developments, and don’t forget to reach out if you want to get involved in any of our upcoming initiatives.