OMSF Project News - March 2025
Greetings! We at OMSF hope you are having a wonderful year so far. As we move into spring, we’d like to dose you with our monthly OMSF project updates.
Staff Announcements
Mallory Tollefson has been working closely with OpenFold as their business development liaison for about a year. We are happy to announce that she accepted a full time position with us as the new project manager not just for OpenFold, but for OpenADMET as well! We are very excited!
Kate Huddleston has also joined OpenADMET as a Research Software Engineer from the University of Florida. Welcome Kate! We are lucky to have you.
In addition, please welcome Feli von Peter, who joins OMSF as its administrative assistant. In a very tangible way, Feli represents the ongoing growth of organization. We are honored to have her!
OMSF Symposium – May 9, 2025
Our annual symposium is shaping up! OMSF will be headed to the Museum of Science in Boston for the 3rd annual OMSF Symposium. The morning will feature keynote sessions, and in the afternoon, we're planning demos, industry talks, and community discussions.
If you are interested, feel free to register - there’s still some space left! There will be another newsletter soon with more information - stay tuned!
Open Force Field
The PTM Workflow Prototype is now available for feedback, showcasing how to load and parameterize a modified protein using OpenFF, including use of an early version of our polymer loader, openff-pablo . Additionally, Jeff will be presenting a showcase of OpenFF and other OMSF tools at the RDKit UGM on April 11..
For users encountering issues with SMIRNOFFTemplateGenerator in OpenMMForceFields, the team recommends upgrading to OpenMMForceFieldsOMMFFs 0.14.3 or downgrading openff-interchange to 0.4.1.
Open Free Energy
The OpenFE team is hard at work on a large benchmarking project in collaboration with their industry partners. They are collecting and analyzing results on both public and private datasets from 13 collaborators to demonstrate the accuracy of their Relative Binding Free Energy protocol. The team is also making progress on new protocols for Absolute Binding Free Energies and a Separated Topologies approach to RBFE.
OpenFE is actively developing a new annual roadmap, so please reach out if you have ideas for a joint project - James Eastwood, Project Manager at Open Free Energy, is eager to hear from you!
OpenFold
Progress continues on OpenFold 3, with model training now halfway complete and an anticipated release before the symposium. The project has also introduced a new logo, and three new contributors have recently joined the team. Check out their updated website to learn more!
OpenADMET
The team’s primary tool, Anvil, is now publicly available on GitHub, with new community driven model architectures and benchmarking data obtained from the ASAP Challenge expected soon following analysis of challenge results. Thanks to all that participated.
OpenADMET continues to fold in additional model architectures, with the addition of graph-convolutional deep learning models as well as improving their model training and model evaluation pipelines. They are also busy developing an active learning pipeline for compound selection from large libraries, with the aim of improving model performance across a broadly defined chemical space through in-the-loop data acquisition with our partners. Follow that journey on their GitHub (linked above)!
OpenADMET is also expanding their team, looking to hire 3-5 new Research Software Engineers. Be on the lookout for new roles on our Job Board!
RosettaCommons
The Winter RosettaCon (WRC) was a success, bringing together ~160 in-person attendees and 180 virtual participants. Looking ahead, RosettaCommons is tentatively scheduling a C Bootcamp in early June and is currently discussing membership structure updates while planning next steps for the Biosecurity Fellowship.
Rosetta is also actively working towards the goals of their POSE grant, and they have two open roles funded by the grant waiting to be filled – if you’re interested in research software product management or technical writing, this is your opportunity to do some impactful work!
Eco-Infra
Our ecosystem infrastructure team has been working on the Software Bill of Materials (SBOM), as a part of the greater effort to understand the software landscape in which OMSF tools exist and our dependencies. The team is also advancing the SPEC0 script, as another critical component for infrastructure improvement.
Meanwhile, the GitHub Actions Runners project (gha-runner) has been migrated to our new GitHub Actions framework. This project enables OMSF projects to use more expansive compute options during continuous integration, allowing for more comprehensive testing of things like GPU code paths. . As OMSF’s technical support team, Eco-Infra continues to assist projects with packaging strategy and investigate ways to improve cloud-based deployment strategies for OMSF-hosted projects.
That's all for this month's updates - thanks so much for reading! See you next month with more updates. Bye!