Karmen Condic-Jurkic
Karmen Condic-Jurkic
@karmencj.bsky.social
We had a few lightening talks presenting the community initiatives supported by OMSF: Free Energy Workshop (feworkshop.org) by Jonah Vilseck, BPDMC (bpdmc.org) by Chris Ball, @bitsinbio.bsky.social by Nelly Tian, and OpenRosetta by Julia Koehler Leman.
May 9, 2025 at 8:45 PM
After our last coffee break, @dwhswenson.net is updating everyone about progress we've made on our #NSF POSE grant, including the release of the first batch of playbooks available at playbooks.omsf.io. We started with the contributor, developer and benchmarking playbooks.
May 9, 2025 at 7:54 PM
Woody Sherman from Psivant provided an industry perspective on molecular modelling, open science, @openfold.io consortium, @omsf.io and future directions for computational molecular sciences. We also got richer for a new expression that received hearty approval -- "free energy landscape artist"
May 9, 2025 at 7:45 PM
Aniket Margakar from Boehringer demonstrated how they use @omsf.io tools in house, praising both the tools and teams -- that's what we like to hear! He highly recommends NAGL and bespokefit for fast charge assignment and parameterization, and @openfree.energy for FE calcs
May 9, 2025 at 6:51 PM
@jenkescheen.bsky.social showcased his work on @asapdiscovery.bsky.social and more recently with CharmTx, combining ML and more traditional free energy calculations. A lot, if not all, of his work is based on @openfree.energy, #openforcefield, and #alchemsicale. Read his papers for more details!
May 9, 2025 at 6:46 PM
After refueling with some sandwiches, Matt Thompson ran a demo connecting OMSF tools in a working workflow (!). You can find the demo notebook here and try it yourself: github.com/openforcefie.... Feedback welcome!
GitHub - openforcefield/joint-demo: Materials for the joint demo at the 2025 OMSF Symposium
Materials for the joint demo at the 2025 OMSF Symposium - openforcefield/joint-demo
github.com
May 9, 2025 at 6:33 PM
@moalquraishi.bsky.social shared some challenges encountered and learnings gained through painful data preparation and multiple training experiments for the next release of OpenFold, which is coming soon!
May 9, 2025 at 4:17 PM
Ryan Renslow and Hugo MacDermott-Opeskin gave a gentle intro to our latest project @openadmet.bsky.social in collaboration with QBI UCSF and Octant Bio, funded by ARPA-H.
May 9, 2025 at 4:09 PM
Next in line is @ialibay.bsky.social with an overview of Open Free Energy and the latest plans and developments. Did I say we have a full house in the lovely Museum of Science in grey Boston?
May 9, 2025 at 1:57 PM
In short, the new release is coming soon, the team is working hard on consistent force fields for small molecules and (bio)polymers, plus some new tools in the belt, like #pablo.
May 9, 2025 at 1:55 PM
Reposted by Karmen Condic-Jurkic
And fantastic to hear from @karmencj.bsky.social on the experiences and challenges of building research infrastructure with @omsf.io !
April 7, 2025 at 7:51 PM