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2023-06-14 All-hands meeting notes

2023-06-14 All-hands meeting notes

Participants

  • @David Mobley

  • @Chapin Cavender

  • @Daniel Cole

  • @James Eastwood

  • @John Chodera

  • @Matt Thompson

  • @Trevor Gokey

  • @Jeffrey Wagner

Discussion topics

Item

Notes

Item

Notes

General updates

  • DM – James Eastwood intro.

  • JW – QC submissions are offline for a while due to QCA server+software migration. New MolSSI QC* release has left old QCA read-only. QCSubmit needs to be updated for new API (much of it is simplification).

    • JC – Could this be an opportunity for new hires to learn the stack?

    • MT – There’s an open PR that DD worked on a few months ago that may be ready to go. Also learning a new software stack is a lot of work and this may not be the best learning task. (JW: DD says more work may be needed.)

    • JW – Is this an org-level decision?

    • DM – Postpone decision until Lily can join

    • JC – PEastman could be willing to help with this as well.

  • JC – How can I help with recruiting new community manager?

    • DM – KCJ is taking point on this, but is swamped by POSE grant paperwork. (POSE = Pathways for sustainment of open source ecosystems(?)). Lots of accounting/reporting requirements to implement.

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Vignettes

JW – https://github.com/openforcefield/2023-workshop-vignettes

  • JW – they put some work into this so people could try new things

  • JW – these are only guaranteed to have worked at the point in time they were demoed. May be able to install same snapshot as was used to reproduce, but not guaranteed to continue to work indefinitely.

  • JW – Vignettes marked as Yellow and Red are particularly interesting since they had a lot of imagination involved

  • JW – Vectorized Representations vignette extracts numpy arrays to allow direct ML on parameters

  • JW – Reaction SMARTS example allows modification of ligand

  • JW – Interchange export and combination things are suitable for testing, but perhaps not yet publishing

  • JW – Custom substructure loading example shows off loading a covalently modified protein, and NAGL used to assign charges. Can use either noncanonical residue charge generation example or NAGL to generate charges for whole molecule.

  • JW – Animations of many vignettes are in my workshop slides: https://docs.google.com/presentation/d/1ErRATwIlkQvjynz_6QAqeYQ36nPqOCR9-JfGbXoiDpI/edit

Action items

Decisions