2020-05-19 All-hands meeting notes

Owned by Karmen Condic-Jurkic
Last updated: May 22, 2020
5 min read

Discussion topics

Item

Presenter

Notes

Item

Presenter

Notes

Confluence tips and updates

Karmen

Virtual meeting impressions

Karmen

  • JDC – pre-recorded talks that can be advertised continuously. We should plan for people not inspecting the talks beforehand and structure the meeting around that.

  • JW – Watching the talks is probably not high on the priority list of the industry folks, being busy and stuff. I wonder if we should have more demos for them to showcase the work done. We might front load it to some extent.

  • OM – We need to keep in mind that interaction in virtual meeting will be around 50%, we should streamline our content.

  • MKG – Instead of- or in addition to- the recorded talk, there could be a really short version given during the meeting. Could also provide brief bullet points. Might tie in with the order of how talks went, with David making the overview talk before most other talks were prepared

  • KCJ – I think that discussion is normally limiting. Short talks will be tricky since they break up discussion and are short on details.

  • MKG – We could focus on the more “provocative” or “attention grabbing” ideas to spur discussion

  • KCJ – That may be a good idea. It’ll take a lot

  • JW – the talks were extraordinarily good, but I will need to manage my time and energy a bit better. The pre-meeting period was a bit stressful, but the meeting was quite relaxed.

  • MKG – May be good to allow a few weekdays between talk recording and meeting, for folks to have more time to watch.

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  • Key deliverables graphic (Y1 / Y2 / Y3)

Karmen

  • Suggestions for improvement metrics

  • MKG – Do we have this or do we need to run this in the future?

  • DM – People like Victoria Lim’s plots, we can reuse that script on new datasets. We could also show a trajectory of improvement on coverage

  • MKG – We might conceptualize protein-ligand thing for Y3 as a benchmark. For a fixed set of systems.

  • JDC – Can we show accuract plots from my meeting slides

  • DM – Were those generated using the perses version with a bug?

  • JDC – Thrombin works well because of the single atom changes, but other systems have other issues.

  • MKG – Let’s make sure we point out this data to pharma folks, and give them the data to hold on to

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Misc

 

  • Hiring a QM person – reaching the full capacity with it

  • MS – @Matt Thompson started to sketch the specifications for System Object, any comments and feedback are welcome. Some additional people are involved. More info here OpenFF System Object Specification

  • DD – Do we want to pursue one-on-ones with pharma partners?

Devs week summary

Jeff Wagner

May 2020 Developers Week Notes

  • Operational experiences

    • When deadlines are approaching, have frequent check-ins to evaluate progress and reschedule deadline if needed

    • Working together on big tasks creates a shared responsibility and makes hard decisions easier

  • Shared package namespace

    • What should namespace be called?

      • openff

    • When should the migration happen?

      • Over the next year

    • Which packages should be under openff namespace?

      • Definitely:

        • Toolkit, Evaluator, Openforcefields, smirnoff99Frosst, QCSubmit (when officially released), System (when released),

      • Suggested, need author approval:

        • CMILES?, Fragmenter?, Chemper?, Smarty?, Taproom (Talk to setiadi/slochower -- coming to OFF organization), PLBenchmarks software (eventual), PLBenchmarks data (eventual)

      • Maybe’s -- Not part of OFF org, maybe will migrate in later? Talk to author

        • Perses? (Talk with Hannah), Freeenergyframework? (talk with Hannah), Gimlet? (Talk with Yuanqing/John -- Probably no)

  • Migrating packages over to GitHub Actions and unifying under one OE license

    • Jaime will be hosting a walk-through session in the next two weeks -- Will post in #maintainers

  • Reorganizing/defining/consolidating the many development-related slack channels

    • Rename maintainers to developers

  • Deciding upon a consistent approach and theme for each repos docs

    • Theme working group: JW, SB, DD, MT, JRG, KCJ

      • Working group will make proposal and infrastructure team will open PRs for changes in all repos

    • Content: Like openff-evaluator

    • Engine: Continue using Sphinx

    • Hosting: Switch to GitHub Actions/Pages

  • Feedback

    • Could have optional sessions and provided schedule ahead of time. Takes a lot of mental stamina to follow less relevant topics. 

    • Technical discussions were interesting, but not directly applicable. Channel naming discussion wasn’t that important. 

    • Put together proposals for each topic -- Present ideas and options clearly. Frame things as “here’s what we want to do, do you have objections?”

    • Could have discussions dedicated to early career researcher topics. Unstructured social time would be very helpful.

    • Career perspectives from older folks? 

      • Probably doesn’t need to be structured/scheduled. This would come up in informal discussion.

      • Chris Bayly story time?

    • Breakout/hacking sessions would be good. Could have sessions where people present problems and we work together to solve them.

Industry 1:1

 

DD – do we want to pursue 1:1 with the industry folks? How do we balance their needs for privacy and their scientific needs?

JW – They mostly want FE calculations, some Schrodinger modules replacements (Macromolecule). We released the conformer CLI tool.

JDC – We don’t know how their workflows look like, which is our greatest liability. They would need to reveal what do they use, which might be tricky.

JW – it might be a good way to have another rounds of 1:1. Scheduling is the biggest challenge, it takes a fair amount of time to organize these.

DD – Planning to review AI book, it’s more general than just NNs. Would anyone else be interested in doing something like 1 chapter/month with me?

  • JC – You should talk to Josh Fass about this. And Karmen could organize him giving a public talk about “lessons learned”

  • KCJ – We’re planning for Josh to give a talk shortly

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Remote organization

 

JDC – Are there other strategic issues we should consider for contiued lockdown?

  • KCJ – VR sets for all?

JW – Time separation issues – how to remove deluge of continuous slack messages and create some space for deep work, while leaving enough time to interact with others?

MW – Similar thoughts, I’d like to make myself more available to the younger folks.

DM – office hours?

OM – It’s harder to ask for mentorship when we’re not in the same room

JDC – I use IDPs, and would revise every 6 months. Journal clubs are helpful, as well as hearing about career trajectories form older folks.

KCJ – Journal clubs can be more effort than they’re worth, especially since our consortium members are already in a lab with existing meetings

MKG – I’ve had varied experiences with journal clubs, but would be willing to give them a shot. Ill advertise to my lab.

KCJ – It seems like journal clubs have petered out during the lockdown, the adjustment period and meeting fatigue probably played a role.

MW – Office hours? Put on OpenFF calendar.

TG – I’d like to share my screen sometimes with someone and knowing when I could do.

JW – We had meetings on Mondays where everyone would say what are they working on. We could reinstate those.

Action items

Decisions