Attendees

• Zach, Eric, Elaine, Greg, TomG, Scooter, TomF

Agenda

• Renew NIAID contract -- SOW
• Work on R01 grant resubmission text, Google doc (link sent by email)
• Create ChimeraX 1.4 roadmap
• Updates:
  • project updates
• New desktop computer hardware
• Review Action Items list below

Discussion Notes

• New NIAID statement of work
  • Drop HuBMAP, Darrell had low interest
  • Keep NIH 3D pipeline, general improvements, multi-person VR, segmentation, dicom.
  • DICOM should focus on VR for use in BCBB BioViz center. Probably rendering improvement and ui controls, rather than past meta-data viewer aim.
  • Segmentation might not mention ITK. Instead focus on reading, viewing, editing segmentations in VR.
  • TomG complains too many of these projects assigned to him.
  • Scooter suggests Zach work on DICOM and segmentation goals but TomG handle the VR and rendering.
  • TomG not clear if DICOM and segmentation may be mostly rendering and VR gui, with reading/writing files a small part that Zach could do.

• Funding and staffing
  • TomG has too many projects: Phenix, Qt 6, M1 port, AlphaFold, VR, EM...
  • Scooter suggest TomG drop all CZI (qt 6, M1 port, pypi wheel) and Zach can take those.
  • Scooter suggests asking him and Tom if other grant projects (e.g. Phenix) need to be shifted onto other developers.
  • If we get R01 renewed we would try to hire another developer.

• R01 resubmission
  • Need to add a half-page on structure prediction machine learning, e.g. AlphaFold and RoseTTAFold.
  • Need to add text to emphasize the importance of integrated tools.
  • Need to add text justifying that this is all a lot of work, budget should not be cut.
  • Will add to progress section the 9 months of work since first submission.
  • Can remove interactive MD that is not related to EM refinement.
  • Resubmission letter will reference new parts of proposal.
  • Resubmission letter can emphasize impact of integrated tools for example that allowed quick implementation of AlphaFold sequence search, matchmarker...

• Web services
  • Scooter suggests Zach give an overview of web services at developer meeting in 2 weeks.

Action Items

• Setup meeting with NIH R01 program officer to discuss resubmission, Tom Ferrin
• Start resubmission process going with C&G -- TEF
• Check update of toolshed to django 4.0 -- Greg
• Move toolshed to it's own IP address -- Greg/Scooter
• Set up toolshed test instance (UCSF only) -- Greg/Scooter
• Clean up VirtualHosts on our web servers -- Greg/Scooter
• Move webservices to https only & test (and test, and test) chimera to make sure it works
• Create self-signed certificate for webservices-test -- ongoing, Greg has run into a weird error
• Document new vpn setup on Linux - Scooter
• Set up 2-factor authentication for hal2 vpn - (waiting to see if VPN will even be allowed by campus IT) - Scooter