Attendees

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

On-site Genentech Hall N436A

Agenda

• TomG NIAID contract progress
• Create ChimeraX 1.4 roadmap
• NIAID contract
• Review Action Items listed below

Discussion Notes

• NIAID contract
  • Scooter met with MSC, UCSF contract people, and Darrell to work out hourly contract.
  • Contract expected to start May 1 and last 10 months.
  • Will have monthly progress reports
  • Includes two 5 day trips for TomG to visit RML and Bethesda.

• Computer security audit
  • UCSF assigned us a system administrator Nick to help with security upgrade tasks.

• CGL email
  • UCSF IT wants to redirect all CGL email through ProofPoint cloud scanning service.
  • Would have 25 Mbyte message size limit, no Python attachments, URLs converted to go through urldefense.
  • This impairs our daily work, mailing list Python attachments, bug report email with large attachments.
  • UCSF IT said understands our special needs and is evaluating.
  • Sali lab email has already converted to ProofPoint scanning.
  • Greg says he sent Sali lab Python script attachment earlier but has not heard back.
  • Possibly in the future we may host Trac and mailing lists offsite (e.g. google groups).
  • Aim is to not disrupt current working systems and keep email functioning well.

• Wynton BeeGFS
  • BeeGFS was patched yesterday and seems to have fixed stability problem.
  • Patch also seemed to give 25% speedup.

• Trac
  • Fewer Trac corrupted database problems recently
  • BeeGFS file system problems may be the cause of those.
  • Trac currently using SQLite and Python 2.
  • Want to upgrade to MariaDB (MySQL) and Python 3.
  • Currently updating Toolshed to MariaDB.

• NIAID progress report for new contract (not yet funded)
  • Eric
    • Uniprot or mmCIF residue numbering now supported.
    • Trying to get NIH 3D presets on toolshed, held up by Toolshed issues.
    • Then will get Philip to install presets bundle in NIH 3D pipeline.
    • Then will switch NIH 3D scripts to use presets, and make pull request with changes.
    • Next task is probably copy/combine GUIs
  • TomG
    • Gave VR demo to NIH VR special interest group organized by Jeremy Swan.
    • About 50 viewers including NASA and other non-NIH people.
    • Video on YouTube.
    • Showed two person VR with Phil Cruz.
    • One participant had funding and collaboration suggestions at end.
    • AlphaFold Database updated, to late January 3rd release, 1 million structures
    • AlphaFold update to 2.2.0 in ChimeraX Colab, Wynton and Minsky in visvault
    • New alphafold error plots advertised in video demo and on twitter and in SBGrid webinar.
  • Zach
    • Today's ChimeraX now handles Jason Rubensteins heart echo cardiogram (4D).
    • Jason sent two more 4D dicom datasets, ChimeraX only sees first time point.
    • TomG will try the first data set in VR since Jason was specifically interested in VR.
    • Jason has VR equipment

Action Items

• Move toolshed to it's own IP address and it's own Apache instance -- 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 and extensively 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 -- Scooter
• Audit followup -- Scooter