Attendees

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

Agenda

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

Discussion Notes

• Covid protocols
  • Not restarting lab meetings onsite - reconsider in february
  • Going in in January requires covid tests.
  • Eric says he has gone in for backups without testing, so not enforced
  • TomF says vending machine covid self-testing available in Genentech Hall (company Color), results as quick as 12 hours.

• log4j computer security vulnerability
  • TomF says UCSF worked over holidays to secure computers
  • Scooter says he believes none of our web services have this vulnerability

• Network security
  • UCSF audit says Chimera web services http need to switch to https
  • CGL vpn will need 2-factor authentication
    • 2-factor works with Duo intermediate between VPN box and Radius server, supported solution
    • To test 2-factor can schedule some cgl vpn downtime
  • TomF says VPN may soon need more than 2-factor authentication to meet UCSF requirements
  • 2-factor not required for web sites in ucsf domain currently
  • Greg asks do we need 2-factor with IMAP for cgl email?
  • UCSF email has turned off IMAP for security
    • Elaine notes cannot get UCSF email even on VPN (probably using IMAP)

• NIAID contract renewal
  • Start writing down next NIAID contract goals
  • May be easier to renew NTT Data contract than all new MSC contract
    • Learned in NIAID meeting Darrell is currently reviewing bids for who will be BCBB new prime contractor starting March 1, so bridge funding for our contract may be needed.

• TomF email with R01 program officer
  • we have new NIGMS program officer for R01
  • former program officer was Christina Liu
  • Christina said NIGMS portfolio reassignments led to ChimeraX reassigned to Han Nguyen who is new
  • Christina say Han's expertise is more in our expertise
  • Han says he and Christina believe we need to resubmit R01 March 5
  • Han needs to review summary statement before meeting with Tom Ferrin
  • Don't expect Han attended our R01 review so won't be able to advise on why they wanted to drastically cut budget
  • Resubmission, needs 1 page letter, can send draft and get feedback from Han
  • We were asked to supply just-in-time documents (TomF and Scooter info) for R01 in case it is funded.

• Staff progress reports
  • Zach
    • web services
  • Greg
    • network security for toolshed, rules for https for virtual hosts
    • Toolshed should use own web service, own IP, own apache instance
  • Elaine
    • user questions, licensing ($50,000 this week), testing new ChimeraX stuff
  • Eric
    • NIH 20 presets bundle
    • will adapt NIH 3d pipeline scripts to use presets
    • improved presets developer tutorial
    • worked on render by attribute gui
    • added command multiple sequence alignment web services
    • started higher performance for sequence viewer
    • working on dock prep
    • started on match align
    • updated some prereqs
    • fixing bugs
  • Tom
    • Gave two class tutorials Jaime Fraser, Aashish Manglik
    • Tested Qt 6 in chimerax on Windows, Mac and Linux
    • Support updated EBI AlphaFold database with Zach
    • Reviewed StarMap Rosetta cryoEM refinement manuscript, Marlovits lab
    • Figuring out how to handle failed mac laptop
      • TomF ordered new Mac laptop before Christmas but shipping date unknown and likely a month out.
    • Sick this week, taking some time off today and tomorrow
    • For Phenix R24 tried calling douse from chimerax, has some problems, Phenix R24 progress report due start of March

Action Items

• Setup meeting with NIH R01 program officer to discuss resubmission, Tom Ferrin
• Get certificate for https at rbvi.org. Expires 6 May 2022 Greg
• Renew certificate for https on vr.ucsf.edu. Expires 11 Dec 2022 Greg
• 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
• 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