Attendees

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

Agenda

• Work on R01 grant resubmission text, Google doc (link sent by email)
• Phenix R24. Tried phenix douse command to place waters.
• Chimera 1.16 release plan.
• Create ChimeraX 1.4 roadmap.
• New desktop computer hardware.
  • Assign host name to new AI machine. minsky.cgl.ucsf.edu?
• Review Action Items list below

Discussion Notes

• Christmas card sent.

• Java critical security log4j bug
  • Scooter dealing with Cytoscape and log4j 2 security vulnerability.
  • Our Apache servers don't use log4j.
  • TomCat uses log4j 1 which does not have plugin weakness.
  • Neo4j was vulnerable and Scooter patched it.
  • Chimera small molecule depiction service uses cdk library, does not have log4j.

• Web services in ChimeraX using REST
  • Would like smiles to 2D depiction without CDK in ChimeraX.
  • Zach working on porting ChimeraX modeller to new web services (replacing opal).
  • Get all services working with ChimeraX, then look at backport to ChimeraX.
  • Everyone will have to run latest Chimera.
  • Zach is testing using webservicestest, then will move to production webservices.

• Web services for Chimera
  • Chimera needs opal service to open mmcif and find ligand templates
  • Might just turn off Chimera services in a year

• Web service status checking
  • Alphafold web services do status checking.
  • Have other ChimeraX web service check a status page on failure.
  • Get this into daily builds.
  • There is a 3 day wynton planned service in February.
    • Can have a static rbvi web site on cglbackup which will stay up during planned service (service is mostly for beegfs).

• Security audit
  • We made many suggestions for corrections to audit report.
  • Who is taking responsibility to update audit report?
  • We can get draft audit report.
  • Scooter sent email to get a reply about requested changes.

• Phenix R24 progress
  • Technical meeting was this morning, Eric, Zach, TomG attended
  • Added ChimeraX Phenix douse command (not yet in daily build), not using REST
  • Phenix nightly build is supposed to have Phenix REST server support tomorro

Action Items

• Send xmas card to Conrad - TomG
• Assign minsky.cgl.ucsf.edu hostname for AI machine - Greg, TomG
• Setup meeting with NIH R01 program officer to discuss resubmission, Tom Ferrin
• Get certificate for https at rbvi.org. Greg
• Renew certificate for https on vr.ucsf.edu. Greg
• Set up 2-factor authentication for hal2 vpn - (waiting to see if VPN will even be allowed by campus IT) - Scooter
• Document new vpn setup on Linux - Scooter