Changes between Version 1 and Version 2 of Dev2025-1-27

Timestamp:

Jan 27, 2025, 4:16:05 PM (9 months ago)

Author:

Tom Goddard

Comment:

--

Dev2025-1-27

@@ -15 +15 @@
 = Discussion =
 
+* N453 door lock
+  - The N453 door keypad lock needs to have the code set to allow keeping door unlocked all day.
+  - Greg will call to have this done.  Greg has chart string for payment.
+
+* Plato home directory changes
+  - Greg, Tom Ferrin and Scooter discussed plato home directory changes last week.
+  - Goal is to remove from plato all wynton PHI or root management access so that plato is only at P1/P2 security level instead of P3.
+  - Plato will use shadow home directories on NAS that can symbolic link either to a NAS home directory or NFS mounted wynton home directory.
+  - Login to log1.wynton.ucsf.edu will always give Wynton home directory (on beegfs).
+  - Wynton LDAP and Kerberos authentication servers are still on plato.  UCSF IT is working on a centralized password management and have chosen a vendor that will replace current LDAP/Kerberos.
+
+* Web update failures
+  - Nightly webpush sometimes fails with emailed traceback saying a directory could not be deleted because it was not empty.
+  - Eric says this usually involves corrective action like another webpush or pcs restart to restart web service.
+  - Greg will look into why.  Says this happens more often with web site on NAS, but used to happen on BeeGFS sometimes.
+  - Problem happens more often with Chimera web site, less often with ChimeraX web site.
+  - Elaine and TomG notice updating web site files sometimes the fails to show them on web page for 30-60 seconds.
+
+* Qt 6.8.2 update
+  - Qt 6.8.2 is not out yet.  Was planned to release Jan 23.  Often they are 1-2 weeks late.
+  - We will update ChimeraX from 6.7 when 6.8.2 comes out.
+  - 6.8.1 had crash on exit on Mac, supposedly fixed in 6.8.2.
+  - Hope is that 6.8 might fix Mac multi-display crashes.
+
+* PySide 6, Python 3.13, Numpy 2 updates
+  - TomG suggests with grant renewal activities in the next 5 months we probably should try updating these major packages since there will not be time to fix all the problems.
+
+* Faster atom specifier parser
+  - Eric says almost ready to try C++ faster atom spec parser.
+  - There will be an option to enable it during a testing phase.
+  - Bugs are expected.
+
+* AlphaFold 3 clones
+  - Tom is looking at Chai-1 and Boltz-1 clones of Alphafold 3.
+  - They have more open license terms.
+  - They may support newer features than AlphaFold 3 such as specifying where ligands or antibodies should bind or using experimental structures as parts of complexes.
+
+* Scooter
+  - Scooter meeting with UCSF HR tomorrow to discuss his leave.
+  - HR said a week ago they didn't know anything, but will investigate and report tomorrow.
+
+* Endowed chair search committee
+  - Tom Ferrin reports that the endowed chair search committee has been formed.
+
+* Speed up sequence conservation
+  - Eric made computing sequence conservation for 50,000 sequences 100x faster.
+  - Was taking 3 minutes because every character lookup was done by C++ copying the entire sequence.
+  - This is for use with new Profile Grid sequence viewer.
+
+* Piet scene progress
+  - Piet will report on scene API progress Feb 13 at group meeting, also Elaine presenting that day.
+
+* ScholAR
+  - Piet has not heard back from Tyler from USC about ScholAR improvements so Piet is currently not working on that.
+
+* ViewDockX
+  - Piet is looking for next project, Eric suggests porting ViewDockX from html/javascript to Qt.
+  - Tom says Brian Schoichet and John Irwin labs still using Chimera ViewDock due to poor function of ViewDockX.
+  - Eric and Elaine will write-up what improvements are needed in the ported ViewDockX and give that to Piet to consider.
 
 --------------------------
 = Action Items =
+
+* Greg will get N453 keypad able to unlock all day by contacting building maintenance.