ChimeraX Developer Meeting

Attendance: Zach, Greg, Tom, Eric

April 22, 2024

Agenda

• Work in progress reports
• ChimeraX 1.8 release candidates.
• Log slow to update when it gets long, Tristan ticket #9909
• Create Grafana dashboards to monitor web services.
• Make Chimera end-of-life bug report and registration changes for 1.18 release in Spring 2024.
• Back up the Chimera build machine to a solid state drive, Windows 7.
• ChimeraX Ideas milestone clean-up.

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Discussion

• Toolshed improvements
  • Greg is adding check that tool category is given when user submits a new bundle. Also will check for other mandatory items.
  • Will prepopulate Toolshed tool description with text from bundle info.
  • Greg working on making Toolshed cache initialization not download metadata on every version of every bundle every submitted. Only use 3 most recent revisions, and only metadata used by ChimeraX.

• ChimeraX 1.8 release candidate date
  • Tentatively aim for May 6 release candidate.
  • Will discuss again at next week's ChimeraX meeting.
  • R01 annual report due May 15, and want to be able to say ChimeraX 1.8 prerelease is out and when release is anticipated.

• Plato backup computer
  • plato-backup has RAID hardware that is deprecated by Rocky 8 and eliminated in Rocky 9.
  • No home directory backups to tape made last 10 days.
  • plato-back connects to tape drives.
  • Scooter is working on getting quote for new hardware.
  • Scooter also is currently working on backups of all wynton home directories, including plato ones.
  • Scooter proposed today at Wynton meeting restricting backups to directories containing less than 10,000 files.

• Profile grids sequence visualization
  • Eric working on profile grid sequence viewer.
  • Wants to get minimum usable features working, that includes cross-talk with selections between structure and sequence and sequence headers.

• UMAP structure plots
  • Tom cleaning up new code that makes 2d plot clustering hundreds or thousands of structures by conformational differences.
  • New command is diffplot.
  • Probably will not be included in 1.8, but will go in daily builds for Klim Verba's lab to try.

• Zach's current projects
  • Adding BLAST command options to simplify use of umap structure plots.
  • Fixing segmentation tool bugs for 1.8 release.
  • Working on raytracing OpenGL code. Trying to improve speed. Comparing to 3D Slicer that has fast implementation.
  • Medical imaging move to Toolshed bundle, made branch where Med Image toolbar has button to install from Toolshed. Need to add capability to populate toolbar tabs. Probably for ChimeraX 1.9

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Action Items