Changes between Version 122 and Version 123 of NTTData

Timestamp:

Jun 9, 2022, 1:39:08 PM (3 years ago)

Author:

Elaine Meng

Comment:

--

NTTData

@@ -727 +727 @@
 
 == 6/9/2022 ==
+
+Phil, Philip, Michal Stolarczyk and David Liou from 3D pipeline team, Meghan (last half); Zach, Eric, Elaine, Greg, TomG, Scooter
+
+Self-introductions from both teams. 
+
+Michal is currently the primary developer working on NIH3D, working for last month on infrastructure.  ChimeraX script has been running without issues, so he hasn't been working on that part. ~10-min slide presentation.
+
+Running Ubuntu 20.4 0 within EC2 instance within VPC within AWS. Involves Prefect and GraphQL. 
+
+Recent updates: 
+- workflow deployment: standardized flow names, external Postgres database
+- workflow handling: https://niaid.github.io/nih_3D_workflows, JSON-based configuration
+
+Planned enhancements:
+- switch to ECS for running flows (to handle more at the same time)
+- increase reproducibility of results by including code versioning
+- use newer version of NIH3D presets provided by Eric
+
+Phil: Eric please explain unified script and presets
+
+Eric: originally all the types of view/displays that could be requested by the user were in a giant script with lots of commands, and we decided to refactor that as a set of presets where each preset generates one type of view. Now a smaller script calls the individual presets as needed. This set of presets is available as a bundle on the ChimeraX toolshed. Would have to re-install if ChimeraX is not persistent between runs.
+
+Michal: ChimeraX is persistent on the same machine, but different machines are used.  When we use ECS it will deploy a docker image that could have the bundle already installed.
+
+Eric: how long to deal with my pull request?  Michal: about a couple of weeks.
+
+Eric: ChimeraX now has "renumber" command, on the way towards having a GUI to do it.
+
+Some discussion of reproducibility, ChimeraX preferences and fetch caching.
+
+Phil: are ChimeraX-calculated values saved somehow? Eric: currently, the script sends them to standard-out with a standardized prefix to facilitate grepping the lines. Could be changed if needed.
+
+TomG: !AlphaFold update