Changes between Version 1 and Version 2 of 2024-8-1

Timestamp:

Aug 2, 2024, 5:15:57 PM (15 months ago)

Author:

Tom Goddard

Comment:

--

2024-8-1

@@ -7 +7 @@
 = Agenda =
 
-* Selina work in progress, or Elaine journal club
+* Selina work in progress
 
 = Discussion Notes =
 
+* Sequence databases
+  - Scooter accidentally deleted BLAST and AlphaFold and ESMFold k-mer sequence databases.
+  - Databases are not backed up and need to be rebuilt.
+  - Cron update scripts rebuilt PDB and NR databases.
+  - Tom restored AlphaFold and ESMFold databases.
+  - Scooter writing a script to update Uniref databases which were 10 years out of date.
+
+* Selina work in progress
+  - Working on CLIP organ segmentation method.
+  - Tested on UCSF PHI data, 72 data sets, only 35 usable.
+  - Also tried unreleased newer nnUnet organ segmentation from John's Hopkins.  Works slightly better than CLIP.
+  - Analyzed different kinds of errors: under segmentation, over segmentation, mixing organs.
+  - Ground truth established by eye.  Selina says boundaries are visually clear.
+  - Selina made prototype web-site showing results.
+  - Scooter suggests next goal is write short paper showing CLIP and nnUnet analysis results.
+  - Also want to make a ChimeraX bundle to call a web service to run CLIP or nnUnet.
+
+* Ion classification
+  - Responding to manuscript reviewers of MIC paper at Nature Communications.
+  - Reviewers wanted a "no ion" class.
+  - Working on making an "open bubble" Python module to calculate molecular neighborhood fingerprinting used by MIC.
+  - Have made a ChimeraX tool to run it.
+  - Will run MIC from ChimeraX on local computer using PyTorch since CPU speed is adequate.
+
 = Action Items =