vcell
vcell copied to clipboard
virtualcell
Microscopy Protocols in alpha fails for membrane species
Gaussian convolution protocol in alpha currently fails for membrane species, with error "solver stopped unexpectedly".
- Test BioModel was created: "Test Gaussian Projection" user ACowan shared with schaff and VCellSupport. 4 Applications - spherical membrane or linear membrane in x, y or z planes.
- The protocol has not worked for a long time in release (and still not not work).
- Late in 2023 the convolution was improperly calculated in alpha but gave a result - looked more like a volume species than a membrane species.
- Subsequently in late 2023 it was fixed and correctly calculated. Sims in Test Gaussian Projection with membrane in a single plain all look correct (results are still available)
- Two days ago was used in another Biomodel, results took a very long time to come back, and convolution function was incorrect (Spherical membrane convolves to a "blob" with value highest in center). See Biomodel "Bacillus Spore Membrane New FRAP Analysis" user ACowan Application Application "half bleach plus convolved" Sim: "8-23 fit bleach Halfbleach_01_1_2".
- Above simulation copied and rerun today (1-23-2-24) now fails "Simulation 'Copy of 8-23 fit bleach Halfbleach_01_1_2' failed solver stopped unexpectedly, Fail found by monitor, slrmJobID=7642707 jobName=V_ALPHA_266871221_0_16 jobState=FAILED.
- Copies and reran sim in Test Gaussian Project Biomodel, new sim now fails with same error message as above.
Tested 2.6.2024 and simulations now are complete. Results seem correct for membrane species in spherical membrane (see sim results for BioModel Test Gaussian Projection Application Spherical Membrane.
