Code

Optimize#15

Code

Merged

eagmon merged 52 commits intomastervivarium-collective/tumor-tcell:masterfrom optimizevivarium-collective/tumor-tcell:optimizeCopy head branch name to clipboardOct 17, 2023

+2,519-842

Commits

Commits on Sep 4, 2023

• make dir

  eagmon

  committed
  6664e2e

• optimization by removing unit operations

  eagmon

  committed
  babcca8

• minor refactor of tumor, still using units in next_update

  eagmon

  committed
  d28133e

Commits on Sep 5, 2023

• minor optimization of diffuse

  eagmon

  committed
  1c6396f

• Editing analysis with new data structure and tumor death options for further testing analysis.

  

  John Hickey

  authored and

  John Hickey

  committed
  2868413

• v0.0.30

  

  John Hickey

  authored and

  John Hickey

  committed
  c8cd3ac

• allow non-master branch to push to pypi

  

  John Hickey

  authored and

  John Hickey

  committed
  100d32e

• v0.0.30

  

  John Hickey

  authored and

  John Hickey

  committed
  ecea7a7

• Additional edits to analysis scripts and trying out slightly larger times and numbers of cells in simulations for analysis.

  

  John Hickey

  authored and

  John Hickey

  committed
  2a0b693

• v0.0.31

  

  John Hickey

  authored and

  John Hickey

  committed
  8ff25c2

• removed need for saving data within experiment and also changing additional data processing

  

  John Hickey

  committed
  2052db2

• v0.0.32

  

  John Hickey

  committed
  d01b979

Commits on Sep 6, 2023

• additional improvements to handle exceptions for analysis

  

  John Hickey

  authored and

  John Hickey

  committed
  bb7f70c

• v0.0.33

  

  John Hickey

  authored and

  John Hickey

  committed
  c25732c

• additional handling of empty death dictionaries

  

  John Hickey

  authored and

  John Hickey

  committed
  b9e8e29

• v0.0.34

  

  John Hickey

  authored and

  John Hickey

  committed
  a16cd02

• Change back parameters to expected values to look at long term behavior

  

  John Hickey

  authored and

  John Hickey

  committed
  74755f3

• v0.0.35

  

  John Hickey

  authored and

  John Hickey

  committed
  29ac3e0

Commits on Sep 7, 2023

• set initial in_transit t-cells state to PD1n

  eagmon

  committed
  7827361

• troubleshoot T cells division in LN

  

  John Hickey

  authored and

  John Hickey

  committed
  2c6ee6b

• v0.0.36

  

  John Hickey

  authored and

  John Hickey

  committed
  4c62786

• get in_transit tcell initialized correctly

  eagmon

  committed
  c587b10

• optimize tumor process by refactoring units to the constructor

  eagmon

  committed
  3252ae8

• v0.0.37

  

  John Hickey

  committed
  3ec99ab

Commits on Sep 11, 2023

• remove division from lymph node and bring into T cell process

  

  John Hickey

  committed
  c1974ec

• v0.0.38

  

  John Hickey

  committed
  5154d97

Commits on Sep 12, 2023

• changed simulation conditions back to normal timescale for longer simulations

  

  John Hickey

  authored and

  John Hickey

  committed
  bd51d6f

• v0.0.39

  

  John Hickey

  authored and

  John Hickey

  committed
  8b8076b

Commits on Sep 13, 2023

• change DC migration assuming there are a subset of already activated DCs pretreatment in LN

  

  John Hickey

  authored and

  John Hickey

  committed
  0a9aa3a

• v0.0.40

  

  John Hickey

  authored and

  John Hickey

  committed
  f90766e

Commits on Sep 15, 2023

• Made changes to main and also analysis based on if we are not using any dendritic cells or doing a lymph node experiment.

  

  John Hickey

  authored and

  John Hickey

  committed
  5272367

• v0.0.41

  

  John Hickey

  authored and

  John Hickey

  committed
  ad5ce1b

Commits on Sep 18, 2023

• Found error with T cell division of PD1n cells and put back correct DC transit time parameter. Both found from long-term simulations.

  

  John Hickey

  committed
  2f3c038

• v0.0.42

  

  John Hickey

  committed
  ea46d6f

Commits on Sep 20, 2023

• Force T cells to enter the tumor instead of the outside from the lymph node.

  

  John Hickey

  authored and

  John Hickey

  committed
  24ed29c

• v0.0.43

  

  John Hickey

  authored and

  John Hickey

  committed
  f0e2c7b

Commits on Sep 22, 2023

• get the timestep through to dendritic process

  eagmon

  committed
  dcf2cbd

• v0.0.44

  

  John Hickey

  authored and

  John Hickey

  committed
  c92da19

Commits on Sep 29, 2023

• fixing IFNg internalization rate post changes with removing IFNg dimensions.

  

  John Hickey

  committed
  ee4439e

• v0.0.46

  

  John Hickey

  committed
  9fe4230

Commits on Oct 15, 2023

• tumor_tcell_model notebook working again

  eagmon

  committed
  de02874

• begin work on diagrams

  eagmon

  committed
  daf1f40

• minor code cleanup

  eagmon

  committed
  208a109

Commits on Oct 16, 2023

• clean up cell process files

  eagmon

  committed
  2e92f91

• clean up

  eagmon

  committed
  e572c82

Commits on Oct 17, 2023

• get no LN composite in same schema, clean up, working on diagram

  eagmon

  committed
  bc498ba

• fix tumor microenvironment test to new schema

  eagmon

  committed
  d6ff47b

• rename TumorCellProcess

  eagmon

  committed
  c2c1c45

• diagrams notebook with individual processes

  eagmon

  committed
  d6ada84

• more process figs

  eagmon

  committed
  d4cbe88

• add individual cell schemas in diagram

  eagmon

  committed
  4071e59

• tumor environment diagram

  eagmon

  committed
  5306818