1.14.2-drbergman-1.3.0

What's Changed

• improving roadrunner implementation
• allow for a single intracellular file as input (must use command-line argument -n path/to/intracellular.xml)
  • see commit details for more info
  • Added a sample project to sample_projects_intracellular/combined/template-combined. Follow these steps to run:
    1. load this project with make template-combined-intras
    2. compile it with make. Note: you may need to run this twice if you have not used libRoadRunner in this PhysiCell repository
    3. run it with ./project -n ./config/sample_combined_sbmls.xml (or project.exe if on Windows)
• Add calls to load initial cells in ode-energy-sample sample project.

See previous release notes for what this release is and how it differs from the upstream 1.14.2 version.

Full Changelog: 1.14.2-drbergman-1.2.1...1.14.2-drbergman-1.3.0

1.14.2-drbergman-1.2.1

Fix bug that caused ic cells to not be copied to output.

See previous release notes for what this release is and how it differs from the upstream 1.14.2 version.

Full Changelog: 1.14.2-drbergman-1.2.0...1.14.2-drbergman-1.2.1

1.14.2-drbergman-1.2.0

Add a command line argument for passing in the dirichlet conditions file. The flag is --ic-dc or simply -d followed by the path to the file. For example

./project -d ./config/dcs.csv

Full Changelog: 1.14.2-drbergman-1.1.0...1.14.2-drbergman-1.2.0

1.14.2-drbergman-1.1.0

Adds the ability to initialize Dirichlet Conditions from a CSV. From that commit message:

provide a CSV file with similar structure to the substrate ICs csv
header row: x,y,z,<substrate_01>,<substrate_02>,...
where the list of substrates need not be all the substrates, only those with DCs being set
each subsequent row is:
<x_coord>,<y_coord>,<z_coord>,<val_01>,<val_02>,...
where the coords must be specified and the vals can either be empty (<val_01>,,<val_03>,...) or a number
If empty, then nothing chagnes for the substrate in that column at that voxel
If a number, then the DC activation for that voxel-substrate pairing is set to the number

A sample project is included dirichlet_from_file. Here's a sample file for making the dcs:

x,y,z,substrate_1,substrate_2
-30,0,0,100,
-10,0,0,50,50
10,0,0,,100

Full Changelog: 1.14.2-drbergman-1.0.0...1.14.2-drbergman-1.1.0

1.14.2-drbergman-1.0.0

My extension of PhysiCell that can integrate with pcvct. See the 1.14.0-drbergman-1.0.0 release for more information. Here are all the differences with 1.14.2:

• ArgumentParser to allow for command line arguments (BREAKING CHANGE FROM 1.14.1). See this sample_projects/template/main.cpp for how to use the ArgumentParser to start the main function.
• initialize cells with nonzero velocity
  • if they are motile
  • without this, cells that otherwise move the entirety of the simulation are stationary on average for their persistence time when the sim starts
• PhysiECM addon to do continuum modeling of the ECM
• PhysiPKPD addon to do PKPD modeling
• allow for transmembrane diffusion as secretion model
• allow for rules to be passed in as XML

Full Changelog: 1.14.1-drbergman-1.0.0...1.14.2-drbergman-1.0.0

1.14.1-drbergman-1.0.0

My extension of PhysiCell that can integrate with pcvct. See the 1.14.0-drbergman-1.0.0 release for more information. Here are all the differences with 1.14.1:

• ArgumentParser to allow for command line arguments (BREAKING CHANGE FROM 1.14.1)
• initialize cells with nonzero velocity
  • if they are motile
  • without this, cells that otherwise move the entirety of the simulation are stationary on average for their persistence time when the sim starts
• PhysiECM addon to do continuum modeling of the ECM
• PhysiPKPD addon to do PKPD modeling
• allow for transmembrane diffusion as secretion model
• allow for rules to be passed in as XML

Full Changelog: 1.14.0-drbergman-1.0.0...1.14.1-drbergman-1.0.0

1.14.0-drbergman-1.0.0

My extension of PhysiCell that can integrate with what is for now called pcvct. The version format indicates the latest PhysiCell release this builds off of (1.14.0), my fork (drbergman), and the version of this extension off of 1.14.0 (1.0.0; i.e. a breaking release). The one breaking change is the ArgumentParser that allows for command line arguments for passing in the output folder, initial conditions, and rules. Other minor changes (minor only in that they don't break backwards compatibility):

• initialize cells with nonzero velocity
  • if they are motile
  • without this, cells that otherwise move the entirety of the simulation are stationary on average for their persistence time when the sim starts
• PhysiECM addon to do continuum modeling of the ECM
• PhysiPKPD addon to do PKPD modeling
• allow for transmembrane diffusion as secretion model
• allow for rules to be passed in as XML

This also includes some of the fixes under consideration for 1.14.1, but not yet released:

• fix bug reading large random seeds
• fix bug in export rules
• fix buffer bug in writing coords in xml
• initialize total_attack_time to 0.0
• handle abspath for output folder creation
• make output folder if it does not exist
• conserved quantities are transferred by default during phagocytosis
• preserve internalized substrates and custom data in Cell:convert_to_cell_definition function
• standard asym div
• read in attack_duration from config