Set path for SBML files

See template for how to set the folder for SBML files now. They no longer need to be in the config folder.
Full Changelog: v1.0.9...v1.0.10

Set path to csv dose schedule for PK

Now can set the path to the PK dosing schedule in the schedule element as follows:

<schedule format="csv">
  <folder>./config</folder>
  <filename>S_dose_schedule.csv</filename>
</schedule>

Replace ./config and S_dose_schedule.csv with your path info.
Full Changelog: v1.0.8...v1.0.9

Constant PKs

Now can set constant PKs. Using a CSV file as before for 1C and 2C models, specify the times at which the circulation concentration changes, i.e. the times at which the Dirichlet conditions change. The first column of the csv is the times the concentration changes. The second column is the value it changes to. The concentration will stay fixed at that value until the next time it is set.

Full Changelog: v1.0.7...v1.0.8

Minor bug fixes

• Fix bug in displaying studio commands for Windows
• Fix bug in deleting temporary makefile

Full Changelog: v1.0.6...v1.0.7

More protections in editing PhysiCell files

Full Changelog: v1.0.5...v1.0.6

First search for the lines to be added before committing to adding them.

Error handling in get_ and add_

• return meaningful messages if add_physipkpd.py is supplied with a missing directory
• puts addons in if missing
• handles if main.cpp is not found when add_physipkpd.py-ing with error message
• better print statements for how to run studio afterwards

Improve get_ and add_ scripts

Better functioning of get_physipkpd.py and add_physipkpd.py scripts. They're also now easier to read and cleaner.

Use the following to start a new PhysiPKPD project or add PhysiPKPD to an existing project:

python get_physipkpd.py --dir path/to/project/dir --studio

python add_physipkpd.py path/to/project/dir --studio

Add PhysiPKPD to an existing PhysiCell project

Using add_physipkpd.py, you can quickly add PhysiPKPD to an existing PhysiCell project. If you have a project in path-to-project, then run this script as

python add_physipkpd.py path-to-project --studio

The output will guide you to editing it directly or with studio. Make sure you use the correct config file though!

Script setup

A python script to set up your own PhysiPKPD project. Download the script to a directory you want to hold your PhysiPKPD project and run it from there with python get_physipkpd.py. It will not touch any of your current files or folders, but will download new PhysiCell and PhysiPKPD copies and combine into a single folder. Follow instructions in output to go about making a project.

PhysiPKPD: rules and studio integration

PhysiPKPD now integrates with PhysiCell's rules grammar and has PhysiCell-Studio support.

To get started with your own project do the following:

• Download the attached python script
• Rename to get_physipkpd.py
• Run python get_physipkpd.py (will set up a folder called PhysiPKPD_Project that is ready to use with PhysiPKPD from its development-rules-integration-studio-version branch that integrates with this release)
• Run make pkpd-template to load up the template project
• Run python [path-to-this-studio] -c ./config/pkpd_model.xml -e pkpd_model --pkpd

get_physipkpd.txt