Re-Addition Modeler

A python based GUI to model kinetic data that contains re-additions.

Install

• make sure COPASI is installed (https://copasi.org/Download/)

• Create and activate a dedicated environment

• pip install re_add_modeler

• download and unzip 'python implementation of COPASI': https://drive.google.com/file/d/1cVNLU4SBsz0JhC48MO69wVSLH-RpyIt6/view?usp=sharing

• OR clone github repo of 'python implementation of COPASI' https://gitlab.com/heingroup/py_copasi

• create a text file named copasi_path.txt in the folder you want to run the GUI from

• add the path to the previously downloaded 'python implementation of COPASI' to copasi_path.txt

• create a folder named output in the folder you want to run the GUI from

• open cmd in the folder you want to run the GUI from

• python

• import re_add_modeler

This should open the GUI. All relevant information will be stored in the previously created output folder sorted by date and time.

How to use

• drag and drop csv files to be modeled into the csv field

• for re-additions either manually or from json click the additions button for the correct csv file

• type out mechanisms the names of the species must match the names in the csv file

• all non-zero starting concentrations need to be defined in the csv file (for unknow concentrations such as catalyst only give it the initial value and leave all other entries blank)

• to exclude a k-value from optimization (remove backwards reaction for irreversible processes) add a "$" in front of the known value

• add complete mechanisms with the "+" button on the top right

• switch to modeling tab on the top

• confirm the text box on the left does not indicate an error (it is red)

• set the species COPASI uses for fitting on the bottom right. Species names must match the names in the csv file separated by a comma (",")

• set number of generations and population size for COPASI to use on the bottom left

• click "Run Evaluation"

• wait for optimization to finish

• swap to results tab on the top

• click through data and mechanisms

Known issues

• only accepts csv files and not excel for now
• deleting files you want to model on requires a restart of the GUI