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Parameter Sweeps	<link href="styles.css" rel="stylesheet"/>

Overview

This script is a generic way to setup parameter sweeps of system biology models. The specific application here is Copasi but the ultimate goal is to work with all types of application. Very broadly it takes some input data from the user in a specific format. The input specifies the parameter sweep which is a list of parameter combinations. This script mainly generates the sweep space, runs a particular task for each element of the space and stores the corresponding output in different formats. Any subset of this space can be selected for plotting or individual queries. The same setup will also be used for global and local sensitivity analysis.

How to Run

This package has been made as self-contained as possible. The required packages are listed in the file requirements.txt. In a new machine the most convenient way to setup the system is to create a python virtual environment with the virtualenv package. Use the following steps for installation

1. Clone the package using git clone.

2. Install virtualenv if not already available using the instructions from the homepage.

3. Create a new virtual environment in the directory using the following command

$ virtualenv ./pyenv

Note: The required python version is 2.7 so make sure the default system python is > 2.7.6. If not point to an alternate python 2.7 interpreter using the --python flag for the virtualenv command.

4. Switch to the new environment using

$ source ./pyenv/bin/activate
(pyenv) $

This should change the prompt as above.

5. Install the necessary packages using pip

(pyenv) $ pip install -r requirements.txt

6. Download the Copasi executable from the download page and add the path to the executable file CopasiSE in system PATH environment variable.

7. Make a test run by running the following command

(pyenv) $ python visualize.py Sweep_Information.json

If this runs without any error then the system has been setup correctly.

7. (Optionally) Deactivate the environment after completing run.

(pyenv) $ deactivate
$

Code

The code consists of the following modules

Sweep

This gets model parameter names and values to be altered in a specific format (necessary to locate the element in xml) and generates the overall sweep space. An example run is shown below for a small dictionary

test_sweep = { "a" : [1,2], "b" : [1,2] }
for elem in Generate_Sweeps(test_sweep):
    print elem

This produces the following output

$ python sweep.py
{'a': 1, 'b': 1}
{'a': 1, 'b': 2}
{'a': 2, 'b': 1}
{'a': 2, 'b': 2}

Since there are two different values for each of the keys the code produces four different combinations of the keys as a sweep space.

Change

Run

Collect