README.md

<h1><strong>Mechanistic Modeling of Implantable Bioresorbable Drug Release Systems</strong></h1>
<p><img alt="Representative Image" src="images/ToC_small.jpg" /></p>
<p>This repository contains the model scripts for the paper <strong><em>Mechanistic Modeling of Implantable Bioresorbable Drug Release Systems</em></strong>: </p>
<p>Patrick A. Giolando, Kelsey Hopkins, Barrett Davis, Joseph Rispoli,
Nicole Vike, Adib Ahmadzadegan, Arezoo Arekandi, Pavlos Vlachos, Luis Solorio,
Tamara L. Kinzer-Ursem, "Mechanistic Modeling of Implantable Bioresorbable Drug Release Systems," <em>Advanced Materials</em>. 2023. [Accepted].
<ul>
<li>Purdue Research Repository Link: <a href="https://doi.org/10.4231/ASPM-SY16">link</a> </li>
<li>Advanced Materials: <a href="https://doi.org/10.1002/adma.202301698">link</a></li>
</ul>
<h3>Repository contents</h3>
<ul>
<li><code>implant_model.py</code>: main modeling script</li>
<li><code>implant_model_10um.py</code>: modeling script for 10 µm beads</li>
<li><code>diffusivity_fitter.py</code>: script to calibrate diffusivity parameters</li>
<li><code>precipitation_fitter.py</code>: script to calibrate polymer precipitation parameters</li>
</ul>
<h3>Installation</h3>
<h4>Unix/macOS</h4>
<p>To download, edit, and run the files included in this repository, users are recommended to first install or update the python package manager <code>pip</code> and virtual environment tool <code>virtualenv</code>.</p>
<pre>python3 -m ensurepip --upgrade
python3 -m pip install --user virtualenv</pre>
<p>A new, virtual environment can then be created and activated. Here, this environment will be called <code>isfi</code>. </p>
<pre>python3 -m venv isfi       
source isfi/bin/activate</pre>
<p>All necessary packages can then be installed with the requirements file <code>requirements.txt</code>.</p>
<pre>python3 -m pip install -r requirements.txt</pre>
<p>And the contents of this repository cloned (shown below) or manually downloaded from this page. Change directories into the newly-created folder to run its contents. See <a href="https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository?tool=desktop&amp;platform=mac">this page</a> for further help on cloning a repository. </p>
<pre>git clone https://github.itap.purdue.edu/TamaraKinzerursemGroup/DrugReleaseSystemModel.git
cd DrugReleaseSystemModel</pre>
<p>To confirm installation was successful, call the model file <code>implant_model.py</code>. </p>
<pre>python3 ImplantModel.py</pre>
<h4>Windows</h4>
<p>To download, edit, and run the files included in this repository, users are recommended to first install or update the python package manager <code>pip</code> and virtual environment tool <code>virtualenv</code>.</p>
<pre>py -m ensurepip --upgrade
py -m pip install --user virtualenv</pre>
<p>A new, virtual environment can then be created and activated. Here, this environment will be called <code>isfi</code>. </p>
<pre>py -m venv isfi
.\env\Scripts\activate</pre>
<p>All necessary packages can then be installed with the requirements file <code>requirements.txt</code>.</p>
<pre>py -m pip install -r requirements.txt</pre>
<p>And the contents of this repository cloned (shown below) or manually downloaded from this page. Change directories into the newly-created folder to run its contents. See <a href="https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository?tool=desktop&amp;platform=mac">this page</a> for further help on cloning a repository. </p>
<pre>git clone https://github.itap.purdue.edu/TamaraKinzerursemGroup/DrugReleaseSystemModel.git
cd DrugReleaseSystemModel</pre>
<p>To confirm installation was successful, call the model file <code>implant_model.py</code>. </p>
<pre>py ImplantModel.py</pre>
<h3>Example Output</h3>
<p>A successful call to the model file <code>implant_model.py</code> will print timepoints to the users terminal or command prompt during the simulated experimental timecourse. </p>
<pre>Day = 0     DrugLeft = 0.979
Day = 1     DrugLeft = 0.822
Day = 2     DrugLeft = 0.802
...
Day = 21    DrugLeft = 0.017
Day = 22    DrugLeft = 0.010</pre>
<p>Ultimately, this will generate a figure as below. 
<img alt="Representative Image" src="images/drug_release_implant_model.png" />
<em>Normalized drug release (navy) vs experimental data (black).</em></p>
<hr />
<p><em>Last Updated: 2023-05-09</em></p>