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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<meta http-equiv="Cache-Control" content="no-store" />
<title>MSCBIO 2025: Schedule</title>
<link href="default.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div class="main">
<h1>Schedule</h1>
<h3>Subject to change</h3>
<table width=100% style="border-collapse: collapse;">
<thead>
<th>Date</th><th>Instructor</th><th>Topic</th><th>Links</th>
</thead>
<tbody>
<tr style='background-color: #ede1f7'>
<td>08/29</td><td>DK</td><td>Introduction/Linux Commandline Basics</td>
<td style='display: inline-block; width: 200px;'> <a href="notes/intro2023.pdf" target="_blank">intro</a> <a href="notes/bash.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/bash.ipynb" target="_blank">notebook</a> <a href="notes/bash_cheatsheet.pdf" target="_blank">reference</a> </td>
<tr class='endweek' style='background-color: #dec6f5'>
<td>08/31</td><td>DK</td><td>Linux Commandline File Processing</td>
<td style='display: inline-block; width: 200px;'><a href="notes/bash2.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/bash2.ipynb" target="_blank">notebook</a> </td>
<tr class='A'><td>09/05</td><td></td><td colspan=1>Assignment 1 Due 11:59pm</td><td></td></tr>
<tr style='background-color: #ace3af'>
<td>09/05</td><td>JB</td><td>Getting Started with Python</td>
<td style='display: inline-block; width: 200px;'><a href="notes/pythonintro.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/pythonintro.ipynb" target="_blank">notebook</a> </td>
<tr class='endweek' style='background-color: #76db7a'>
<td>09/07</td><td>JB</td><td>Control Flow and Basic Data Visualization with <a href='http://matplotlib.org/'>matplotlib</a></td>
<td style='display: inline-block; width: 200px;'><a href="notes/pyandplot.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/pyandplot.ipynb" target="_blank">notebook</a> </td>
<tr class='A'><td>09/12</td><td></td><td colspan=1>Assignment 2 Due 11:59pm</td><td></td></tr>
<tr style='background-color: #ace3af'>
<td>09/12</td><td>JB</td><td><a href='http://www.numpy.org/'>numpy</a> Arrays</td>
<td style='display: inline-block; width: 200px;'><a href="notes/numpy.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/numpy.ipynb" target="_blank">notebook</a> </td>
<tr class='endweek' style='background-color: #f2c9ed'>
<td>09/14</td><td>JF</td><td>Systems Biology with <a href='http://pysb.org/'>PySB</a></td>
<td style='display: inline-block; width: 200px;'><a href="notes/pysb.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/pysb.ipynb" target="_blank">notebook</a> </td>
<tr class='A'><td>09/19</td><td></td><td colspan=1>Assignment 3 Due 11:59pm</td><td></td></tr>
<tr style='background-color: #ace3af'>
<td>09/19</td><td>JB</td><td>Dictionaries and Sets and Function Fitting</td>
<td style='display: inline-block; width: 200px;'><a href="notes/numpy2dict.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/numpy2dict.ipynb" target="_blank">notebook</a> </td>
<tr class='endweek' style='background-color: #76db7a'>
<td>09/21</td><td>JB</td><td>Sequence Analysis with <a href='http://biopython.org/wiki/Biopython'>Biopython</a></td>
<td style='display: inline-block; width: 200px;'><a href="notes/biopython.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/biopython.ipynb" target="_blank">notebook</a> </td>
<tr class='A'><td>09/26</td><td></td><td colspan=1>Assignment 4 Due 11:59pm</td><td></td></tr>
<tr style='background-color: #ace3af'>
<td>09/26</td><td>JB</td><td>More Sequence Analysis</td>
<td style='display: inline-block; width: 200px;'><a href="notes/seqcont.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/seqcont.ipynb" target="_blank">notebook</a> </td>
<tr class='endweek' style='background-color: #76db7a'>
<td>09/28</td><td>JB</td><td>EMR with <a href='http://pandas.pydata.org/'>pandas</a></td>
<td style='display: inline-block; width: 200px;'><a href="notes/emr.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/emr.ipynb" target="_blank">notebook</a> </td>
<tr class='A'><td>10/03</td><td></td><td colspan=1>Assignment 5 Due 11:59pm</td><td></td></tr>
<tr style='background-color: #c6eaf7'>
<td>10/03</td><td>MG</td><td>Structure Analysis with <a href='http://prody.csb.pitt.edu/'>ProDy</a></td>
<td style='display: inline-block; width: 200px;'><a href="notes/prody1.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/prody1.ipynb" target="_blank">notebook</a> </td>
<tr class='endweek' style='background-color: #b0e4f7'>
<td>10/05</td><td>MG</td><td>Protein Analysis Continued</td>
<td style='display: inline-block; width: 200px;'><a href="notes/prody2.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/prody2.ipynb" target="_blank">notebook</a> </td>
<tr class='A'><td>10/10</td><td></td><td colspan=1>Assignment 6 Due 11:59pm</td><td></td></tr>
<tr style='background-color: #c6eaf7'>
<td>10/10</td><td>MG</td><td>Molecular Dynamics (<a href='http://www.mdanalysis.org/'>mdanalysis</a>)</td>
<td style='display: inline-block; width: 200px;'><a href="notes/mdanalysis.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/mdanalysis.ipynb" target="_blank">notebook</a> </td>
<tr class='endweek' style='background-color: #b0e4f7'>
<td>10/12</td><td>MG</td><td>More Molecular Dynamics</td>
<td style='display: inline-block; width: 200px;'><a href="notes/md2.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/md2.ipynb" target="_blank">notebook</a> </td>
<tr class='A'><td>10/17</td><td></td><td colspan=1>Assignment 7 Due 11:59pm</td><td></td></tr>
<tr style='background-color: #c6eaf7'>
<td>10/17</td><td>MG</td><td>Clustering</td>
<td style='display: inline-block; width: 200px;'><a href="notes/clustering.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/clustering.ipynb" target="_blank">notebook</a> </td>
<tr class='endweek' style='background-color: #dec6f5'>
<td>10/19</td><td>DK</td><td>Regular Expressions</td>
<td style='display: inline-block; width: 200px;'><a href="notes/regex.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/regex.ipynb" target="_blank">notebook</a> </td>
<tr class='A'><td>10/24</td><td></td><td colspan=1>Assignment 8 Due 11:59pm</td><td></td></tr>
<tr style='background-color: #ede1f7'>
<td>10/24</td><td>DK</td><td>Web Services and Communication Protocols</td>
<td style='display: inline-block; width: 200px;'><a href="notes/web.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/web.ipynb" target="_blank">notebook</a> </td>
<tr class='endweek' style='background-color: #dec6f5'>
<td>10/26</td><td>DK</td><td>From Data to Model to the World Web Web</td>
<td style='display: inline-block; width: 200px;'><a href="notes/webprogramming.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/webprogramming.ipynb" target="_blank">notebook</a> </td>
<tr class='A'><td>10/31</td><td></td><td colspan=1>Assignment 9 Due 11:59pm</td><td></td></tr>
<tr style='background-color: #ede1f7'>
<td>10/31</td><td>DK</td><td>Cheminformatics (<a href='http://openbabel.org/docs/dev/UseTheLibrary/Python_Pybel.html'>Pybel</a>)</td>
<td style='display: inline-block; width: 200px;'><a href="notes/cheminformatics.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/cheminformatics.ipynb" target="_blank">notebook</a> </td>
<tr class='endweek' style='background-color: #eff584'>
<td>11/02</td><td>SU</td><td>Dimensionality Reduction</td>
<td style='display: inline-block; width: 200px;'><a href="notes/dimred.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/dimred.ipynb" target="_blank">notebook</a> </td>
<tr class='A'><td>11/07</td><td></td><td colspan=1>Assignment 10 Due 11:59pm</td><td></td></tr>
<tr style='background-color: #fbffb3'>
<td>11/07</td><td>SU</td><td>Machine Learning with <a href='http://scikit-learn.org/stable/'>sklearn</a></td>
<td style='display: inline-block; width: 200px;'><a href="notes/machinelearning.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/machinelearning.ipynb" target="_blank">notebook</a> </td>
<tr class='endweek' style='background-color: #dec6f5'>
<td>11/09</td><td>DK</td><td>Process Control with <a href='https://docs.python.org/3/library/subprocess.html'>subprocess</a></td>
<td style='display: inline-block; width: 200px;'><a href="notes/subprocess.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/subprocess.ipynb" target="_blank">notebook</a> </td>
<tr class='A'><td>11/14</td><td></td><td colspan=1>Assignment 11 Due 11:59pm</td><td></td></tr>
<tr style='background-color: #fbffb3'>
<td>11/14</td><td>SU</td><td>Bioimaging I</td>
<td style='display: inline-block; width: 200px;'><a href="notes/bioimaging.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/bioimaging.ipynb" target="_blank">notebook</a> </td>
<tr class='endweek' style='background-color: #eff584'>
<td>11/16</td><td>SU</td><td>Bioimaging II</td>
<td style='display: inline-block; width: 200px;'><a href="notes/bioimaging2.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/bioimaging2.ipynb" target="_blank">notebook</a> </td>
<tr class='B'><td>11/21</td><td></td><td colspan=1>Thanksgiving Break</td><td></td></tr>
<tr class='B endweek'><td>11/23</td><td></td><td colspan=1>Thanksgiving Break</td><td></td></tr>
<tr class='A'><td>11/28</td><td></td><td colspan=1>Assignment 12 Due 11:59pm</td><td></td></tr>
<tr style='background-color: #fbffb3'>
<td>11/28</td><td>SU</td><td>Deep Learning</td>
<td style='display: inline-block; width: 200px;'><a href="notes/deeplearning.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/deeplearning.ipynb" target="_blank">notebook</a> </td>
<tr class='endweek' style='background-color: #dec6f5'>
<td>11/30</td><td>DK</td><td>multiprocessing</td>
<td style='display: inline-block; width: 200px;'><a href="notes/multiprocessing.slides.html" target="_blank">slides</a> <a href="https://nbviewer.org/urls/mscbio2025.net/notes/multiprocessing.ipynb" target="_blank">notebook</a> </td>
<tr style='background-color: #ffe8e8'>
<td>12/05</td><td></td><td><b>Project Presentations</b></td>
<td style='display: inline-block; width: 200px;'></td>
<tr class='endweek' style='background-color: #ffe8e8'>
<td>12/07</td><td></td><td><b>Project Presentations</b></td>
<td style='display: inline-block; width: 200px;'></td>
<tr style='background-color: #ffe8e8'>
<td>12/12</td><td></td><td><b>Movie and Pizza</td>
<td style='display: inline-block; width: 200px;'></td>
</tbody>
</table>
</div>
</body>
</html>