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index.html

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<!doctype html>
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<html>
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<head>
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<meta charset="utf-8">
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<meta http-equiv="X-UA-Compatible" content="chrome=1">
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<title>Scientific Programming in Python by scientificprogrammingUOS</title>
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<link rel="stylesheet" href="stylesheets/styles.css">
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<link rel="stylesheet" href="stylesheets/github-light.css">
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<meta name="viewport" content="width=device-width">
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<!--[if lt IE 9]>
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<script src="//html5shiv.googlecode.com/svn/trunk/html5.js"></script>
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<![endif]-->
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</head>
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<body>
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<div class="wrapper">
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<header>
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<h1>Scientific Programming in Python</h1>
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<p>Lectures for the course &quot;Scientific Programming in Python&quot; at Osnabrück University</p>
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<p class="view"><a href="https://github.com/scientificprogrammingUOS/lectures">View the Project on GitHub <small>scientificprogrammingUOS/lectures</small></a></p>
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<ul>
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<li><a href="https://github.com/scientificprogrammingUOS/lectures/zipball/master">Download <strong>ZIP File</strong></a></li>
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<li><a href="https://github.com/scientificprogrammingUOS/lectures/tarball/master">Download <strong>TAR Ball</strong></a></li>
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<li><a href="https://github.com/scientificprogrammingUOS/lectures">View On <strong>GitHub</strong></a></li>
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</ul>
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</header>
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<section>
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<p><a href="https://mybinder.org/v2/gh/scientificprogrammingUOS/lectures/master?urlpath=lab"><img src="https://mybinder.org/badge_logo.svg" alt="Binder"></a></p>
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<h1>
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<a id="lectures-in-scientific-computing-in-python" class="anchor" href="#lectures-in-scientific-computing-in-python" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Lectures in Scientific Computing in Python</h1>
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<p>This repository contains all lectures from the course
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<em>Scientific programming in Python</em> that is part of the Cognitive Science program
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at the University Osnabrück. Each lecture is accompanied by a Jupyter notebook
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that explains each topic with a combination of code and text. You
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can view the notebooks directly on GitHub or run them locally and play
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with the code. If you do not want to install anything, click on the Binder
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logo above to run all the notebooks in a ready to use environment in the cloud.</p>
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<h2>
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<a id="recordings" class="anchor" href="#recordings" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Recordings</h2>
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<p>All lecture recordings from 2018 and 2019 can be viewed on <a href="https://www.youtube.com/channel/UC_FUSDNAoX8woYbGXaFdtvw">Youtube</a> and on the Opencast platform (which is available only to students of the University of Osnabrück).</p>
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<table>
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<thead>
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<tr>
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<th>Lecture</th>
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<th>YouTube 2018</th>
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<th>Youtube 2019</th>
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<th>Opencast 2018</th>
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<th>Opencast 2019</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td>Introduction</td>
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<td><a href="https://www.youtube.com/watch?v=UmVC3XxkXhI&amp;list=PL7Rs54JKuEjFRyyhtJy2eDOhqTtmWpXzl&amp;index=1">View</a></td>
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<td>
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<a href="https://www.youtube.com/watch?v=uLYuLW_H7c0&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1">Part 1</a>, <a href="https://www.youtube.com/watch?v=835JkTU--9E&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1">Part 2</a>
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</td>
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<td><a href="https://video4.virtuos.uos.de/engage/theodul/ui/core.html?cid=a18d5bd1b862d194bcd7b56bca95c32f&amp;id=b0079cbf-51b7-47c1-8a38-21147935d249">View</a></td>
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<td>
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<a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=1581f0ee-b9c7-44ef-a483-0897d3c3de68">Part 1</a>, <a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=a7acc8d9-a374-44e7-b538-b98fb2f5f51e">Part 2</a>
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</td>
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</tr>
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<tr>
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<td>Basic Python</td>
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<td><a href="https://www.youtube.com/watch?v=awAl94Rx0u8&amp;index=2&amp;list=PL7Rs54JKuEjFRyyhtJy2eDOhqTtmWpXzl">View</a></td>
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<td>
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<a href="https://www.youtube.com/watch?v=-I37mS8_7Dc&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1">Part 1</a>, <a href="https://www.youtube.com/watch?v=7GdEJkcoHvI&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1">Part 2</a>
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</td>
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<td><a href="https://video4.virtuos.uos.de/engage/theodul/ui/core.html?cid=a18d5bd1b862d194bcd7b56bca95c32f&amp;id=f41dc9ef-c846-4f07-a7a8-b87b92cd82f9">View</a></td>
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<td>
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<a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=342723fe-5c97-4d19-9f30-f43c5d0bc9d8">Part 1</a>, <a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=1c46a715-f965-4c63-92c1-b6d022d22c52">Part 2</a>
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</td>
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</tr>
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<tr>
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<td>Advanced Python</td>
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<td><a href="https://www.youtube.com/watch?v=s01yqt2fxwk&amp;index=3&amp;list=PL7Rs54JKuEjFRyyhtJy2eDOhqTtmWpXzl">View</a></td>
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<td>
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<a href="https://www.youtube.com/watch?v=L-C9mwFmxpc&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1&amp;index=6">Part 1</a>, <a href="https://www.youtube.com/watch?v=YDHlRnwoWQg&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1&amp;index=7">Part 2</a>
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</td>
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<td><a href="https://video4.virtuos.uos.de/engage/theodul/ui/core.html?cid=a18d5bd1b862d194bcd7b56bca95c32f&amp;id=fcb80388-4dc3-4336-bec4-a294ccc096de">View</a></td>
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<td>
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<a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=e0415562-98d4-4a21-95c9-484acb775119">Part 1</a>, <a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=a0fd26c4-85a8-48a7-8d3f-f085532b5548">Part 2</a>
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</td>
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</tr>
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<tr>
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<td>Numpy</td>
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<td><a href="https://www.youtube.com/watch?v=oxo-3fDJE6M&amp;list=PL7Rs54JKuEjFRyyhtJy2eDOhqTtmWpXzl&amp;index=4">View</a></td>
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<td>
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<a href="https://www.youtube.com/watch?v=v603JUrsIr4&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1&amp;index=8">Part 1</a>, <a href="https://www.youtube.com/watch?v=DH6FuWjxQiA&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1&amp;index=9">Part 2</a>
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</td>
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<td><a href="https://video4.virtuos.uos.de/engage/theodul/ui/core.html?cid=a18d5bd1b862d194bcd7b56bca95c32f&amp;id=f695daea-8ee4-473b-8684-c46cbef62586">View</a></td>
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<td>
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<a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=b1410913-3857-485b-ab6c-2acf89dfce87">Part 1</a>, <a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=3921cc73-a4ee-450f-8002-22344b9e3260">Part 2</a>
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</td>
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</tr>
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<tr>
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<td>Matplotlib</td>
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<td><a href="https://www.youtube.com/watch?v=VmWEcqdcqa4&amp;index=5&amp;list=PL7Rs54JKuEjFRyyhtJy2eDOhqTtmWpXzl">View</a></td>
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<td>
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<a href="https://www.youtube.com/watch?v=phfZTV94qp8&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1&amp;index=10">Part 1</a>, <a href="https://www.youtube.com/watch?v=oJy2SyWFc20&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1&amp;index=11">Part 2</a>
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</td>
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<td><a href="https://video4.virtuos.uos.de/engage/theodul/ui/core.html?cid=a18d5bd1b862d194bcd7b56bca95c32f&amp;id=3a01b270-efc0-4d38-8457-586ec2fc6886">View</a></td>
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<td>
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<a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=bcc3363e-9ab4-4212-bec8-b89054fe33ae">Part 1</a>, <a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=39f91b82-c484-4765-88e1-3df771c9cbbb">Part 2</a>
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</td>
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</tr>
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<tr>
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<td>Basic Pandas</td>
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<td><a href="https://www.youtube.com/watch?v=AHXj14joofo&amp;list=PL7Rs54JKuEjFRyyhtJy2eDOhqTtmWpXzl&amp;index=6">View</a></td>
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<td>
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<a href="https://www.youtube.com/watch?v=P4t3E5PgCI8&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1&amp;index=12">Part 1</a>, <a href="https://www.youtube.com/watch?v=u92m5yRUHJc&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1&amp;index=13">Part 2</a>
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</td>
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<td><a href="https://video4.virtuos.uos.de/engage/theodul/ui/core.html?cid=a18d5bd1b862d194bcd7b56bca95c32f&amp;id=0b158123-ecdb-4081-a13a-4a13c57cfeac">View</a></td>
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<td>
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<a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=fefe0cf1-4aed-4bbe-88e0-5902b54c3c41">Part 1</a>, <a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=e0015e0f-504d-4ed6-945e-4404a2494d60">Part 2</a>
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</td>
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</tr>
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<tr>
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<td>Pandas: Cleaning Data</td>
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<td><a href="https://www.youtube.com/watch?v=Yw2uqr__5-M&amp;list=PL7Rs54JKuEjFRyyhtJy2eDOhqTtmWpXzl&amp;index=7">View</a></td>
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<td>
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<a href="https://www.youtube.com/watch?v=A_xLroDojDc&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1&amp;index=14">Part 1</a>, <a href="https://www.youtube.com/watch?v=rH0oehOhixY&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1&amp;index=15">Part 2</a>
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</td>
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<td><a href="https://video4.virtuos.uos.de/engage/theodul/ui/core.html?cid=a18d5bd1b862d194bcd7b56bca95c32f&amp;id=e077a983-89b3-40f7-818c-4cd34906f41f">View</a></td>
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<td>
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<a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=df86ac4b-332f-4554-8d54-116696ba668b">Part 1</a>, <a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=b2c16421-5c00-438a-8e4a-50493062950c">Part 2</a>
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</td>
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</tr>
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<tr>
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<td>Pandas: Analyzing Data &amp; Time Series</td>
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<td><a href="https://www.youtube.com/watch?v=QAiFhPNZ4hU&amp;index=8&amp;list=PL7Rs54JKuEjFRyyhtJy2eDOhqTtmWpXzl">View</a></td>
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<td>
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<a href="https://www.youtube.com/watch?v=sU3SJG_mJL0&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1&amp;index=16">Part 1</a>, <a href="https://www.youtube.com/watch?v=_OsV2hlPAIQ&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1&amp;index=17">Part 2</a>
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</td>
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<td><a href="https://video4.virtuos.uos.de/engage/theodul/ui/core.html?cid=a18d5bd1b862d194bcd7b56bca95c32f&amp;id=4f440f84-8de7-4336-8f3f-b8f5764d84f3">View</a></td>
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<td>
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<a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=d2a54683-4c1f-4b0e-976a-649e21bc9f00">Part 1</a>, <a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=5bbdc5c5-723c-4608-993d-2882c0638547">Part 2</a>
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</td>
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</tr>
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<tr>
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<td>Debugging in Pycharm</td>
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<td></td>
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<td><a href="https://www.youtube.com/watch?v=RKgCuN3jg0w&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1&amp;index=18">View</a></td>
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<td></td>
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<td><a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=6e0b9236-a71f-45fb-be6f-8128eb9c11ee">View</a></td>
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</tr>
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<tr>
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<td>Statistical Visualization (ggplot, seaborn)</td>
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<td><a href="https://www.youtube.com/watch?v=k371NeL-7tM&amp;list=PL7Rs54JKuEjFRyyhtJy2eDOhqTtmWpXzl&amp;index=9">View</a></td>
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<td>
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<a href="https://www.youtube.com/watch?v=bIVrkNMjOx8&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1&amp;index=21">Part 1</a>, <a href="https://www.youtube.com/watch?v=3wkbry7YiAI&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1&amp;index=22">Part 2</a>
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</td>
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<td><a href="https://video4.virtuos.uos.de/engage/theodul/ui/core.html?cid=a18d5bd1b862d194bcd7b56bca95c32f&amp;id=79bce1f2-48e3-407b-8a1d-caf2a74e5517">View</a></td>
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<td>
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<a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=cef6e799-ac3f-4612-ba85-505e5ca6ef9d">Part 1</a>, <a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=f3f364cf-fcfe-464c-91f4-35580bbe1d2d">Part 2</a>
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</td>
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</tr>
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<tr>
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<td>Statistical Modeling (statsmodels)</td>
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<td><a href="https://www.youtube.com/watch?v=1Ba9LmyJ1ko&amp;list=PL7Rs54JKuEjFRyyhtJy2eDOhqTtmWpXzl&amp;index=10">View</a></td>
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<td>
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<a href="https://www.youtube.com/watch?v=npM0J-e-35s&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1&amp;index=23">Part 1</a>, <a href="https://www.youtube.com/watch?v=WXR-AEjOUNI&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1&amp;index=24&amp;t=0s">Part 2</a>
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</td>
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<td><a href="https://video4.virtuos.uos.de/engage/theodul/ui/core.html?cid=a18d5bd1b862d194bcd7b56bca95c32f&amp;id=634cd5c8-0227-4c19-9400-e348b53b2bf0">View</a></td>
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<td>
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<a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=90d3b2ee-f346-4932-84c1-69de535fc901">Part 1</a>, <a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=40f29cc0-b24b-427c-bf83-548411644450">Part 2</a>
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</td>
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</tr>
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<tr>
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<td>Experiments (expyriment)</td>
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<td><a href="https://www.youtube.com/watch?v=YEt6Eww26s4&amp;index=11&amp;list=PL7Rs54JKuEjFRyyhtJy2eDOhqTtmWpXzl">View</a></td>
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<td>
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<a href="https://www.youtube.com/watch?v=9lR2Uk0nRD0&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1&amp;index=19">Part 1</a>, <a href="https://www.youtube.com/watch?v=RTwzombMuls&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1&amp;index=20">Part 2</a>
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</td>
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<td><a href="https://video4.virtuos.uos.de/engage/theodul/ui/core.html?cid=a18d5bd1b862d194bcd7b56bca95c32f&amp;id=a34a0164-19da-406b-b1e1-3570ebcdc8d4">View</a></td>
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<td>
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<a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=f4510a77-f4d7-4065-9426-360a7f848d6e">Part 1</a>, <a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=8114a025-fbcf-49f9-8ba8-cfc47755a1db">Part 2</a>
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</td>
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</tr>
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<tr>
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<td>Study: A to Z, Scikit-Learn, Parallelism</td>
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<td><a href="https://www.youtube.com/watch?v=BV35GhsqmuE&amp;list=PL7Rs54JKuEjFRyyhtJy2eDOhqTtmWpXzl&amp;index=12">View</a></td>
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<td></td>
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<td><a href="https://video4.virtuos.uos.de/engage/theodul/ui/core.html?cid=a18d5bd1b862d194bcd7b56bca95c32f&amp;id=6d4e5f5e-727f-4834-80db-4322a86b0a96">View</a></td>
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<td></td>
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</tr>
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<tr>
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<td>Interactive Visualization (Widgets, Altair)</td>
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<td></td>
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<td><a href="https://www.youtube.com/watch?v=o1ApUz6dEi8&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1&amp;index=25">View</a></td>
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<td></td>
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<td><a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=2a67645e-8aab-4444-8e9a-8455dfff107c">View</a></td>
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</tr>
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<tr>
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<td>Data Exploration, Performance-Optimization</td>
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<td></td>
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<td><a href="https://www.youtube.com/watch?v=b_hL6ITo0aM&amp;list=PL7Rs54JKuEjE5PV8m3ksRuq_-DxLP8Kq1&amp;index=26">View</a></td>
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<td></td>
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<td><a href="https://video4.virtuos.uni-osnabrueck.de/paella/ui/watch.html?cid=48c679d3c81e6414ab61bba835ecae97&amp;id=ccb55af9-2081-445f-a76e-7b36fa4313e0">View</a></td>
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</tr>
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</tbody>
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<p>To view the Jupyter Notebooks corresponding to the videos of the respective years, access this repository's state from <a href="https://github.com/scientificprogrammingUOS/lectures/tree/v2018">2018</a> or <a href="https://github.com/scientificprogrammingUOS/lectures/tree/v2019">2019</a>, respectively. To access the videos in the better Opencast-player, make sure you're logged into Myuos before clicking the link.</p>
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<h2>
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<a id="installation" class="anchor" href="#installation" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Installation</h2>
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<p>Create a virtual Python environment, name e.g. <em>scientific</em>, for example using <code>conda</code>.</p>
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<pre><code>$ conda env create -f environment.yml
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</code></pre>
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<p>Activate the environment</p>
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<pre><code>$ conda activate scientific
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</code></pre>
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<p>you might see some error like <code>your shell has not been set up to use conda activate</code>. Follow the instructions given in your shell to make it work.</p>
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<p>then start JupyterLab</p>
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<pre><code>$ jupyter lab
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</code></pre>
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<p>JupyterLab should open in your browser. From there you can navigate to the notebooks
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and interact with them.</p>
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<h2>
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<a id="contributing" class="anchor" href="#contributing" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Contributing</h2>
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<p>Before committing changes, run the whole notebook from top to bottom using (for <code>fish</code>)</p>
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<pre><code>$ env RUNALL=1 jupyter nbconvert --execute --allow-errors --inplace lecture.ipynb
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</code></pre>
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<p>for <code>bash</code></p>
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<pre><code>$ export RUNALL=1 jupyter nbconvert --execute --allow-errors --inplace lecture.ipynb
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</code></pre>
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<p>To make new interactive exercises install <a href="https://github.com/rmotr/jupyterlab-solutions">jupyter-solutions</a> and set up as teacher, by setting</p>
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<pre><code>c.JupyterLabRmotrSolutions.role = "teacher"
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</code></pre>
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<p>in the repositories <code>jupyter_notebook_config.py</code>.</p>
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<p>Only use markdown headers to structure the lectures. Numbering will be automatically handled by the <a href="https://github.com/jupyterlab/jupyterlab-toc">jupyterlab-toc extension</a>.
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Also use markdown to talk about the content of the lecture and the next cells. Use comments only if you want to highlight something in a specific line of code.
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If you write comments, write them in full sentences.</p>
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<p>Use <a href="https://github.com/jupyter/nbdime"><code>nbdime</code></a> to make working with notebooks and git easier</p>
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<pre><code>pip install nbdime
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nbdime config-git --enable
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</code></pre>
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<h2>
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<a id="acknowledgments" class="anchor" href="#acknowledgments" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Acknowledgments</h2>
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<ul>
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<li>Some parts of this lecture base on Jake VanderPlas' <a href="https://jakevdp.github.io/PythonDataScienceHandbook/">Python Data Science Handbook</a>, which is a very good source for Scientific Python.</li>
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<li>Thanks to <a href="https://github.com/aauss">Auss Abbood</a> for making 2018's videos YouTube ready!</li>
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</ul>
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</section>
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<footer>
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<p>This project is maintained by <a href="https://github.com/scientificprogrammingUOS">scientificprogrammingUOS</a></p>
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<p><small>Hosted on GitHub Pages &mdash; Theme by <a href="https://github.com/orderedlist">orderedlist</a></small></p>
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