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<!doctype html>
<html>
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="chrome=1">
<title>Jmichel80.GitHub.io by jmichel80</title>
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<header>
<h1>Jmichel80.GitHub.io</h1>
<p>My GitHub Pages home page</p>
<p class="view"><a href="https://github.com/jmichel80">View the Project on GitHub <small>jmichel80</small></a></p>
<ul>
<li class="single"><a href="https://github.com/jmichel80/jmichel80.github.io">View On <strong>GitHub</strong></a></li>
</ul>
</header>
<section>
<h3>
<a id="welcome-to-github-pages" class="anchor" href="#welcome-to-github-pages" aria-hidden="true"><span class="octicon octicon-link"></span></a>Welcome to the CECAM extented software development workshop website:
Developing interoperable and portable molecular simulation software libraries</h3>
<h3>
<a id="summary" class="anchor" href="#summary" aria-hidden="true"><span class="octicon octicon-link"></span></a>Summary</h3>
<p>This workshop will be held on October 19-20th 2015 at CECAM-DE-JUELICH. </p>
<p></p>This workshop will bring together developers to share their experience of developing molecular
simulation software toolkits. Emphasis will be placed on discussing best-practices for code sharing,
code re-use and code extensibility, as well as strategies to facilitate software maintenance.
In addition two mini ‘hands-on’ workshops will be organised to teach delegates how to develop
code with the molecular simulation library OpenMM (https://simtk.org/home/openmm), and the free
energy calculations library Plumed (http://www.plumed-code.org/). Delegates will also have the opportunity
to suggest coding problems they would like to work on with OpenMM and/or Plumed during the workshop.
</p>
<h3>
<a id="target-audience" class="anchor" href="#target-audience" aria-hidden="true"><span class="octicon octicon-link"></span></a>Target audience</h3>
* Software developers with expertise in molecular simulation software development</br>
* Computational scientists with an interest in learning how to use OpenMM and/or Plumed to write new code.</br>
</br>
<h3>
<a id="invited-speakers" class="anchor" href="#invited-speakers" aria-hidden="true"><span class="octicon octicon-link"></span></a>The following invited speakers have confirmed attendance</h3>
<pre><code>
John Chodera (Memorial Sloan Kettering Cancer Center)
Peter Eastman (Stanford University)
Gareth Tribello (Queen’s University Belfast)
Christopher Woods (University of Bristol)
</code>
</pre>
<h3>
<a id="schedule" class="anchor" href="#schedule" aria-hidden="true"><span class="octicon octicon-link"></span></a>Schedule</h3>
<p><strong>Draft Programme</strong></p>
<p><em>Monday 19 October 2015</em></p>
<ul>
<li>0900 – 0930 Welcome and Introduction to the workshop</li>
<li>0930 – 1000 Christopher Woods. <a href=http://chryswoods.com/talks/ target="_blank">How Who is the What, When and Why of Programming</a></li>
<li>1000 – 1030 Gareth Tribello. "Learning from mistakes: Reflections on writing software for molecular simulation"</li>
<li>1030 – 1100 Coffee break</li>
<li>1100 – 1130 Peter Eastman. "Architecting Scientific Software"</li>
<li>1130 – 1200 John Chodera, <a href=https://github.com/choderalab/cecam-2015-julich-workshop/blob/master/slides/2015-10-19%20CECACM%20Simulation%20Software%20Interoperability%20-%20Monday%20talk.pdf target="_blank">Redesigning drug design (with open source software)</a></li>
<li>1200 – 1230 Group discussion on best practices for the field</li>
<li>1230 – 1330 Lunch</li>
<li>1330 – 1500 Plumed workshop </li>
<li>1500 – 1530 Coffee break </li>
<li>1530 – 1700 Plumed workshop (continued)</li>
<li>1700 – 1715 Wrap up </li>
</ul>
<p><em>Tuesday 20 October 2015</em></p>
<ul>
<li>0900 – 1030 OpenMM workshop </li>
<li>1030 – 1100 Coffee break </li>
<li>1100 – 1230 OpenMM workshop (continued)</li>
<li>1230 – 1330 Lunch</li>
<li>1330 – 1500 Free form workshop </li>
<li>1500 – 1530 Coffee break </li>
<li>1530 – 1700 Free form workshop (continued)</li>
<li>1700 – 1715 Wrap up </li>
</ul>
<h3>
<a id="schedule" class="anchor" href="#schedule" aria-hidden="true"><span class="octicon octicon-link"></span></a>Workshop preparation</h3>
<p>Delegates should have downloaded and installed on their laptop OpenMM and Plumed to follow the practical workshops.</p>
<p>For the OpenMM workshop</p>
<ul>
<li>please download a copy from <a href=http://openmm.org/ target="_blank">http://openmm.org/openmm.org</a></li>
<li>Follow installation instructions at <a href=http://docs.openmm.org/6.3.0/userguide/application.html#installing-openmm target="_blank">http://docs.openmm.org/6.3.0/userguide/application.html#installing-openmm</a></li>
</ul>
<p>For the Plumed workshop</p>
<ul>
<li>Please download the latest release version of the code from <a href=http://www.plumed-code.org/git target="_blank">http://www.plumed-code.org/git</a> </li>
<li>Follow installation instructions from the user manual at <a href=http://plumed.github.io/doc-master/user-doc/html/index.html target="_blank">http://plumed.github.io/doc-master/user-doc/html/index.html</a></li>
<li>The link for the developer manual is <a href=http://plumed.github.io/doc-master/developer-doc/html/index.html target="_blank">http://plumed.github.io/doc-master/developer-doc/html/index.html</a></li>
</ul>
<h3>
<a id="forum" class="anchor" href="#forum" aria-hidden="true"><span class="octicon octicon-link"></span></a>Forum</h3>
Please use the issues tracker (Workshop forum link) to post queries/issues/questions to the workshop organisers.</br>
NOTE: You need to have a github account to be able to post on the forum. Go to <a href=https://github.com/>https://github.com/</a>
if you need to create one.
<br/>
<br/>
<p>
</p>
<a href=https://github.com/jmichel80/jmichel80.github.io/issues target="_blank">Workshop forum</a>
<br/>
<br/>
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