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		<title>Open Source in Science: Challenges and Opportunities</title>

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				<section>
					<h1>Open Source in Science</h1>
					<h2>Challenges and Opportunities</h2>
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					<h1>Personal background</h1>
					<ul>
						<li>studied mathematics, genetics, psychology,</li>
						<li>got involved in the <a href="https://git-scm.com/">Git</a> project,</li>
						<li>started and maintained the <a href="https://fiji.sc/">Fiji</a> project, an extensible scientific image processing framework,</li>
						<li>now maintaining <a href="https://gitforwindows.org/">Git for Windows</a></li>
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					<h1>A Day in the Life of a maintainer</h1>
					<ul>
						<li>Read emails. Lots of 'em. Field usage questions.</li>
						<li>Take care of contributions, vulnerabilities, sometimes new features</li>
						<li>Mentor engineers</li>
						<li>etc</li>
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					<h1>Open Source and Science, a natural match</h1>
					It's all about sharing knowledge
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					<h1>Opportunity: impact</h1>
					<ul>
						<li>Exhibit A: Fiji, cited <a href="https://scholar.google.com/scholar?q=fiji+schindelin">31k+ times and counting</a><br /><a class="doi" href="https://doi.org/10.1038/nmeth.2019">https://doi.org/10.1038/nmeth.2019</a></li>
						<li>Exhibit B: <a href="https://matplotlib.org/">Matplotlib</a>, cited <a href="https://scholar.google.com/scholar?q=matplotlib">almost 16k times</a><br /><a class="doi" href="https://doi.org/10.1109/MCSE.2007.55">https://doi.org/10.1109/MCSE.2007.55</a></li>
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					<h1>Primary challenge: funding</h1>
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						Everybody loves free stuff, nobody likes to pay for it.
						<div class="fragment">... unless they can slap their name on it?</div>
						<div class="fragment">e.g. <a href="https://chanzuckerberg.com/blog/importance-open-source-science-software/">Chan Zuckerberg Initiative</a></div>
						<div class="fragment">e.g. Fiji vs DFG, Fiji vs MotionTracker, Fiji vs Icy</div>
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					<h1>Challenge: publishing</h1>
					Originally: nobody would accept software papers. Now: <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008390">high standards</a> (industry-grade code quality expected from non-CS researchers)
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					<h1>Challenge: best practices</h1>
					<ul>
						<li>Code Comments</li>
						<li>Object-Oriented Design, Functional Programming</li>
						<li>Regression Testing (mock objects)</li>
						<li>Continuous Integration</li>
						<li>etc</li>
					</ul>
				</section>
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					<h1>Challenge: maintenance</h1>
					<ul>
						<li>Tending to the bug tracker,</li>
						<li>answering questions about usage,</li>
						<li>helping contributors getting started,</li>
						<li>etc</li>
					</ul>
					<p>
						<a href="https://www.nature.com/articles/d41586-019-02046-0">How to support open-source software and stay sane</a> <a class="doi" href="https://doi.org/10.1038/d41586-019-02046-0">https://doi.org/10.1038/d41586-019-02046-0</a>
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					<h1>Challenge: community building</h1>
					<a href="https://cmustrudel.github.io/papers/raman20toxicity.pdf">Stress and Burnout in Open Source</a><br /><a class="doi" href="https://doi.org/10.1145/3377816.3381732">https://doi.org/10.1145/3377816.3381732</a>
				</section>
				<section>
					<h1>Opportunity: stand on giants' shoulders</h1>
					<li><a href="https://www.researchgate.net/topic/Open-Source-Scientific-Software/publications">https://www.researchgate.net/topic/Open-Source-Scientific-Software/publications</a></li>
					<li><a href="https://github.com/topics/science">https://github.com/topics/science</a></li>
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					<h1>Questions?</h1>
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