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MichaelRimler committed Dec 4, 2023
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Binary file modified Open-Source-Technology-in-Clinical-Data-Analysis.docx
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41 changes: 26 additions & 15 deletions index.html
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Expand Up @@ -265,13 +265,11 @@ <h2 id="toc-title">Table of contents</h2>
<ul>
<li><a href="#preface" id="toc-preface" class="nav-link active" data-scroll-target="#preface">Preface</a>
<ul class="collapse">
<li><a href="#draft" id="toc-draft" class="nav-link" data-scroll-target="#draft">DRAFT</a>
<ul class="collapse">
<li><a href="#do-not-cite" id="toc-do-not-cite" class="nav-link" data-scroll-target="#do-not-cite">Do not cite</a></li>
<li><a href="#learn-more" id="toc-learn-more" class="nav-link" data-scroll-target="#learn-more">Learn more</a></li>
<li><a href="#draft" id="toc-draft" class="nav-link" data-scroll-target="#draft">DRAFT</a></li>
<li><a href="#how-to-contribute" id="toc-how-to-contribute" class="nav-link" data-scroll-target="#how-to-contribute">How to Contribute</a></li>
<li><a href="#guidance" id="toc-guidance" class="nav-link" data-scroll-target="#guidance">Guidance</a></li>
<li><a href="#thank-you" id="toc-thank-you" class="nav-link" data-scroll-target="#thank-you">Thank you</a></li>
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Expand Down Expand Up @@ -319,25 +317,38 @@ <h1 class="unnumbered">Preface</h1>
<h2 class="anchored" data-anchor-id="draft">DRAFT</h2>
<p>The information contained in this <a href="https://quarto.org/" target="_blank">Quarto</a> book aims to comprehensively address the most important questions related to deploying open source solutions for clinical data analytics in the pharmaceutical and vaccine development industry.</p>
<ul>
<li>What questions have been asked and <u><strong><em>already</em></strong></u> answered?</li>
<li>What questions have been asked and <u><strong><em>nearly</em></strong></u> answered?</li>
<li>What questions have been asked and <u><strong><em>not yet</em></strong></u> answered?</li>
<li>What questions have been asked and [<strong><em>already answered</em></strong>]?</li>
<li>What questions have been asked and [<strong><em>nearly answered</em></strong>]?</li>
<li>What questions have been asked and [<strong><em>not yet answered</em></strong>]?</li>
</ul>
<p>We are developing this manuscript in the open and accepting contributions by the community via our GitHub repository’s <a href="https://github.com/phuse-org/OSTCDA/discussions" target="_blank">Discussions</a> tab. Please contribute your thoughts, perspectives, references, citations, and links through that mechanism. We’d like to be able to attribute your ideas to you, so providing the rationale supporting your thoughts will strengthen your argument. Please be as thoughtful and thorough in your contributions as you can! You can also upvote questions and/or responses that you find particularly valuable.</p>
<section id="do-not-cite" class="level3">
<h3 class="anchored" data-anchor-id="do-not-cite">Do not cite</h3>
<section id="do-not-cite" class="level4">
<h4 class="anchored" data-anchor-id="do-not-cite">DO NOT CITE</h4>
<p>At the moment, this document is in draft form, hence please <u><strong><em>DO NOT CITE</em></strong></u> it as a reference.</p>
</section>
<section id="learn-more" class="level3">
<h3 class="anchored" data-anchor-id="learn-more">Learn more</h3>
<section id="learn-more" class="level4">
<h4 class="anchored" data-anchor-id="learn-more">LEARN MORE</h4>
<p>To learn more about this initiative, please watch our <strong>[2023 R in Pharma]</strong>(https://rinpharma.com/){target=“_blank”} lightning talk: <a href="https://www.youtube.com/watch?v=cbFzcXMOfTM" target="_blank">The State of Open Source Technology in Clinical Data Analysis, Reporting, and Submissions</a>.</p>
</section>
<section id="thank-you" class="level3">
<h3 class="anchored" data-anchor-id="thank-you">Thank you</h3>
</section>
<section id="how-to-contribute" class="level2">
<h2 class="anchored" data-anchor-id="how-to-contribute">How to Contribute</h2>
<p>Contribute to the discussion here in GitHub Discussions:<br>
<a href="https://github.com/phuse-org/OSTCDA/discussions/1" target="_blank">What is open source?</a></p>
</section>
<section id="guidance" class="level2">
<h2 class="anchored" data-anchor-id="guidance">Guidance</h2>
<ul>
<li>Provide your thoughts and perspectives</li>
<li>Provide references to articles, webinars, presentations (citations, links)</li>
<li>Be respectful in this community</li>
</ul>
</section>
<section id="thank-you" class="level2">
<h2 class="anchored" data-anchor-id="thank-you">Thank you</h2>
<p>Thank you to <a href="https://phuse.global/" target="_blank">PHUSE</a> for supporting this endeavor. And thank you to <strong><em>YOU</em></strong> for your thoughtful contributions to the effort.</p>


</section>
</section>
</section>

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43 changes: 32 additions & 11 deletions search.json
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28 changes: 13 additions & 15 deletions summary.html
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Expand Up @@ -262,12 +262,10 @@
<h2 id="toc-title">Table of contents</h2>

<ul>
<li><a href="#what-is-open-source" id="toc-what-is-open-source" class="nav-link active" data-scroll-target="#what-is-open-source"><span class="header-section-number">2</span> What is Open Source?</a>
<ul class="collapse">
<li><a href="#how-to-contribute" id="toc-how-to-contribute" class="nav-link" data-scroll-target="#how-to-contribute"><span class="header-section-number">2.1</span> How to Contribute</a></li>
<li><a href="#guidance" id="toc-guidance" class="nav-link" data-scroll-target="#guidance"><span class="header-section-number">2.2</span> Guidance</a></li>
<li><a href="#examples" id="toc-examples" class="nav-link" data-scroll-target="#examples"><span class="header-section-number">2.3</span> Examples</a></li>
</ul></li>
<li><a href="#what-is-open-source" id="toc-what-is-open-source" class="nav-link active" data-scroll-target="#what-is-open-source"><span class="header-section-number">1.1</span> What is Open Source?</a></li>
<li><a href="#how-to-contribute" id="toc-how-to-contribute" class="nav-link" data-scroll-target="#how-to-contribute"><span class="header-section-number">1.2</span> How to Contribute</a></li>
<li><a href="#guidance" id="toc-guidance" class="nav-link" data-scroll-target="#guidance"><span class="header-section-number">1.3</span> Guidance</a></li>
<li><a href="#examples" id="toc-examples" class="nav-link" data-scroll-target="#examples"><span class="header-section-number">1.4</span> Examples</a></li>
</ul>
</nav>
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Expand All @@ -291,8 +289,8 @@ <h1 class="title"><span class="chapter-number">1</span>&nbsp; <span class="chapt

</header>

<section id="what-is-open-source" class="level1" data-number="2">
<h1 data-number="2"><span class="header-section-number">2</span> What is Open Source?</h1>
<section id="what-is-open-source" class="level2" data-number="1.1">
<h2 data-number="1.1" class="anchored" data-anchor-id="what-is-open-source"><span class="header-section-number">1.1</span> What is Open Source?</h2>
<p>When someone says ‘open source’ - what does that mean to you?<br>
What are the important characteristics of something that is regarded as ‘open source’?</p>
<ul>
Expand All @@ -301,21 +299,22 @@ <h1 data-number="2"><span class="header-section-number">2</span> What is Open So
<li>Does the ability to reuse the code matter?</li>
<li>Does the ability to modify the code matter?</li>
</ul>
<section id="how-to-contribute" class="level2" data-number="2.1">
<h2 data-number="2.1" class="anchored" data-anchor-id="how-to-contribute"><span class="header-section-number">2.1</span> How to Contribute</h2>
</section>
<section id="how-to-contribute" class="level2" data-number="1.2">
<h2 data-number="1.2" class="anchored" data-anchor-id="how-to-contribute"><span class="header-section-number">1.2</span> How to Contribute</h2>
<p>Contribute to the discussion here in GitHub Discussions:<br>
<a href="https://github.com/phuse-org/OSTCDA/discussions/1" target="_blank">What is open source?</a></p>
</section>
<section id="guidance" class="level2" data-number="2.2">
<h2 data-number="2.2" class="anchored" data-anchor-id="guidance"><span class="header-section-number">2.2</span> Guidance</h2>
<section id="guidance" class="level2" data-number="1.3">
<h2 data-number="1.3" class="anchored" data-anchor-id="guidance"><span class="header-section-number">1.3</span> Guidance</h2>
<ul>
<li><p>Provide your thoughts and perspectives</p></li>
<li><p>Provide references to articles, webinars, presentations (citations, links)</p></li>
<li><p>Be respectful in this community</p></li>
</ul>
</section>
<section id="examples" class="level2" data-number="2.3">
<h2 data-number="2.3" class="anchored" data-anchor-id="examples"><span class="header-section-number">2.3</span> Examples</h2>
<section id="examples" class="level2" data-number="1.4">
<h2 data-number="1.4" class="anchored" data-anchor-id="examples"><span class="header-section-number">1.4</span> Examples</h2>
<p><u><strong>Example 1:</strong></u> The Open Source Initiative provides a <a href="https://opensource.org/osd/">definition</a>:</p>
<ul>
<li><p>Free distribution</p></li>
Expand All @@ -325,7 +324,6 @@ <h2 data-number="2.3" class="anchored" data-anchor-id="examples"><span class="he
<p><u><strong>Example 2:</strong></u> <a href="#0" style="font-size: 11.4pt;">Merriam-Webster</a> defines open source as “having the source code freely available for possible modification and redistribution”.</p>


</section>
</section>

</main> <!-- /main -->
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