From 5b3034d4e2a63217544bd80c35098eb31b72fcf0 Mon Sep 17 00:00:00 2001
From: MichaelRimler <47422662+MichaelRimler@users.noreply.github.com>
Date: Wed, 4 Sep 2024 10:32:26 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20phuse-or?=
 =?UTF-8?q?g/OSTCDA@64b8e94c006c29adeb806bb443dd0d941f230905=20?=
 =?UTF-8?q?=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 OSmodels.html   |  2 +-
 art.html        |  2 +-
 cost.html       |  2 +-
 doc_trust.html  |  2 +-
 fundOS.html     |  2 +-
 index.html      |  6 +++---
 legal.html      |  2 +-
 liability.html  |  2 +-
 longrun.html    |  2 +-
 match.html      |  2 +-
 references.html |  2 +-
 reg_accept.html |  2 +-
 search.json     | 16 +++-------------
 summary.html    | 44 ++++++++++++++++++++++----------------------
 trust.html      |  2 +-
 user_dev.html   |  2 +-
 users.html      |  2 +-
 whatelse.html   |  2 +-
 why.html        |  2 +-
 19 files changed, 44 insertions(+), 54 deletions(-)
diff --git a/OSmodels.html b/OSmodels.html
index e0a7fe4..a0982ea 100644
--- a/OSmodels.html
+++ b/OSmodels.html
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diff --git a/art.html b/art.html
index 85dad96..70c46e2 100644
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+++ b/art.html
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diff --git a/cost.html b/cost.html
index 88f42f8..2896228 100644
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+++ b/cost.html
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index cb14bb6..c79d3f1 100644
--- a/doc_trust.html
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diff --git a/fundOS.html b/fundOS.html
index 4990034..b2b6457 100644
--- a/fundOS.html
+++ b/fundOS.html
@@ -2,7 +2,7 @@
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 <meta charset="utf-8">
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diff --git a/index.html b/index.html
index be711ae..3e134a0 100644
--- a/index.html
+++ b/index.html
@@ -2,12 +2,12 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.56">
+<meta name="generator" content="quarto-1.5.57">
 
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 <meta name="author" content="PHUSE">
-<meta name="dcterms.date" content="2024-08-22">
+<meta name="dcterms.date" content="2024-09-04">
 
 <title>Open Source Technology in Clinical Data Analysis</title>
 <style>
@@ -302,7 +302,7 @@ <h1 class="title">Open Source Technology in Clinical Data Analysis</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">August 22, 2024</p>
+      <p class="date">September 4, 2024</p>
     </div>
   </div>
   
diff --git a/legal.html b/legal.html
index a96e152..039a868 100644
--- a/legal.html
+++ b/legal.html
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diff --git a/liability.html b/liability.html
index f02a8ee..8216cc5 100644
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diff --git a/longrun.html b/longrun.html
index b0760e8..6bb7d42 100644
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 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.56">
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diff --git a/match.html b/match.html
index 5913dfb..4ae84e1 100644
--- a/match.html
+++ b/match.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.5.56">
+<meta name="generator" content="quarto-1.5.57">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
diff --git a/references.html b/references.html
index 8515212..ce30899 100644
--- a/references.html
+++ b/references.html
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 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
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diff --git a/reg_accept.html b/reg_accept.html
index 158f4a2..188dd5c 100644
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+++ b/reg_accept.html
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diff --git a/search.json b/search.json
index f94f97f..fb2fd46 100644
--- a/search.json
+++ b/search.json
@@ -54,7 +54,7 @@
     "href": "summary.html",
     "title": "1  What is Open Source?",
     "section": "",
-    "text": "1.1 What is Open Source?\nWhen someone says ‘open source’ - what does that mean to you?\nWhat are the important characteristics of something that is regarded as ‘open source’?",
+    "text": "1.1 What is Open Source?\nThe Open Source Initiative delineates a number of characteristics of what it means to be open source, including free distribution, available source code, and the ability to create derived works.\nAccording to Merriam-Webster, open source is “having the source code freely available for possible modification and redistribution”.\nWikipedia defines open-source software (OSS) as a computer software that is released under a license in which the copyright holder grants users the rights to use, study, change and distribute the software and its source code to anyone and for any purpose.\nAll three of these sources refer to the ability to see the code, use the code, change the code, and share the code. And to be able to do so without any cost.",
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     "title": "1  What is Open Source?",
     "section": "",
-    "text": "Does the cost matter?\nDoes the ability to review the code matter?\nDoes the ability to reuse the code matter?\nDoes the ability to modify the code matter?",
+    "text": "1.1.1 How is this enabled?\nFundamentally, the code is owned by someone - by some entity, whether an individual, an organization, or a group of other entities. The owner of the code have the right to disseminate the code openly and describe how it can be used by others. This is accomplished through a license agreement (discussed in another section). For any piece of open source code, the owner of that code has decided to release it publicly with an associated license that defines how others may use or modify the code.\nIn a paper entitled *Open Source Technologies in Clinical Research, as part of the 2020 PHUSE US Connect, Bruce Wienckowski et al. write that “open source software includes permission to use the source code, design documents, or content of the product.” This is in contrast to proprietary software which is not typically distributed free of charge and “typically has licensed limitations on how that software can be used.”\nData submitted for review by a health authority to approve a medicine, therapy, or vaccine into the market it governs are expected to be accurate, reproducible, and traceable from the point of collection to the final analytic report. The ability to demonstrate the integrity of all data transformations has been perceived to be more challenging with open source solutions (relative to proprietary or commercial solutions).\nIn this publication, we aim to explore the numerous questions that have been raised by practitioners of data analytics for clinical research. These questions are aimed at managing the perceived risk of leveraging tools built on open source software for analyzing clinical trial data to support market applications of medicines, therapies, and vaccines based on evidence of safety and efficacy. The answers to some of these questions are becoming well understood in the industry while other answers are less complete. Our objective is to comprehensively compile this knowledge for ease of reference by others.",
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@@ -74,7 +74,7 @@
     "href": "summary.html#how-to-contribute",
     "title": "1  What is Open Source?",
     "section": "1.2 How to Contribute",
-    "text": "1.2 How to Contribute\nContribute to the discussion here in GitHub Discussions:\nWhat is open source?",
+    "text": "1.2 How to Contribute\nYou may continue to contribute to this discussion here in GitHub Discussions:\nWhat is open source?\n\nComment on content already developed\nAdd additional content or perspectives for consideration\nUpvote content that is particularly valuable",
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diff --git a/summary.html b/summary.html
index eb2fb5e..8729954 100644
--- a/summary.html
+++ b/summary.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
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@@ -269,10 +269,12 @@
     <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">1.1</span> What is Open Source?</a></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>
+  <ul class="collapse">
+  <li><a href="#how-is-this-enabled" id="toc-how-is-this-enabled" class="nav-link" data-scroll-target="#how-is-this-enabled"><span class="header-section-number">1.1.1</span> How is this enabled?</a></li>
+  </ul></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>
     </div>
@@ -300,19 +302,27 @@ <h1 class="title"><span class="chapter-number">1</span>&nbsp; <span class="chapt
 
 <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>
-<li>Does the cost matter?</li>
-<li>Does the ability to review the code matter?</li>
-<li>Does the ability to reuse the code matter?</li>
-<li>Does the ability to modify the code matter?</li>
-</ul>
+<p>The <a href="https://opensource.org/osd" target="_blank">Open Source Initiative</a> delineates a number of characteristics of what it means to be <strong>open source</strong>, including free distribution, available source code, and the ability to create derived works.</p>
+<p>According to <a href="https://www.merriam-webster.com/dictionary/open-source" target="_blank">Merriam-Webster</a>, open source is “having the source code freely available for possible modification and redistribution”.</p>
+<p><a href="https://en.wikipedia.org/wiki/Open-source_software" target="_blank">Wikipedia</a> defines open-source software (OSS) as a computer software that is released under a license in which the copyright holder grants users the rights to use, study, change and distribute the software and its source code to anyone and for any purpose.</p>
+<p>All three of these sources refer to the ability to see the code, use the code, change the code, and share the code. And to be able to do so without any cost.</p>
+<section id="how-is-this-enabled" class="level3" data-number="1.1.1">
+<h3 data-number="1.1.1" class="anchored" data-anchor-id="how-is-this-enabled"><span class="header-section-number">1.1.1</span> How is this enabled?</h3>
+<p>Fundamentally, the code is owned by someone - by some entity, whether an individual, an organization, or a group of other entities. The owner of the code have the right to disseminate the code openly and describe how it can be used by others. This is accomplished through a license agreement (discussed in another section). For any piece of <strong>open source code</strong>, the owner of that code has decided to release it publicly with an associated license that defines how others may use or modify the code.</p>
+<p>In a paper entitled *<a href="https://phuse.s3.eu-central-1.amazonaws.com/Archive/2020/Connect/US/Virtual/PAP_TT10.pdf" target="_blank">Open Source Technologies in Clinical Research</a>, as part of the 2020 PHUSE US Connect, Bruce Wienckowski et al.&nbsp;write that “open source software includes permission to use the source code, design documents, or content of the product.” This is in contrast to proprietary software which is not typically distributed free of charge and “typically has licensed limitations on how that software can be used.”</p>
+<p>Data submitted for review by a health authority to approve a medicine, therapy, or vaccine into the market it governs are expected to be <strong><em>accurate</em></strong>, <strong><em>reproducible</em></strong>, and <strong><em>traceable</em></strong> from the point of collection to the final analytic report. The ability to demonstrate the integrity of all data transformations has been perceived to be more challenging with open source solutions (relative to proprietary or commercial solutions).</p>
+<p>In this publication, we aim to explore the numerous questions that have been raised by practitioners of data analytics for clinical research. These questions are aimed at managing the perceived risk of leveraging tools built on open source software for analyzing clinical trial data to support market applications of medicines, therapies, and vaccines based on evidence of safety and efficacy. The answers to some of these questions are becoming well understood in the industry while other answers are less complete. Our objective is to comprehensively compile this knowledge for ease of reference by others.</p>
+</section>
 </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>
+<p>You may continue to contribute to this discussion here in GitHub Discussions:<br>
 <a href="https://github.com/phuse-org/OSTCDA/discussions/1" target="_blank">What is open source?</a></p>
+<ul>
+<li><p>Comment on content already developed</p></li>
+<li><p>Add additional content or perspectives for consideration</p></li>
+<li><p>Upvote content that is particularly valuable</p></li>
+</ul>
 </section>
 <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>
@@ -321,16 +331,6 @@ <h2 data-number="1.3" class="anchored" data-anchor-id="guidance"><span class="he
 <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="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>
-<li><p>Available source code</p></li>
-<li><p>Derived works possible</p></li>
-</ul>
-<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>
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index b66f94e..dbafd16 100644
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index 6fafbc7..1deb4ed 100644
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