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-rw-r--r--doc/blog/using-covid-19-pubseq-part1.org7
-rw-r--r--doc/blog/using-covid-19-pubseq-part2.org16
-rw-r--r--doc/blog/using-covid-19-pubseq-part3.html286
-rw-r--r--doc/blog/using-covid-19-pubseq-part3.org30
4 files changed, 339 insertions, 0 deletions
diff --git a/doc/blog/using-covid-19-pubseq-part1.org b/doc/blog/using-covid-19-pubseq-part1.org
index b1edbad..5a749d6 100644
--- a/doc/blog/using-covid-19-pubseq-part1.org
+++ b/doc/blog/using-covid-19-pubseq-part1.org
@@ -1,5 +1,12 @@
#+TITLE: COVID-19 PubSeq (part 1)
#+AUTHOR: Pjotr Prins
+# C-c C-e h h publish
+# C-c ! insert date (use . for active agenda, C-u C-c ! for date, C-u C-c . for time)
+# C-c C-t task rotate
+# RSS_IMAGE_URL: http://xxxx.xxxx.free.fr/rss_icon.png
+
+#+HTML_LINK_HOME: http://covid19.genenetwork.org
+#+HTML_HEAD: <link rel="Blog stylesheet" type="text/css" href="blog.css" />
As part of the COVID-19 Biohackathon 2020 we formed a working group
to create a COVID-19 Public Sequence Resource (COVID-19 PubSeq) for
diff --git a/doc/blog/using-covid-19-pubseq-part2.org b/doc/blog/using-covid-19-pubseq-part2.org
index d61bf42..d2a1cbc 100644
--- a/doc/blog/using-covid-19-pubseq-part2.org
+++ b/doc/blog/using-covid-19-pubseq-part2.org
@@ -8,6 +8,22 @@
#+HTML_LINK_HOME: http://covid19.genenetwork.org
#+HTML_HEAD: <link rel="Blog stylesheet" type="text/css" href="blog.css" />
+As part of the COVID-19 Biohackathon 2020 we formed a working group to
+create a COVID-19 Public Sequence Resource (COVID-19 PubSeq) for
+Corona virus sequences. The general idea is to create a repository
+that has a low barrier to entry for uploading sequence data using best
+practices. I.e., data published with a creative commons 4.0 (CC-4.0)
+license with metadata using state-of-the art standards and, perhaps
+most importantly, providing standardised workflows that get triggered
+on upload, so that results are immediately available in standardised
+data formats.
+
+* Table of Contents :TOC:noexport:
+ - [[#finding-output-of-workflows][Finding output of workflows]]
+ - [[#introduction][Introduction]]
+ - [[#the-arvados-file-interface][The Arvados file interface]]
+ - [[#using-the-arvados-api][Using the Arvados API]]
+
* Finding output of workflows
As part of the COVID-19 Biohackathon 2020 we formed a working group to
diff --git a/doc/blog/using-covid-19-pubseq-part3.html b/doc/blog/using-covid-19-pubseq-part3.html
new file mode 100644
index 0000000..94d5a2e
--- /dev/null
+++ b/doc/blog/using-covid-19-pubseq-part3.html
@@ -0,0 +1,286 @@
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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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+<head>
+<!-- 2020-05-27 Wed 07:27 -->
+<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
+<meta name="viewport" content="width=device-width, initial-scale=1" />
+<title>COVID-19 PubSeq Uploading Data (part 3)</title>
+<meta name="generator" content="Org mode" />
+<meta name="author" content="Pjotr Prins" />
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+<link rel="Blog stylesheet" type="text/css" href="blog.css" />
+<script type="text/javascript">
+/*
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+JavaScript code in this tag.
+
+Copyright (C) 2012-2020 Free Software Foundation, Inc.
+
+The JavaScript code in this tag is free software: you can
+redistribute it and/or modify it under the terms of the GNU
+General Public License (GNU GPL) as published by the Free Software
+Foundation, either version 3 of the License, or (at your option)
+any later version. The code is distributed WITHOUT ANY WARRANTY;
+without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU GPL for more details.
+
+As additional permission under GNU GPL version 3 section 7, you
+may distribute non-source (e.g., minimized or compacted) forms of
+that code without the copy of the GNU GPL normally required by
+section 4, provided you include this license notice and a URL
+through which recipients can access the Corresponding Source.
+
+
+@licend The above is the entire license notice
+for the JavaScript code in this tag.
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+</head>
+<body>
+<div id="content">
+<h1 class="title">COVID-19 PubSeq Uploading Data (part 3)</h1>
+<div id="table-of-contents">
+<h2>Table of Contents</h2>
+<div id="text-table-of-contents">
+<ul>
+<li><a href="#orgb387609">1. Uploading Data</a></li>
+<li><a href="#org7dd876c">2. What does this mean?</a></li>
+</ul>
+</div>
+</div>
+
+<div id="outline-container-orgb387609" class="outline-2">
+<h2 id="orgb387609"><span class="section-number-2">1</span> Uploading Data</h2>
+<div class="outline-text-2" id="text-1">
+<p>
+<i>Work in progress!</i>
+</p>
+
+<p>
+As part of the COVID-19 Biohackathon 2020 we formed a working group to
+create a COVID-19 Public Sequence Resource (COVID-19 PubSeq) for
+Corona virus sequences. The general idea is to create a repository
+that has a low barrier to entry for uploading sequence data using best
+practices. I.e., data published with a creative commons 4.0 (CC-4.0)
+license with metadata using state-of-the art standards and, perhaps
+most importantly, providing standardised workflows that get triggered
+on upload, so that results are immediately available in standardised
+data formats.
+</p>
+</div>
+</div>
+
+<div id="outline-container-org7dd876c" class="outline-2">
+<h2 id="org7dd876c"><span class="section-number-2">2</span> What does this mean?</h2>
+</div>
+</div>
+<div id="postamble" class="status">
+<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-05-27 Wed 07:27</small>.
+</div>
+</body>
+</html>
diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org
index c147ba3..d088f78 100644
--- a/doc/blog/using-covid-19-pubseq-part3.org
+++ b/doc/blog/using-covid-19-pubseq-part3.org
@@ -1,2 +1,32 @@
+#+TITLE: COVID-19 PubSeq Uploading Data (part 3)
+#+AUTHOR: Pjotr Prins
+# C-c C-e h h publish
+# C-c ! insert date (use . for active agenda, C-u C-c ! for date, C-u C-c . for time)
+# C-c C-t task rotate
+# RSS_IMAGE_URL: http://xxxx.xxxx.free.fr/rss_icon.png
+
+#+HTML_HEAD: <link rel="Blog stylesheet" type="text/css" href="blog.css" />
+
+* Uploading Data
+
/Work in progress!/
+As part of the COVID-19 Biohackathon 2020 we formed a working group to
+create a COVID-19 Public Sequence Resource (COVID-19 PubSeq) for
+Corona virus sequences. The general idea is to create a repository
+that has a low barrier to entry for uploading sequence data using best
+practices. I.e., data published with a creative commons 4.0 (CC-4.0)
+license with metadata using state-of-the art standards and, perhaps
+most importantly, providing standardised workflows that get triggered
+on upload, so that results are immediately available in standardised
+data formats.
+
+* Table of Contents :TOC:noexport:
+ - [[#uploading-data][Uploading Data]]
+ - [[#table-of-contents][Table of Contents]]
+ - [[#what-does-this-mean][What does this mean?]]
+
+* Table of Contents :TOC:noexport:
+ - [[#what-does-this-mean][What does this mean?]]
+
+* What does this mean?
generated by cgit v1.2.3 (git 2.45.2) at 2024-11-25 15:54:18 +0000