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| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part1.org | 7 | ||||
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part2.org | 16 | ||||
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part3.html | 286 | ||||
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part3.org | 30 |
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 @@ +<?xml version="1.0" encoding="utf-8"?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" +"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> +<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" /> +<style type="text/css"> + <!--/*--><![CDATA[/*><!--*/ + .title { text-align: center; + margin-bottom: .2em; } + .subtitle { text-align: center; + font-size: medium; + font-weight: bold; + margin-top:0; } + .todo { font-family: monospace; color: red; } + .done { font-family: monospace; color: green; } + .priority { font-family: monospace; color: orange; } + .tag { background-color: #eee; font-family: monospace; + padding: 2px; font-size: 80%; font-weight: normal; } + .timestamp { color: #bebebe; } + .timestamp-kwd { color: #5f9ea0; } + .org-right { margin-left: auto; margin-right: 0px; text-align: right; } + .org-left { margin-left: 0px; margin-right: auto; text-align: left; } + .org-center { margin-left: auto; margin-right: auto; text-align: center; } + .underline { text-decoration: underline; } + #postamble p, #preamble p { font-size: 90%; margin: .2em; } + p.verse { margin-left: 3%; } + pre { + border: 1px solid #ccc; + box-shadow: 3px 3px 3px #eee; + padding: 8pt; + font-family: monospace; + overflow: auto; + margin: 1.2em; + } + pre.src { + position: relative; + overflow: visible; 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+ text-align: center; + width: 100%; + } + .equation { + vertical-align: middle; + } + .equation-label { + display: table-cell; + text-align: right; + vertical-align: middle; + } + .inlinetask { + padding: 10px; + border: 2px solid gray; + margin: 10px; + background: #ffffcc; + } + #org-div-home-and-up + { text-align: right; font-size: 70%; white-space: nowrap; } + textarea { overflow-x: auto; } + .linenr { font-size: smaller } + .code-highlighted { background-color: #ffff00; } + .org-info-js_info-navigation { border-style: none; } + #org-info-js_console-label + { font-size: 10px; font-weight: bold; white-space: nowrap; } + .org-info-js_search-highlight + { background-color: #ffff00; color: #000000; font-weight: bold; } + .org-svg { width: 90%; } + /*]]>*/--> +</style> +<link rel="Blog stylesheet" type="text/css" href="blog.css" /> +<script type="text/javascript"> +/* +@licstart The following is the entire license notice for the +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. +*/ +<!--/*--><![CDATA[/*><!--*/ + function CodeHighlightOn(elem, id) + { + var target = document.getElementById(id); + if(null != target) { + elem.cacheClassElem = elem.className; + elem.cacheClassTarget = target.className; + target.className = "code-highlighted"; + elem.className = "code-highlighted"; + } + } + function CodeHighlightOff(elem, id) + { + var target = document.getElementById(id); + if(elem.cacheClassElem) + elem.className = elem.cacheClassElem; + if(elem.cacheClassTarget) + target.className = elem.cacheClassTarget; + } +/*]]>*///--> +</script> +</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? |