aboutsummaryrefslogtreecommitdiff
path: root/doc/blog
diff options
context:
space:
mode:
Diffstat (limited to 'doc/blog')
-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 @@
+<?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;
+ padding-top: 1.2em;
+ }
+ pre.src:before {
+ display: none;
+ position: absolute;
+ background-color: white;
+ top: -10px;
+ right: 10px;
+ padding: 3px;
+ border: 1px solid black;
+ }
+ pre.src:hover:before { display: inline;}
+ /* Languages per Org manual */
+ pre.src-asymptote:before { content: 'Asymptote'; }
+ pre.src-awk:before { content: 'Awk'; }
+ pre.src-C:before { content: 'C'; }
+ /* pre.src-C++ doesn't work in CSS */
+ pre.src-clojure:before { content: 'Clojure'; }
+ pre.src-css:before { content: 'CSS'; }
+ pre.src-D:before { content: 'D'; }
+ pre.src-ditaa:before { content: 'ditaa'; }
+ pre.src-dot:before { content: 'Graphviz'; }
+ pre.src-calc:before { content: 'Emacs Calc'; }
+ pre.src-emacs-lisp:before { content: 'Emacs Lisp'; }
+ pre.src-fortran:before { content: 'Fortran'; }
+ pre.src-gnuplot:before { content: 'gnuplot'; }
+ pre.src-haskell:before { content: 'Haskell'; }
+ pre.src-hledger:before { content: 'hledger'; }
+ pre.src-java:before { content: 'Java'; }
+ pre.src-js:before { content: 'Javascript'; }
+ pre.src-latex:before { content: 'LaTeX'; }
+ pre.src-ledger:before { content: 'Ledger'; }
+ pre.src-lisp:before { content: 'Lisp'; }
+ pre.src-lilypond:before { content: 'Lilypond'; }
+ pre.src-lua:before { content: 'Lua'; }
+ pre.src-matlab:before { content: 'MATLAB'; }
+ pre.src-mscgen:before { content: 'Mscgen'; }
+ pre.src-ocaml:before { content: 'Objective Caml'; }
+ pre.src-octave:before { content: 'Octave'; }
+ pre.src-org:before { content: 'Org mode'; }
+ pre.src-oz:before { content: 'OZ'; }
+ pre.src-plantuml:before { content: 'Plantuml'; }
+ pre.src-processing:before { content: 'Processing.js'; }
+ pre.src-python:before { content: 'Python'; }
+ pre.src-R:before { content: 'R'; }
+ pre.src-ruby:before { content: 'Ruby'; }
+ pre.src-sass:before { content: 'Sass'; }
+ pre.src-scheme:before { content: 'Scheme'; }
+ pre.src-screen:before { content: 'Gnu Screen'; }
+ pre.src-sed:before { content: 'Sed'; }
+ pre.src-sh:before { content: 'shell'; }
+ pre.src-sql:before { content: 'SQL'; }
+ pre.src-sqlite:before { content: 'SQLite'; }
+ /* additional languages in org.el's org-babel-load-languages alist */
+ pre.src-forth:before { content: 'Forth'; }
+ pre.src-io:before { content: 'IO'; }
+ pre.src-J:before { content: 'J'; }
+ pre.src-makefile:before { content: 'Makefile'; }
+ pre.src-maxima:before { content: 'Maxima'; }
+ pre.src-perl:before { content: 'Perl'; }
+ pre.src-picolisp:before { content: 'Pico Lisp'; }
+ pre.src-scala:before { content: 'Scala'; }
+ pre.src-shell:before { content: 'Shell Script'; }
+ pre.src-ebnf2ps:before { content: 'ebfn2ps'; }
+ /* additional language identifiers per "defun org-babel-execute"
+ in ob-*.el */
+ pre.src-cpp:before { content: 'C++'; }
+ pre.src-abc:before { content: 'ABC'; }
+ pre.src-coq:before { content: 'Coq'; }
+ pre.src-groovy:before { content: 'Groovy'; }
+ /* additional language identifiers from org-babel-shell-names in
+ ob-shell.el: ob-shell is the only babel language using a lambda to put
+ the execution function name together. */
+ pre.src-bash:before { content: 'bash'; }
+ pre.src-csh:before { content: 'csh'; }
+ pre.src-ash:before { content: 'ash'; }
+ pre.src-dash:before { content: 'dash'; }
+ pre.src-ksh:before { content: 'ksh'; }
+ pre.src-mksh:before { content: 'mksh'; }
+ pre.src-posh:before { content: 'posh'; }
+ /* Additional Emacs modes also supported by the LaTeX listings package */
+ pre.src-ada:before { content: 'Ada'; }
+ pre.src-asm:before { content: 'Assembler'; }
+ pre.src-caml:before { content: 'Caml'; }
+ pre.src-delphi:before { content: 'Delphi'; }
+ pre.src-html:before { content: 'HTML'; }
+ pre.src-idl:before { content: 'IDL'; }
+ pre.src-mercury:before { content: 'Mercury'; }
+ pre.src-metapost:before { content: 'MetaPost'; }
+ pre.src-modula-2:before { content: 'Modula-2'; }
+ pre.src-pascal:before { content: 'Pascal'; }
+ pre.src-ps:before { content: 'PostScript'; }
+ pre.src-prolog:before { content: 'Prolog'; }
+ pre.src-simula:before { content: 'Simula'; }
+ pre.src-tcl:before { content: 'tcl'; }
+ pre.src-tex:before { content: 'TeX'; }
+ pre.src-plain-tex:before { content: 'Plain TeX'; }
+ pre.src-verilog:before { content: 'Verilog'; }
+ pre.src-vhdl:before { content: 'VHDL'; }
+ pre.src-xml:before { content: 'XML'; }
+ pre.src-nxml:before { content: 'XML'; }
+ /* add a generic configuration mode; LaTeX export needs an additional
+ (add-to-list 'org-latex-listings-langs '(conf " ")) in .emacs */
+ pre.src-conf:before { content: 'Configuration File'; }
+
+ table { border-collapse:collapse; }
+ caption.t-above { caption-side: top; }
+ caption.t-bottom { caption-side: bottom; }
+ td, th { vertical-align:top; }
+ th.org-right { text-align: center; }
+ th.org-left { text-align: center; }
+ th.org-center { text-align: center; }
+ td.org-right { text-align: right; }
+ td.org-left { text-align: left; }
+ td.org-center { text-align: center; }
+ dt { font-weight: bold; }
+ .footpara { display: inline; }
+ .footdef { margin-bottom: 1em; }
+ .figure { padding: 1em; }
+ .figure p { text-align: center; }
+ .equation-container {
+ display: table;
+ 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?
generated by cgit v1.2.3 (git 2.45.2) at 2024-11-22 09:16:22 +0000