aboutsummaryrefslogtreecommitdiff
path: root/doc
diff options
context:
space:
mode:
authorPjotr Prins2020-08-22 09:49:11 +0100
committerPjotr Prins2020-08-22 09:49:11 +0100
commit0a23018b8afced6a145d96efbe5bffe86f092cce (patch)
treedbd275195d25e92fb6b4afaa77d702c9ee5f1eb5 /doc
parente184e5e61590c3988b810fdf956cf839477efc39 (diff)
downloadbh20-seq-resource-0a23018b8afced6a145d96efbe5bffe86f092cce.tar.gz
bh20-seq-resource-0a23018b8afced6a145d96efbe5bffe86f092cce.tar.lz
bh20-seq-resource-0a23018b8afced6a145d96efbe5bffe86f092cce.zip
Small text fixes
Diffstat (limited to 'doc')
-rw-r--r--doc/blog/using-covid-19-pubseq-part5.org4
-rw-r--r--doc/web/about.html1522
-rw-r--r--doc/web/about.org12
3 files changed, 580 insertions, 958 deletions
diff --git a/doc/blog/using-covid-19-pubseq-part5.org b/doc/blog/using-covid-19-pubseq-part5.org
index 78eea66..99c8ebf 100644
--- a/doc/blog/using-covid-19-pubseq-part5.org
+++ b/doc/blog/using-covid-19-pubseq-part5.org
@@ -23,8 +23,8 @@ The public sequence resource uses multiple data formats listed on the
for RDF and semantic web/linked data ontologies. This technology
allows for querying data in unprescribed ways - that is, you can
formulate your own queries without dealing with a preset model of that
-data (so typical of CSV files and SQL tables). Examples of exploring
-data are listed [[http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part1][here]].
+data (which is how one has to approach CSV files and SQL
+tables). Examples of exploring data are listed [[http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part1][here]].
In this BLOG we are going to look at the metadata entered on the
COVID-19 PubSeq website (or command line client). It is important to
diff --git a/doc/web/about.html b/doc/web/about.html
index c971a4e..a4ab186 100644
--- a/doc/web/about.html
+++ b/doc/web/about.html
@@ -1,964 +1,582 @@
<?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">
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
- <!-- 2020-07-18 Sat 03:27 -->
- <meta http-equiv="Content-Type" content="text/html;charset=utf-8"/>
- <meta name="viewport" content="width=device-width, initial-scale=1"/>
- <title>About/FAQ</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>
- <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>
+<!-- 2020-08-22 Sat 03:48 -->
+<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
+<meta name="viewport" content="width=device-width, initial-scale=1" />
+<title>About/FAQ</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; }
+ .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>
+<script type="text/javascript">
+/*
+@licstart The following is the entire license notice for the
+JavaScript code in this tag.
+
+Copyright (C) 2012-2018 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">About/FAQ</h1>
- <div id="table-of-contents">
- <h2>Table of Contents</h2>
- <div id="text-table-of-contents">
- <ul>
- <li><a href="#org0db9061">1. What is the 'public sequence resource' about?</a></li>
- <li><a href="#org983877d">2. Who created the public sequence resource?</a></li>
- <li><a href="#org83093c3">3. How does the public sequence resource compare to other data resources?</a>
- </li>
- <li><a href="#org9b31fd4">4. Why should I upload my data here?</a></li>
- <li><a href="#org4e92cb5">5. Why should I not upload by data here?</a></li>
- <li><a href="#orgdfe72f6">6. How does the public sequence resource work?</a></li>
- <li><a href="#orgd0c5abb">7. Who uses the public sequence resource?</a></li>
- <li><a href="#org56f4a54">8. How can I contribute?</a></li>
- <li><a href="#org2240ef7">9. Is this about open data?</a></li>
- <li><a href="#orgbb655e0">10. Is this about free software?</a></li>
- <li><a href="#org4e779f4">11. How do I upload raw data?</a></li>
- <li><a href="#org83f6b7b">12. How do I change metadata?</a></li>
- <li><a href="#org1bc6dab">13. How do I change the work flows?</a></li>
- <li><a href="#org1140d62">14. How do I change the source code?</a></li>
- <li><a href="#orge182714">15. Should I choose CC-BY or CC0?</a></li>
- <li><a href="#orgf4a692b">16. How do I deal with private data and privacy?</a></li>
- <li><a href="#org7757574">17. How do I communicate with you?</a></li>
- <li><a href="#org194006f">18. Who are the sponsors?</a></li>
- </ul>
- </div>
- </div>
-
- <div id="outline-container-org0db9061" class="outline-2">
- <h2 id="org0db9061"><span class="section-number-2">1</span> What is the 'public sequence resource' about?</h2>
- <div class="outline-text-2" id="text-1">
- <p>
- The <b>public sequence resource</b> aims to provide a generic and useful
- resource for COVID-19 research. The focus is on providing the best
- possible sequence data with associated metadata that can be used for
- sequence comparison and protein prediction.
- </p>
- <p>
- We were at the <strong>Bioinformatics Community Conference 2020</strong>! Have a look at the
- <a href="https://bcc2020.sched.com/event/coLw">video talk</a></li>
- (<a href="https://drive.google.com/file/d/1skXHwVKM_gl73-_4giYIOQ1IlC5X5uBo/view?usp=sharing">alternative link</a>)
- and the <a href="https://drive.google.com/file/d/1vyEgfvSqhM9yIwWZ6Iys-QxhxtVxPSdp/view?usp=sharing">poster</a>.
- </p>
- </div>
- </div>
-
- <div id="outline-container-org983877d" class="outline-2">
- <h2 id="org983877d"><span class="section-number-2">2</span> Who created the public sequence resource?</h2>
- <div class="outline-text-2" id="text-2">
- <p>
- The <b>public sequence resource</b> is an initiative by <a
- href="https://github.com/arvados/bh20-seq-resource/graphs/contributors">bioinformatics</a> and
- ontology experts who want to create something agile and useful for the
- wider research community. The initiative started at the COVID-19
- biohackathon in April 2020 and is ongoing. The main project drivers
- are Pjotr Prins (UTHSC), Peter Amstutz (Curii), Andrea Guarracino
- (University of Rome Tor Vergata), Michael Crusoe (Common Workflow
- Language), Thomas Liener (consultant, formerly EBI), Erik Garrison
- (UCSC) and Jerven Bolleman (Swiss Institute of Bioinformatics).
- </p>
-
- <p>
- Notably, as this is a free software initiative, the project represents
- major work by hundreds of software developers and ontology and data
- wrangling experts. Thank you everyone!
- </p>
- </div>
- </div>
-
- <div id="outline-container-org83093c3" class="outline-2">
- <h2 id="org83093c3"><span class="section-number-2">3</span> How does the public sequence resource compare to
- other data resources?</h2>
- <div class="outline-text-2" id="text-3">
- <p>
- The short version is that we use state-of-the-art practices in
- bioinformatics using agile methods. Unlike the resources from large
- institutes we can improve things on a dime and anyone can contribute
- to building out this resource! Sequences from GenBank, EBI/ENA and
- others are regularly added to PubSeq. We encourage people to everyone
- to submit on PubSeq because of its superior live tooling and metadata
- support (see the next question).
- </p>
-
- <p>
- Importantly: all data is published under either the <a
- href="https://creativecommons.org/licenses/by/4.0/">Creative Commons
- 4.0 attribution license</a> or the <a
- href="https://creativecommons.org/share-your-work/public-domain/cc0/">CC0 “No Rights Reserved”
- license</a> which
- means it data can be published and workflows can run in public
- environments allowing for improved access for research and
- reproducible results. This contrasts with some other public resources,
- such as GISAID.
- </p>
- </div>
- </div>
-
- <div id="outline-container-org9b31fd4" class="outline-2">
- <h2 id="org9b31fd4"><span class="section-number-2">4</span> Why should I upload my data here?</h2>
- <div class="outline-text-2" id="text-4">
- <ol class="org-ol">
- <li>We champion truly shareable data without licensing restrictions - with proper
- attribution
- </li>
- <li>We provide full metadata support using state-of-the-art ontology's</li>
- <li>We provide a web-based sequence uploader and a command-line version
- for bulk uploads
- </li>
- <li>We provide a live SPARQL end-point for all metadata</li>
- <li>We provide free data analysis and sequence comparison triggered on data upload</li>
- <li>We do real work for you, with this <a
- href="https://workbench.lugli.arvadosapi.com/container_requests/lugli-xvhdp-bhhk4nxx1lch5od">link</a>
- you can see the last
- run took 5.5 hours!
- </li>
- <li>We provide free downloads of all computed output</li>
- <li>There is no need to set up pipelines and/or compute clusters</li>
- <li>All workflows get triggered on uploading a new sequence</li>
- <li>When someone (you?) improves the software/workflows and everyone benefits</li>
- <li>Your data gets automatically integrated with the Swiss Institure of
- Bioinformatics COVID-19 knowledge base
- <a href="https://covid-19-sparql.expasy.org/">https://covid-19-sparql.expasy.org/</a> (Elixir
- Switzerland)
- </li>
- <li>Your data will be used to develop drug targets</li>
- </ol>
-
- <p>
- Finally, if you upload your data here we have workflows that output
- formatted data suitable for <a
- href="http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part6">uploading to EBI
- resources</a> (and soon
- others). Uploading your data here get your data ready for upload to
- multiple resources.
- </p>
- </div>
- </div>
-
- <div id="outline-container-org4e92cb5" class="outline-2">
- <h2 id="org4e92cb5"><span class="section-number-2">5</span> Why should I not upload by data here?</h2>
- <div class="outline-text-2" id="text-5">
- <p>
- Funny question. There are only good reasons to upload your data here
- and make it available to the widest audience possible.
- </p>
-
- <p>
- In fact, you can upload your data here as well as to other
- resources. It is your data after all. No one can prevent you from
- uploading your data to multiple resources.
- </p>
-
- <p>
- We recommend uploading to EBI and NCBI resources using our data
- conversion tools. It means you only enter data once and make the
- process smooth. You can also use our command line data uploader
- for bulk uploads!
- </p>
- </div>
- </div>
-
- <div id="outline-container-orgdfe72f6" class="outline-2">
- <h2 id="orgdfe72f6"><span class="section-number-2">6</span> How does the public sequence resource work?</h2>
- <div class="outline-text-2" id="text-6">
- <p>
- On uploading a sequence with metadata it will automatically be
- processed and incorporated into the public pangenome with metadata
- using workflows from the High Performance Open Biology Lab defined
- <a href="https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate">here</a>.
- </p>
- </div>
- </div>
-
- <div id="outline-container-orgd0c5abb" class="outline-2">
- <h2 id="orgd0c5abb"><span class="section-number-2">7</span> Who uses the public sequence resource?</h2>
- <div class="outline-text-2" id="text-7">
- <p>
- The Swiss Institute of Bioinformatics has included this data in
- <a href="https://covid-19-sparql.expasy.org/">https://covid-19-sparql.expasy.org/</a> and made it part
- of <a href="https://www.uniprot.org/">Uniprot</a>.
- </p>
-
- <p>
- The Pantograph <a href="https://graph-genome.github.io/">viewer</a> uses PubSeq data for their
- visualisations.
- </p>
-
- <p>
- <a href="https://uthsc.edu">UTHSC</a> (USA), <a href="https://www.esr.cri.nz/">ESR</a> (New Zealand) and
- <a href="https://www.ornl.gov/news/ornl-fight-against-covid-19">ORNL</a> (USA) use COVID-19 PubSeq data
- for monitoring, protein prediction and drug development.
- </p>
- </div>
- </div>
-
- <div id="outline-container-org56f4a54" class="outline-2">
- <h2 id="org56f4a54"><span class="section-number-2">8</span> How can I contribute?</h2>
- <div class="outline-text-2" id="text-8">
- <p>
- You can contribute by submitting sequences, updating metadata, submit
- issues on our issue tracker, and more importantly add functionality.
- See 'How do I change the source code' below. Read through our online
- documentation at <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a>
- as a starting
- point.
- </p>
- </div>
- </div>
-
- <div id="outline-container-org2240ef7" class="outline-2">
- <h2 id="org2240ef7"><span class="section-number-2">9</span> Is this about open data?</h2>
- <div class="outline-text-2" id="text-9">
- <p>
- All data is published under a <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons
- 4.0 attribution license</a>
- (CC-BY-4.0). You can download the raw and published (GFA/RDF/FASTA)
- data and store it for further processing.
- </p>
- </div>
- </div>
-
- <div id="outline-container-orgbb655e0" class="outline-2">
- <h2 id="orgbb655e0"><span class="section-number-2">10</span> Is this about free software?</h2>
- <div class="outline-text-2" id="text-10">
- <p>
- Absolutely. Free software allows for fully reproducible pipelines. You
- can take our workflows and data and run it elsewhere!
- </p>
- </div>
- </div>
-
- <div id="outline-container-org4e779f4" class="outline-2">
- <h2 id="org4e779f4"><span class="section-number-2">11</span> How do I upload raw data?</h2>
- <div class="outline-text-2" id="text-11">
- <p>
- We are preparing raw sequence data pipelines (fastq and BAM). The
- reason is that we want the best data possible for downstream analysis
- (including protein prediction and test development). The current
- approach where people publish final sequences of SARS-CoV-2 is lacking
- because it hides how this sequence was created. For reasons of
- reproducible and improved results we want/need to work with the raw
- sequence reads (both short reads and long reads) and take alternative
- assembly variations into consideration. This is all work in progress.
- </p>
- </div>
- </div>
-
- <div id="outline-container-org83f6b7b" class="outline-2">
- <h2 id="org83f6b7b"><span class="section-number-2">12</span> How do I change metadata?</h2>
- <div class="outline-text-2" id="text-12">
- <p>
- See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a>!
- </p>
- </div>
- </div>
-
- <div id="outline-container-org1bc6dab" class="outline-2">
- <h2 id="org1bc6dab"><span class="section-number-2">13</span> How do I change the work flows?</h2>
- <div class="outline-text-2" id="text-13">
- <p>
- Workflows are on <a href="https://github.com/arvados/bh20-seq-resource/tree/master/workflows">github</a>
- and can be modified. See also the BLOG
- <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a> on workflows.
- </p>
- </div>
- </div>
-
- <div id="outline-container-org1140d62" class="outline-2">
- <h2 id="org1140d62"><span class="section-number-2">14</span> How do I change the source code?</h2>
- <div class="outline-text-2" id="text-14">
- <p>
- Go to our <a href="https://github.com/arvados/bh20-seq-resource">source code repositories</a>,
- fork/clone the repository, change
- something and submit a <a href="https://github.com/arvados/bh20-seq-resource/pulls">pull request</a>
- (PR). That easy! Check out how
- many PRs we already merged.
- </p>
- </div>
- </div>
-
- <div id="outline-container-orge182714" class="outline-2">
- <h2 id="orge182714"><span class="section-number-2">15</span> Should I choose CC-BY or CC0?</h2>
- <div class="outline-text-2" id="text-15">
- <p>
- Restrictive data licenses are hampering data sharing and reproducible
- research. CC0 is the preferred license because it gives researchers
- the most freedom. Since we provide metadata there is no reason for
- others not to honour your work. We also provide CC-BY as an option
- because we know people like the attribution clause.
- </p>
-
- <p>
- In all honesty: we prefer both data and software to be free.
- </p>
- </div>
- </div>
-
- <div id="outline-container-orgf4a692b" class="outline-2">
- <h2 id="orgf4a692b"><span class="section-number-2">16</span> How do I deal with private data and privacy?</h2>
- <div class="outline-text-2" id="text-16">
- <p>
- A public sequence resource is about public data. Metadata can refer to
- private data. You can use your own (anonymous) identifiers. We also
- plan to combine identifiers with clinical data stored securely at
- <a href="https://redcap-covid19.elixir-luxembourg.org/redcap/">REDCap</a>. See the relevant <a
- href="https://github.com/arvados/bh20-seq-resource/issues/21">tracker</a> for more information and
- contributing.
- </p>
- </div>
- </div>
-
- <div id="outline-container-org7757574" class="outline-2">
- <h2 id="org7757574"><span class="section-number-2">17</span> How do I communicate with you?</h2>
- <div class="outline-text-2" id="text-17">
- <p>
- We use a <a
- href="https://gitter.im/arvados/pubseq?utm_source=share-link&amp;utm_medium=link&amp;utm_campaign=share-link">gitter
- channel</a> you can join.
- </p>
- </div>
- </div>
-
- <div id="outline-container-org194006f" class="outline-2">
- <h2 id="org194006f"><span class="section-number-2">18</span> Who are the sponsors?</h2>
- <div class="outline-text-2" id="text-18">
- <p>
- The main sponsors are listed in the footer. In addition to the time
- generously donated by many contributors we also acknowledge Amazon AWS
- for donating COVID-19 related compute time.
- </p>
- </div>
- </div>
+<h1 class="title">About/FAQ</h1>
+<div id="table-of-contents">
+<h2>Table of Contents</h2>
+<div id="text-table-of-contents">
+<ul>
+<li><a href="#org99c4553">1. What is the 'public sequence resource' about?</a></li>
+<li><a href="#orga3b6187">2. Presentations</a></li>
+<li><a href="#orgeb109f2">3. Who created the public sequence resource?</a></li>
+<li><a href="#org631e2c7">4. How does the public sequence resource compare to other data resources?</a></li>
+<li><a href="#org319a852">5. Why should I upload my data here?</a></li>
+<li><a href="#org08313ab">6. Why should I not upload by data here?</a></li>
+<li><a href="#orgc4d533c">7. How does the public sequence resource work?</a></li>
+<li><a href="#org345c019">8. Who uses the public sequence resource?</a></li>
+<li><a href="#orgd764100">9. How can I contribute?</a></li>
+<li><a href="#orgd3c405f">10. Is this about open data?</a></li>
+<li><a href="#orga0a0123">11. Is this about free software?</a></li>
+<li><a href="#org37a9339">12. How do I upload raw data?</a></li>
+<li><a href="#org7e7ca3e">13. How do I change metadata?</a></li>
+<li><a href="#org8a0a2be">14. How do I change the work flows?</a></li>
+<li><a href="#orgd811284">15. How do I change the source code?</a></li>
+<li><a href="#org8c01c1e">16. Should I choose CC-BY or CC0?</a></li>
+<li><a href="#orgae29ab5">17. Are there also variant in the RDF databases? *</a></li>
+<li><a href="#org2fe4b9b">18. How do I deal with private data and privacy?</a></li>
+<li><a href="#orgeb974e3">19. Do you have any checks or concerns if human sequence accidentally submitted to your service as part of a fastq? *</a></li>
+<li><a href="#orgd6002f0">20. Does PubSeq support only SARS-CoV-2 data? *</a></li>
+<li><a href="#orgdfdd5c4">21. How do I communicate with you?</a></li>
+<li><a href="#orgdde7304">22. Who are the sponsors?</a></li>
+</ul>
+</div>
+</div>
+
+<div id="outline-container-org99c4553" class="outline-2">
+<h2 id="org99c4553"><span class="section-number-2">1</span> What is the 'public sequence resource' about?</h2>
+<div class="outline-text-2" id="text-1">
+<p>
+The <b>public sequence resource</b> aims to provide a generic and useful
+resource for COVID-19 research. The focus is on providing the best
+possible sequence data with associated metadata that can be used for
+sequence comparison and protein prediction.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orga3b6187" class="outline-2">
+<h2 id="orga3b6187"><span class="section-number-2">2</span> Presentations</h2>
+<div class="outline-text-2" id="text-2">
+<p>
+We presented at the BOSC 2020 Have a look at the <a href="https://bcc2020.sched.com/event/coLw">video</a> (<a href="https://drive.google.com/file/d/1skXHwVKM_gl73-_4giYIOQ1IlC5X5uBo/view?usp=sharing">alternative
+link</a>) and the <a href="https://drive.google.com/file/d/1vyEgfvSqhM9yIwWZ6Iys-QxhxtVxPSdp/view?usp=sharing">poster</a>.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orgeb109f2" class="outline-2">
+<h2 id="orgeb109f2"><span class="section-number-2">3</span> Who created the public sequence resource?</h2>
+<div class="outline-text-2" id="text-3">
+<p>
+The <b>public sequence resource</b> is an initiative by <a href="https://github.com/arvados/bh20-seq-resource/graphs/contributors">bioinformatics</a> and
+ontology experts who want to create something agile and useful for the
+wider research community. The initiative started at the COVID-19
+biohackathon in April 2020 and is ongoing. The main project drivers
+are Pjotr Prins (UTHSC), Peter Amstutz (Curii), Andrea Guarracino
+(University of Rome Tor Vergata), Michael Crusoe (Common Workflow
+Language), Thomas Liener (consultant, formerly EBI), Erik Garrison
+(UCSC) and Jerven Bolleman (Swiss Institute of Bioinformatics).
+</p>
+
+<p>
+Notably, as this is a free software initiative, the project represents
+major work by hundreds of software developers and ontology and data
+wrangling experts. Thank you everyone!
+</p>
+</div>
+</div>
+
+<div id="outline-container-org631e2c7" class="outline-2">
+<h2 id="org631e2c7"><span class="section-number-2">4</span> How does the public sequence resource compare to other data resources?</h2>
+<div class="outline-text-2" id="text-4">
+<p>
+The short version is that we use state-of-the-art practices in
+bioinformatics using agile methods. Unlike the resources from large
+institutes we can improve things on a dime and anyone can contribute
+to building out this resource! Sequences from GenBank, EBI/ENA and
+others are regularly added to PubSeq. We encourage people to everyone
+to submit on PubSeq because of its superior live tooling and metadata
+support (see the next question).
+</p>
+
+<p>
+Importantly: all data is published under either the <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons
+4.0 attribution license</a> or the <a href="https://creativecommons.org/share-your-work/public-domain/cc0/">CC0 “No Rights Reserved” license</a> which
+means it data can be published and workflows can run in public
+environments allowing for improved access for research and
+reproducible results. This contrasts with some other public resources,
+such as GISAID.
+</p>
+</div>
+</div>
+
+<div id="outline-container-org319a852" class="outline-2">
+<h2 id="org319a852"><span class="section-number-2">5</span> Why should I upload my data here?</h2>
+<div class="outline-text-2" id="text-5">
+<ol class="org-ol">
+<li>We champion truly shareable data without licensing restrictions - with proper
+attribution</li>
+<li>We provide full metadata support using state-of-the-art ontology's</li>
+<li>We provide a web-based sequence uploader and a command-line version
+for bulk uploads</li>
+<li>We provide a live SPARQL end-point for all metadata</li>
+<li>We provide free data analysis and sequence comparison triggered on data upload</li>
+<li>We do real work for you, with this <a href="https://workbench.lugli.arvadosapi.com/container_requests/lugli-xvhdp-bhhk4nxx1lch5od">link</a> you can see the last
+run took 5.5 hours!</li>
+<li>We provide free downloads of all computed output</li>
+<li>There is no need to set up pipelines and/or compute clusters</li>
+<li>All workflows get triggered on uploading a new sequence</li>
+<li>When someone (you?) improves the software/workflows and everyone benefits</li>
+<li>Your data gets automatically integrated with the Swiss Institure of
+Bioinformatics COVID-19 knowledge base
+<a href="https://covid-19-sparql.expasy.org/">https://covid-19-sparql.expasy.org/</a> (Elixir Switzerland)</li>
+<li>Your data will be used to develop drug targets</li>
+</ol>
+
+<p>
+Finally, if you upload your data here we have workflows that output
+formatted data suitable for <a href="http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part6">uploading to EBI resources</a> (and soon
+others). Uploading your data here get your data ready for upload to
+multiple resources.
+</p>
+</div>
+</div>
+
+<div id="outline-container-org08313ab" class="outline-2">
+<h2 id="org08313ab"><span class="section-number-2">6</span> Why should I not upload by data here?</h2>
+<div class="outline-text-2" id="text-6">
+<p>
+Funny question. There are only good reasons to upload your data here
+and make it available to the widest audience possible.
+</p>
+
+<p>
+In fact, you can upload your data here as well as to other
+resources. It is your data after all. No one can prevent you from
+uploading your data to multiple resources.
+</p>
+
+<p>
+We recommend uploading to EBI and NCBI resources using our data
+conversion tools. It means you only enter data once and make the
+process smooth. You can also use our command line data uploader
+for bulk uploads!
+</p>
+</div>
+</div>
+
+<div id="outline-container-orgc4d533c" class="outline-2">
+<h2 id="orgc4d533c"><span class="section-number-2">7</span> How does the public sequence resource work?</h2>
+<div class="outline-text-2" id="text-7">
+<p>
+On uploading a sequence with metadata it will automatically be
+processed and incorporated into the public pangenome with metadata
+using workflows from the High Performance Open Biology Lab defined
+<a href="https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate">here</a>.
+</p>
+</div>
+</div>
+
+<div id="outline-container-org345c019" class="outline-2">
+<h2 id="org345c019"><span class="section-number-2">8</span> Who uses the public sequence resource?</h2>
+<div class="outline-text-2" id="text-8">
+<p>
+The Swiss Institute of Bioinformatics has included this data in
+<a href="https://covid-19-sparql.expasy.org/">https://covid-19-sparql.expasy.org/</a> and made it part of <a href="https://www.uniprot.org/">Uniprot</a>.
+</p>
+
+<p>
+The Pantograph <a href="https://graph-genome.github.io/">viewer</a> uses PubSeq data for their visualisations.
+</p>
+
+<p>
+<a href="https://uthsc.edu">UTHSC</a> (USA), <a href="https://www.esr.cri.nz/">ESR</a> (New Zealand) and <a href="https://www.ornl.gov/news/ornl-fight-against-covid-19">ORNL</a> (USA) use COVID-19 PubSeq data
+for monitoring, protein prediction and drug development.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orgd764100" class="outline-2">
+<h2 id="orgd764100"><span class="section-number-2">9</span> How can I contribute?</h2>
+<div class="outline-text-2" id="text-9">
+<p>
+You can contribute by submitting sequences, updating metadata, submit
+issues on our issue tracker, and more importantly add functionality.
+See 'How do I change the source code' below. Read through our online
+documentation at <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a> as a starting
+point.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orgd3c405f" class="outline-2">
+<h2 id="orgd3c405f"><span class="section-number-2">10</span> Is this about open data?</h2>
+<div class="outline-text-2" id="text-10">
+<p>
+All data is published under a <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons 4.0 attribution license</a>
+(CC-BY-4.0). You can download the raw and published (GFA/RDF/FASTA)
+data and store it for further processing.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orga0a0123" class="outline-2">
+<h2 id="orga0a0123"><span class="section-number-2">11</span> Is this about free software?</h2>
+<div class="outline-text-2" id="text-11">
+<p>
+Absolutely. Free software allows for fully reproducible pipelines. You
+can take our workflows and data and run it elsewhere!
+</p>
+</div>
+</div>
+
+<div id="outline-container-org37a9339" class="outline-2">
+<h2 id="org37a9339"><span class="section-number-2">12</span> How do I upload raw data?</h2>
+<div class="outline-text-2" id="text-12">
+<p>
+We are preparing raw sequence data pipelines (fastq and BAM). The
+reason is that we want the best data possible for downstream analysis
+(including protein prediction and test development). The current
+approach where people publish final sequences of SARS-CoV-2 is lacking
+because it hides how this sequence was created. For reasons of
+reproducible and improved results we want/need to work with the raw
+sequence reads (both short reads and long reads) and take alternative
+assembly variations into consideration. This is all work in progress.
+</p>
+</div>
+</div>
+
+<div id="outline-container-org7e7ca3e" class="outline-2">
+<h2 id="org7e7ca3e"><span class="section-number-2">13</span> How do I change metadata?</h2>
+<div class="outline-text-2" id="text-13">
+<p>
+See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a>!
+</p>
+</div>
+</div>
+
+<div id="outline-container-org8a0a2be" class="outline-2">
+<h2 id="org8a0a2be"><span class="section-number-2">14</span> How do I change the work flows?</h2>
+<div class="outline-text-2" id="text-14">
+<p>
+Workflows are on <a href="https://github.com/arvados/bh20-seq-resource/tree/master/workflows">github</a> and can be modified. See also the BLOG
+<a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a> on workflows.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orgd811284" class="outline-2">
+<h2 id="orgd811284"><span class="section-number-2">15</span> How do I change the source code?</h2>
+<div class="outline-text-2" id="text-15">
+<p>
+Go to our <a href="https://github.com/arvados/bh20-seq-resource">source code repositories</a>, fork/clone the repository, change
+something and submit a <a href="https://github.com/arvados/bh20-seq-resource/pulls">pull request</a> (PR). That easy! Check out how
+many PRs we already merged.
+</p>
+</div>
+</div>
+
+<div id="outline-container-org8c01c1e" class="outline-2">
+<h2 id="org8c01c1e"><span class="section-number-2">16</span> Should I choose CC-BY or CC0?</h2>
+<div class="outline-text-2" id="text-16">
+<p>
+Restrictive data licenses are hampering data sharing and reproducible
+research. CC0 is the preferred license because it gives researchers
+the most freedom. Since we provide metadata there is no reason for
+others not to honour your work. We also provide CC-BY as an option
+because we know people like the attribution clause.
+</p>
+
+<p>
+In all honesty: we prefer both data and software to be free.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orgae29ab5" class="outline-2">
+<h2 id="orgae29ab5"><span class="section-number-2">17</span> Are there also variant in the RDF databases? *</h2>
+<div class="outline-text-2" id="text-17">
+<p>
+We do output a RDF file with the pangenome built in, and you can parse it because it has variants implicitly.
+</p>
+
+<p>
+We are also writing tools to generate VCF files directly from the pangenome.
+</p>
+</div>
+</div>
+
+<div id="outline-container-org2fe4b9b" class="outline-2">
+<h2 id="org2fe4b9b"><span class="section-number-2">18</span> How do I deal with private data and privacy?</h2>
+<div class="outline-text-2" id="text-18">
+<p>
+A public sequence resource is about public data. Metadata can refer to
+private data. You can use your own (anonymous) identifiers. We also
+plan to combine identifiers with clinical data stored securely at
+<a href="https://redcap-covid19.elixir-luxembourg.org/redcap/">REDCap</a>. See the relevant <a href="https://github.com/arvados/bh20-seq-resource/issues/21">tracker</a> for more information and contributing.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orgeb974e3" class="outline-2">
+<h2 id="orgeb974e3"><span class="section-number-2">19</span> Do you have any checks or concerns if human sequence accidentally submitted to your service as part of a fastq? *</h2>
+<div class="outline-text-2" id="text-19">
+<p>
+We are planning to remove reads that match the human reference.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orgd6002f0" class="outline-2">
+<h2 id="orgd6002f0"><span class="section-number-2">20</span> Does PubSeq support only SARS-CoV-2 data? *</h2>
+<div class="outline-text-2" id="text-20">
+<p>
+To date, PubSeq is a resource specific to SARS-CoV-2, but we are designing it to be able to support other species in the future.
+</p>
+</div>
+</div>
+
+
+<div id="outline-container-orgdfdd5c4" class="outline-2">
+<h2 id="orgdfdd5c4"><span class="section-number-2">21</span> How do I communicate with you?</h2>
+<div class="outline-text-2" id="text-21">
+<p>
+We use a <a href="https://gitter.im/arvados/pubseq?utm_source=share-link&amp;utm_medium=link&amp;utm_campaign=share-link">gitter channel</a> you can join.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orgdde7304" class="outline-2">
+<h2 id="orgdde7304"><span class="section-number-2">22</span> Who are the sponsors?</h2>
+<div class="outline-text-2" id="text-22">
+<p>
+The main sponsors are listed in the footer. In addition to the time
+generously donated by many contributors we also acknowledge Amazon AWS
+for donating COVID-19 related compute time.
+</p>
+</div>
+</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 2020-07-18 Sat 03:27</small>.
+<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 2020-08-22 Sat 03:48</small>.
</div>
</body>
</html>
diff --git a/doc/web/about.org b/doc/web/about.org
index 29a80bf..5f864e9 100644
--- a/doc/web/about.org
+++ b/doc/web/about.org
@@ -3,6 +3,7 @@
* Table of Contents :TOC:noexport:
- [[#what-is-the-public-sequence-resource-about][What is the 'public sequence resource' about?]]
+ - [[#presentations][Presentations]]
- [[#who-created-the-public-sequence-resource][Who created the public sequence resource?]]
- [[#how-does-the-public-sequence-resource-compare-to-other-data-resources][How does the public sequence resource compare to other data resources?]]
- [[#why-should-i-upload-my-data-here][Why should I upload my data here?]]
@@ -17,10 +18,10 @@
- [[#how-do-i-change-the-work-flows][How do I change the work flows?]]
- [[#how-do-i-change-the-source-code][How do I change the source code?]]
- [[#should-i-choose-cc-by-or-cc0][Should I choose CC-BY or CC0?]]
- - [[#are-there-also-variant-in-the-RDF-databases]][Are there also variant in the RDF databases?]
+ - [[#are-there-also-variant-in-the-rdf-databases-][Are there also variant in the RDF databases? *]]
- [[#how-do-i-deal-with-private-data-and-privacy][How do I deal with private data and privacy?]]
- - [[#do-you-have-any-checks-or-concerns-if-human-sequence-accidentally-submitted-to-your-service-as-part-of-a-fastq][Do you have any checks or concerns if human sequence accidentally submitted to your service as part of a fastq?]
- - [[#does-PubSeq-support-only-SARS-CoV-2=data]][Does PubSeq support only SARS-CoV-2 data?]
+ - [[#do-you-have-any-checks-or-concerns-if-human-sequence-accidentally-submitted-to-your-service-as-part-of-a-fastq-][Do you have any checks or concerns if human sequence accidentally submitted to your service as part of a fastq? *]]
+ - [[#does-pubseq-support-only-sars-cov-2-data-][Does PubSeq support only SARS-CoV-2 data? *]]
- [[#how-do-i-communicate-with-you][How do I communicate with you?]]
- [[#who-are-the-sponsors][Who are the sponsors?]]
@@ -31,7 +32,10 @@ resource for COVID-19 research. The focus is on providing the best
possible sequence data with associated metadata that can be used for
sequence comparison and protein prediction.
-We were at the *Bioinformatics Community Conference 2020*! Have a look at the [[https://bcc2020.sched.com/event/coLw]][video talk] ([[https://drive.google.com/file/d/1skXHwVKM_gl73-_4giYIOQ1IlC5X5uBo/view?usp=sharing]][alternative link]) and the [[https://drive.google.com/file/d/1vyEgfvSqhM9yIwWZ6Iys-QxhxtVxPSdp/view?usp=sharing]][poster].
+* Presentations
+
+We presented at the BOSC 2020 Have a look at the [[https://bcc2020.sched.com/event/coLw][video]] ([[https://drive.google.com/file/d/1skXHwVKM_gl73-_4giYIOQ1IlC5X5uBo/view?usp=sharing][alternative
+link]]) and the [[https://drive.google.com/file/d/1vyEgfvSqhM9yIwWZ6Iys-QxhxtVxPSdp/view?usp=sharing][poster]].
* Who created the public sequence resource?
generated by cgit v1.2.3 (git 2.44.0) at 2024-05-19 11:14:16 +0000