From 8e052cb7355eed7ce4d7075b23c9b0439285f84e Mon Sep 17 00:00:00 2001
From: AndreaGuarracino
Date: Sun, 26 Jul 2020 18:02:41 +0200
Subject: updated org files, removing unuseful information and adding the
BCC2020 video talk and poster links in the about page
---
doc/blog/using-covid-19-pubseq-part2.html | 33 +-
doc/blog/using-covid-19-pubseq-part2.org | 25 +-
doc/blog/using-covid-19-pubseq-part3.html | 2 +-
doc/blog/using-covid-19-pubseq-part3.org | 2 +-
doc/web/about.html | 1489 ++++++++++++++++++-----------
doc/web/about.org | 2 +
6 files changed, 960 insertions(+), 593 deletions(-)
diff --git a/doc/blog/using-covid-19-pubseq-part2.html b/doc/blog/using-covid-19-pubseq-part2.html
index c047441..c041ebe 100644
--- a/doc/blog/using-covid-19-pubseq-part2.html
+++ b/doc/blog/using-covid-19-pubseq-part2.html
@@ -259,39 +259,12 @@ for the JavaScript code in this tag.
</ul>
</div>
</div>
-<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 id="outline-container-org7942167" class="outline-2">
<h2 id="org7942167"><span class="section-number-2">1</span> Finding output of workflows</h2>
<div class="outline-text-2" id="text-1">
-<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-org0022bbe" class="outline-2">
-<h2 id="org0022bbe"><span class="section-number-2">2</span> Introduction</h2>
-<div class="outline-text-2" id="text-2">
-<p>
+ <p>
We are using Arvados to run common workflow language (CWL) pipelines.
The most recent output is on display on a <a href="https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca">web page</a> (with time stamp)
and a full list is generated <a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/">here</a>. It is nice to start up, but for
@@ -302,7 +275,7 @@ want to wade through thousands of output files!
</div>
<div id="outline-container-org3929710" class="outline-2">
-<h2 id="org3929710"><span class="section-number-2">3</span> The Arvados file interface</h2>
+<h2 id="org3929710"><span class="section-number-2">2</span> The Arvados file interface</h2>
<div class="outline-text-2" id="text-3">
<p>
Arvados has the web server, but it also has a REST API and associated
@@ -384,7 +357,7 @@ arv-get 2be6af7b4741f2a5c5f8ff2bc6152d73+1955623+Ab9ad65d7fe958a053b3a57d545839d
</div>
<div id="outline-container-orgc4dba6e" class="outline-2">
-<h2 id="orgc4dba6e"><span class="section-number-2">4</span> Using the Arvados API</h2>
+<h2 id="orgc4dba6e"><span class="section-number-2">3</span> TODO Using the Arvados API</h2>
</div>
</div>
<div id="postamble" class="status">
diff --git a/doc/blog/using-covid-19-pubseq-part2.org b/doc/blog/using-covid-19-pubseq-part2.org
index d2a1cbc..349fd06 100644
--- a/doc/blog/using-covid-19-pubseq-part2.org
+++ b/doc/blog/using-covid-19-pubseq-part2.org
@@ -8,36 +8,13 @@
#+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
-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.
-
-* Introduction
-
We are using Arvados to run common workflow language (CWL) pipelines.
The most recent output is on display on a [[https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca][web page]] (with time stamp)
and a full list is generated [[https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/][here]]. It is nice to start up, but for
@@ -81,4 +58,4 @@ its listed UUID:
: arv-get 2be6af7b4741f2a5c5f8ff2bc6152d73+1955623+Ab9ad65d7fe958a053b3a57d545839de18290843a@5ed7f3c5
-* Using the Arvados API
+* TODO Using the Arvados API
diff --git a/doc/blog/using-covid-19-pubseq-part3.html b/doc/blog/using-covid-19-pubseq-part3.html
index 91879b0..df4a286 100644
--- a/doc/blog/using-covid-19-pubseq-part3.html
+++ b/doc/blog/using-covid-19-pubseq-part3.html
@@ -625,7 +625,7 @@ The web interface using this exact same script so it should just work
<h3 id="org39adf09"><span class="section-number-3">6.2</span> Example: uploading bulk GenBank sequences</h3>
<div class="outline-text-3" id="text-6-2">
<p>
-We also use above script to bulk upload GenBank sequences with a <a href="https://github.com/arvados/bh20-seq-resource/blob/master/scripts/from_genbank_to_fasta_and_yaml.py">FASTA
+We also use above script to bulk upload GenBank sequences with a <a href="https://github.com/arvados/bh20-seq-resource/blob/master/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py">FASTA
and YAML</a> extractor specific for GenBank. This means that the steps we
took above for uploading a GenBank sequence are already automated.
</p>
diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org
index 03f37ab..e8fee36 100644
--- a/doc/blog/using-covid-19-pubseq-part3.org
+++ b/doc/blog/using-covid-19-pubseq-part3.org
@@ -234,6 +234,6 @@ The web interface using this exact same script so it should just work
** Example: uploading bulk GenBank sequences
-We also use above script to bulk upload GenBank sequences with a [[https://github.com/arvados/bh20-seq-resource/blob/master/scripts/from_genbank_to_fasta_and_yaml.py][FASTA
+We also use above script to bulk upload GenBank sequences with a [[https://github.com/arvados/bh20-seq-resource/blob/master/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py][FASTA
and YAML]] extractor specific for GenBank. This means that the steps we
took above for uploading a GenBank sequence are already automated.
diff --git a/doc/web/about.html b/doc/web/about.html
index dfd4252..c971a4e 100644
--- a/doc/web/about.html
+++ b/doc/web/about.html
@@ -1,549 +1,964 @@
<?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;
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- pre.src-asymptote:before { content: 'Asymptote'; }
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- /* pre.src-C++ doesn't work in CSS */
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- /* additional languages in org.el's org-babel-load-languages alist */
- pre.src-forth:before { content: 'Forth'; }
- pre.src-io:before { content: 'IO'; }
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- 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
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- pre.src-bash:before { content: 'bash'; }
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- /* add a generic configuration mode; LaTeX export needs an additional
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- display: table;
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-
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-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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- }
-/*]]>*///-->
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+ <!-- 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';
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</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>
-</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&utm_medium=link&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="#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&utm_medium=link&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>
</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 2020-07-18 Sat 03:27</small>.
</div>
</body>
</html>
diff --git a/doc/web/about.org b/doc/web/about.org
index 39fb667..8a954bb 100644
--- a/doc/web/about.org
+++ b/doc/web/about.org
@@ -28,6 +28,8 @@ 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].
+
* Who created the public sequence resource?
The *public sequence resource* is an initiative by [[https://github.com/arvados/bh20-seq-resource/graphs/contributors][bioinformatics]] and
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