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authorPjotr Prins2020-05-28 08:42:05 -0500
committerPjotr Prins2020-05-28 08:42:05 -0500
commitd12a580db8146f8ebc511119698e63e3a5de0147 (patch)
tree9e9108aba5423edcfd470fd4df7b181990168e3f /doc/web/about.html
parent76ba8143c576b99fba404dd0c053e1e77da9e366 (diff)
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Added Who uses the public sequence resource? to the FAQ
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@@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
-<!-- 2020-05-27 Wed 07:08 -->
+<!-- 2020-05-28 Thu 08:40 -->
<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>
@@ -247,28 +247,29 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
-<li><a href="#org2fe6bec">1. What is the 'public sequence resource' about?</a></li>
-<li><a href="#org9946c6e">2. Who created the public sequence resource?</a></li>
-<li><a href="#org947d1d7">3. How does the public sequence resource compare to other data resources?</a></li>
-<li><a href="#org84cfcc3">4. Why should I upload my data here?</a></li>
-<li><a href="#orgf0aeec4">5. Why should I not upload by data here?</a></li>
-<li><a href="#orgdfa56b7">6. How does the public sequence resource work?</a></li>
-<li><a href="#org18d42bb">7. Is this about open data?</a></li>
-<li><a href="#orge4f73e2">8. Is this about free software?</a></li>
-<li><a href="#org2329f25">9. How do I upload raw data?</a></li>
-<li><a href="#org0a77739">10. How do I change metadata?</a></li>
-<li><a href="#orgc390505">11. How do I change the work flows?</a></li>
-<li><a href="#org22e65a5">12. How do I change the source code?</a></li>
-<li><a href="#org414bffe">13. Should I choose CC-BY or CC0?</a></li>
-<li><a href="#orga36bf3d">14. How do I deal with private data and privacy?</a></li>
-<li><a href="#org9f4676e">15. How do I communicate with you?</a></li>
-<li><a href="#org9bb4341">16. Who are the sponsors?</a></li>
+<li><a href="#org43f7738">1. What is the 'public sequence resource' about?</a></li>
+<li><a href="#orgde86ccd">2. Who created the public sequence resource?</a></li>
+<li><a href="#orgdd37e45">3. How does the public sequence resource compare to other data resources?</a></li>
+<li><a href="#org9edb5aa">4. Why should I upload my data here?</a></li>
+<li><a href="#orgfbf8cae">5. Why should I not upload by data here?</a></li>
+<li><a href="#org847ae99">6. How does the public sequence resource work?</a></li>
+<li><a href="#orgf5b82cd">7. Who uses the public sequence resource?</a></li>
+<li><a href="#orgb98ff9a">8. Is this about open data?</a></li>
+<li><a href="#org1bd01df">9. Is this about free software?</a></li>
+<li><a href="#org9b933c4">10. How do I upload raw data?</a></li>
+<li><a href="#org3425b34">11. How do I change metadata?</a></li>
+<li><a href="#org7ef551b">12. How do I change the work flows?</a></li>
+<li><a href="#org2bdd0eb">13. How do I change the source code?</a></li>
+<li><a href="#org0468035">14. Should I choose CC-BY or CC0?</a></li>
+<li><a href="#org246712c">15. How do I deal with private data and privacy?</a></li>
+<li><a href="#org29eb659">16. How do I communicate with you?</a></li>
+<li><a href="#orgce9d1ee">17. Who are the sponsors?</a></li>
</ul>
</div>
</div>
-<div id="outline-container-org2fe6bec" class="outline-2">
-<h2 id="org2fe6bec"><span class="section-number-2">1</span> What is the 'public sequence resource' about?</h2>
+<div id="outline-container-org43f7738" class="outline-2">
+<h2 id="org43f7738"><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
@@ -279,8 +280,8 @@ sequence comparison and protein prediction.
</div>
</div>
-<div id="outline-container-org9946c6e" class="outline-2">
-<h2 id="org9946c6e"><span class="section-number-2">2</span> Who created the public sequence resource?</h2>
+<div id="outline-container-orgde86ccd" class="outline-2">
+<h2 id="orgde86ccd"><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
@@ -300,8 +301,8 @@ wrangling experts. Thank you everyone!
</div>
</div>
-<div id="outline-container-org947d1d7" class="outline-2">
-<h2 id="org947d1d7"><span class="section-number-2">3</span> How does the public sequence resource compare to other data resources?</h2>
+<div id="outline-container-orgdd37e45" class="outline-2">
+<h2 id="orgdd37e45"><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
@@ -320,8 +321,8 @@ public resources, including GISAID.
</div>
</div>
-<div id="outline-container-org84cfcc3" class="outline-2">
-<h2 id="org84cfcc3"><span class="section-number-2">4</span> Why should I upload my data here?</h2>
+<div id="outline-container-org9edb5aa" class="outline-2">
+<h2 id="org9edb5aa"><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
@@ -338,6 +339,7 @@ for bulk uploads</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>
@@ -349,8 +351,8 @@ multiple resources.
</div>
</div>
-<div id="outline-container-orgf0aeec4" class="outline-2">
-<h2 id="orgf0aeec4"><span class="section-number-2">5</span> Why should I not upload by data here?</h2>
+<div id="outline-container-orgfbf8cae" class="outline-2">
+<h2 id="orgfbf8cae"><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
@@ -372,8 +374,8 @@ for bulk uploads!
</div>
</div>
-<div id="outline-container-orgdfa56b7" class="outline-2">
-<h2 id="orgdfa56b7"><span class="section-number-2">6</span> How does the public sequence resource work?</h2>
+<div id="outline-container-org847ae99" class="outline-2">
+<h2 id="org847ae99"><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
@@ -384,10 +386,25 @@ using workflows from the High Performance Open Biology Lab defined
</div>
</div>
-<div id="outline-container-org18d42bb" class="outline-2">
-<h2 id="org18d42bb"><span class="section-number-2">7</span> Is this about open data?</h2>
+<div id="outline-container-orgf5b82cd" class="outline-2">
+<h2 id="orgf5b82cd"><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>
+<a href="https://uthsc.edu">UTHSC</a> and <a href="https://www.ornl.gov/news/ornl-fight-against-covid-19">ORNL</a> use COVID-19 PubSeq data for protein prediction and
+drug development.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orgb98ff9a" class="outline-2">
+<h2 id="orgb98ff9a"><span class="section-number-2">8</span> Is this about open data?</h2>
+<div class="outline-text-2" id="text-8">
+<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.
@@ -395,9 +412,9 @@ data and store it for further processing.
</div>
</div>
-<div id="outline-container-orge4f73e2" class="outline-2">
-<h2 id="orge4f73e2"><span class="section-number-2">8</span> Is this about free software?</h2>
-<div class="outline-text-2" id="text-8">
+<div id="outline-container-org1bd01df" class="outline-2">
+<h2 id="org1bd01df"><span class="section-number-2">9</span> Is this about free software?</h2>
+<div class="outline-text-2" id="text-9">
<p>
Absolutely. Free software allows for fully reproducible pipelines. You
can take our workflows and data and run it elsewhere!
@@ -405,9 +422,9 @@ can take our workflows and data and run it elsewhere!
</div>
</div>
-<div id="outline-container-org2329f25" class="outline-2">
-<h2 id="org2329f25"><span class="section-number-2">9</span> How do I upload raw data?</h2>
-<div class="outline-text-2" id="text-9">
+<div id="outline-container-org9b933c4" class="outline-2">
+<h2 id="org9b933c4"><span class="section-number-2">10</span> How do I upload raw data?</h2>
+<div class="outline-text-2" id="text-10">
<p>
We are preparing raw sequence data pipelines (fastq and BAM). The
reason is that we want the best data possible for downstream analysis
@@ -421,27 +438,27 @@ assembly variations into consideration. This is all work in progress.
</div>
</div>
-<div id="outline-container-org0a77739" class="outline-2">
-<h2 id="org0a77739"><span class="section-number-2">10</span> How do I change metadata?</h2>
-<div class="outline-text-2" id="text-10">
+<div id="outline-container-org3425b34" class="outline-2">
+<h2 id="org3425b34"><span class="section-number-2">11</span> How do I change metadata?</h2>
+<div class="outline-text-2" id="text-11">
<p>
See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a>!
</p>
</div>
</div>
-<div id="outline-container-orgc390505" class="outline-2">
-<h2 id="orgc390505"><span class="section-number-2">11</span> How do I change the work flows?</h2>
-<div class="outline-text-2" id="text-11">
+<div id="outline-container-org7ef551b" class="outline-2">
+<h2 id="org7ef551b"><span class="section-number-2">12</span> How do I change the work flows?</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-org22e65a5" class="outline-2">
-<h2 id="org22e65a5"><span class="section-number-2">12</span> How do I change the source code?</h2>
-<div class="outline-text-2" id="text-12">
+<div id="outline-container-org2bdd0eb" class="outline-2">
+<h2 id="org2bdd0eb"><span class="section-number-2">13</span> How do I change the source code?</h2>
+<div class="outline-text-2" id="text-13">
<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
@@ -450,9 +467,9 @@ many PRs we already merged.
</div>
</div>
-<div id="outline-container-org414bffe" class="outline-2">
-<h2 id="org414bffe"><span class="section-number-2">13</span> Should I choose CC-BY or CC0?</h2>
-<div class="outline-text-2" id="text-13">
+<div id="outline-container-org0468035" class="outline-2">
+<h2 id="org0468035"><span class="section-number-2">14</span> Should I choose CC-BY or CC0?</h2>
+<div class="outline-text-2" id="text-14">
<p>
Restrictive data licenses are hampering data sharing and reproducible
research. CC0 is the preferred license because it gives researchers
@@ -467,9 +484,9 @@ In all honesty: we prefer both data and software to be free.
</div>
</div>
-<div id="outline-container-orga36bf3d" class="outline-2">
-<h2 id="orga36bf3d"><span class="section-number-2">14</span> How do I deal with private data and privacy?</h2>
-<div class="outline-text-2" id="text-14">
+<div id="outline-container-org246712c" class="outline-2">
+<h2 id="org246712c"><span class="section-number-2">15</span> How do I deal with private data and privacy?</h2>
+<div class="outline-text-2" id="text-15">
<p>
A public sequence resource is about public data. Metadata can refer to
private data. You can use your own (anonymous) identifiers. We also
@@ -479,18 +496,18 @@ plan to combine identifiers with clinical data stored securely at
</div>
</div>
-<div id="outline-container-org9f4676e" class="outline-2">
-<h2 id="org9f4676e"><span class="section-number-2">15</span> How do I communicate with you?</h2>
-<div class="outline-text-2" id="text-15">
+<div id="outline-container-org29eb659" class="outline-2">
+<h2 id="org29eb659"><span class="section-number-2">16</span> How do I communicate with you?</h2>
+<div class="outline-text-2" id="text-16">
<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-org9bb4341" class="outline-2">
-<h2 id="org9bb4341"><span class="section-number-2">16</span> Who are the sponsors?</h2>
-<div class="outline-text-2" id="text-16">
+<div id="outline-container-orgce9d1ee" class="outline-2">
+<h2 id="orgce9d1ee"><span class="section-number-2">17</span> Who are the sponsors?</h2>
+<div class="outline-text-2" id="text-17">
<p>
The main sponsors are listed in the footer. In addition to the time
generously donated by many contributors we also acknowledge Amazon AWS
@@ -500,7 +517,7 @@ for donating COVID-19 related compute time.
</div>
</div>
<div id="postamble" class="status">
-<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-05-27 Wed 07:08</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 2020-05-28 Thu 08:40</small>.
</div>
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generated by cgit v1.2.3 (git 2.45.2) at 2024-11-11 11:33:12 +0000