aboutsummaryrefslogtreecommitdiff
path: root/doc
diff options
context:
space:
mode:
authorPjotr Prins2020-08-22 11:04:56 +0100
committerPjotr Prins2020-08-22 11:04:56 +0100
commitcab2f4ca70c08d9f44442ba01bdfa5639017084b (patch)
treec4d52887fc9b6314d37e45f92c90235a7d9c55c3 /doc
parented0bef1505c50c49479d794bbac6ad2fd2a99db1 (diff)
downloadbh20-seq-resource-cab2f4ca70c08d9f44442ba01bdfa5639017084b.tar.gz
bh20-seq-resource-cab2f4ca70c08d9f44442ba01bdfa5639017084b.tar.lz
bh20-seq-resource-cab2f4ca70c08d9f44442ba01bdfa5639017084b.zip
Repositioning content
Diffstat (limited to 'doc')
-rw-r--r--doc/web/about.html138
-rw-r--r--doc/web/about.org2
-rw-r--r--doc/web/contact.html286
-rw-r--r--doc/web/contact.org20
4 files changed, 376 insertions, 70 deletions
diff --git a/doc/web/about.html b/doc/web/about.html
index a4ab186..f6d1761 100644
--- a/doc/web/about.html
+++ b/doc/web/about.html
@@ -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>
-<!-- 2020-08-22 Sat 03:48 -->
+<!-- 2020-08-22 Sat 04:42 -->
<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>
@@ -234,34 +234,34 @@ for the JavaScript code in this tag.
<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>
+<li><a href="#org43f5d1e">1. What is the 'public sequence resource' about?</a></li>
+<li><a href="#org706e720">2. Presentations</a></li>
+<li><a href="#orge3b0114">3. Who created the public sequence resource?</a></li>
+<li><a href="#org6b86244">4. How does the public sequence resource compare to other data resources?</a></li>
+<li><a href="#org1030148">5. Why should I upload my data here?</a></li>
+<li><a href="#orgdf90c2c">6. Why should I not upload by data here?</a></li>
+<li><a href="#org3294b2e">7. How does the public sequence resource work?</a></li>
+<li><a href="#orgfca20f4">8. Who uses the public sequence resource?</a></li>
+<li><a href="#org0f602e3">9. How can I contribute?</a></li>
+<li><a href="#org441ff7c">10. Is this about open data?</a></li>
+<li><a href="#org42ceb37">11. Is this about free software?</a></li>
+<li><a href="#org1c3275d">12. How do I upload raw data?</a></li>
+<li><a href="#org7cb05f2">13. How do I change metadata?</a></li>
+<li><a href="#org875e3c9">14. How do I change the work flows?</a></li>
+<li><a href="#orgf485768">15. How do I change the source code?</a></li>
+<li><a href="#orgae7cb27">16. Should I choose CC-BY or CC0?</a></li>
+<li><a href="#org765d1a7">17. Are there also variant in the RDF databases? *</a></li>
+<li><a href="#org66263d5">18. How do I deal with private data and privacy?</a></li>
+<li><a href="#org6cd833b">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="#orge8f395f">20. Does PubSeq support only SARS-CoV-2 data? *</a></li>
+<li><a href="#org8f5ae93">21. How do I communicate with you?</a></li>
+<li><a href="#org15ea9a8">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 id="outline-container-org43f5d1e" class="outline-2">
+<h2 id="org43f5d1e"><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
@@ -272,8 +272,8 @@ sequence comparison and protein prediction.
</div>
</div>
-<div id="outline-container-orga3b6187" class="outline-2">
-<h2 id="orga3b6187"><span class="section-number-2">2</span> Presentations</h2>
+<div id="outline-container-org706e720" class="outline-2">
+<h2 id="org706e720"><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
@@ -282,8 +282,8 @@ link</a>) and the <a href="https://drive.google.com/file/d/1vyEgfvSqhM9yIwWZ6Iys
</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 id="outline-container-orge3b0114" class="outline-2">
+<h2 id="orge3b0114"><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
@@ -304,8 +304,8 @@ wrangling experts. Thank you everyone!
</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 id="outline-container-org6b86244" class="outline-2">
+<h2 id="org6b86244"><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
@@ -328,8 +328,8 @@ such as GISAID.
</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 id="outline-container-org1030148" class="outline-2">
+<h2 id="org1030148"><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
@@ -360,8 +360,8 @@ multiple resources.
</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 id="outline-container-orgdf90c2c" class="outline-2">
+<h2 id="orgdf90c2c"><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
@@ -383,8 +383,8 @@ for bulk uploads!
</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 id="outline-container-org3294b2e" class="outline-2">
+<h2 id="org3294b2e"><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
@@ -395,8 +395,8 @@ using workflows from the High Performance Open Biology Lab defined
</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 id="outline-container-orgfca20f4" class="outline-2">
+<h2 id="orgfca20f4"><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
@@ -414,8 +414,8 @@ for monitoring, protein prediction and drug development.
</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 id="outline-container-org0f602e3" class="outline-2">
+<h2 id="org0f602e3"><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
@@ -427,8 +427,8 @@ point.
</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 id="outline-container-org441ff7c" class="outline-2">
+<h2 id="org441ff7c"><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>
@@ -438,8 +438,8 @@ data and store it for further processing.
</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 id="outline-container-org42ceb37" class="outline-2">
+<h2 id="org42ceb37"><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
@@ -448,8 +448,8 @@ can take our workflows and data and run it elsewhere!
</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 id="outline-container-org1c3275d" class="outline-2">
+<h2 id="org1c3275d"><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
@@ -464,8 +464,8 @@ assembly variations into consideration. This is all work in progress.
</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 id="outline-container-org7cb05f2" class="outline-2">
+<h2 id="org7cb05f2"><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>!
@@ -473,8 +473,8 @@ See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork
</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 id="outline-container-org875e3c9" class="outline-2">
+<h2 id="org875e3c9"><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
@@ -483,8 +483,8 @@ Workflows are on <a href="https://github.com/arvados/bh20-seq-resource/tree/mast
</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 id="outline-container-orgf485768" class="outline-2">
+<h2 id="orgf485768"><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
@@ -494,8 +494,8 @@ many PRs we already merged.
</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 id="outline-container-orgae7cb27" class="outline-2">
+<h2 id="orgae7cb27"><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
@@ -511,8 +511,8 @@ In all honesty: we prefer both data and software to be free.
</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 id="outline-container-org765d1a7" class="outline-2">
+<h2 id="org765d1a7"><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.
@@ -524,8 +524,8 @@ We are also writing tools to generate VCF files directly from the pangenome.
</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 id="outline-container-org66263d5" class="outline-2">
+<h2 id="org66263d5"><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
@@ -536,8 +536,8 @@ plan to combine identifiers with clinical data stored securely at
</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 id="outline-container-org6cd833b" class="outline-2">
+<h2 id="org6cd833b"><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.
@@ -545,8 +545,8 @@ We are planning to remove reads that match the human reference.
</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 id="outline-container-orge8f395f" class="outline-2">
+<h2 id="orge8f395f"><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.
@@ -555,17 +555,17 @@ To date, PubSeq is a resource specific to SARS-CoV-2, but we are designing it to
</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 id="outline-container-org8f5ae93" class="outline-2">
+<h2 id="org8f5ae93"><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.
+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. See also <a href="./contact">contact</a>.
</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 id="outline-container-org15ea9a8" class="outline-2">
+<h2 id="org15ea9a8"><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
@@ -576,7 +576,7 @@ 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 2020-08-22 Sat 03:48</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 04:42</small>.
</div>
</body>
</html>
diff --git a/doc/web/about.org b/doc/web/about.org
index 5f864e9..efd914f 100644
--- a/doc/web/about.org
+++ b/doc/web/about.org
@@ -204,7 +204,7 @@ To date, PubSeq is a resource specific to SARS-CoV-2, but we are designing it to
* How do I communicate with you?
-We use a [[https://gitter.im/arvados/pubseq?utm_source=share-link&utm_medium=link&utm_campaign=share-link][gitter channel]] you can join.
+We use a [[https://gitter.im/arvados/pubseq?utm_source=share-link&utm_medium=link&utm_campaign=share-link][gitter channel]] you can join. See also [[./contact][contact]].
* Who are the sponsors?
diff --git a/doc/web/contact.html b/doc/web/contact.html
new file mode 100644
index 0000000..8372743
--- /dev/null
+++ b/doc/web/contact.html
@@ -0,0 +1,286 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
+<head>
+<!-- 2020-08-22 Sat 05:03 -->
+<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
+<meta name="viewport" content="width=device-width, initial-scale=1" />
+<title>CONTACT</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">CONTACT</h1>
+<div id="table-of-contents">
+<h2>Table of Contents</h2>
+<div id="text-table-of-contents">
+<ul>
+<li><a href="#orgd0c1845">1. CONTACT and SUPPORT</a>
+<ul>
+<li><a href="#org5a8566b">1.1. Professional support</a></li>
+<li><a href="#orgccd5ecb">1.2. E-mail</a></li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+
+<div id="outline-container-orgd0c1845" class="outline-2">
+<h2 id="orgd0c1845"><span class="section-number-2">1</span> CONTACT and SUPPORT</h2>
+<div class="outline-text-2" id="text-1">
+<p>
+COVID-19 PubSeq was created by a group of <a href="https://github.com/arvados/bh20-seq-resource/graphs/contributors">bioinformaticians</a> and
+software developers working at leading institutes (see sponsors
+below). You can talk with us directly on a <a href="https://gitter.im/arvados/pubseq?utm_source=share-link&amp;utm_medium=link&amp;utm_campaign=share-link">gitter channel</a>. We are open
+to improving work flows and analysis.
+</p>
+</div>
+
+<div id="outline-container-org5a8566b" class="outline-3">
+<h3 id="org5a8566b"><span class="section-number-3">1.1</span> Professional support</h3>
+<div class="outline-text-3" id="text-1-1">
+<p>
+To use COVID-19 PubSeq solutions for professional purposes you can
+contact <a href="mailto:info@curii.com">Curii</a>, the creators of <a href="https://arvados.org/">Arvados</a>, directly.
+</p>
+
+<p>
+COVID-19 is built on Arvados using CWL workflows.
+</p>
+</div>
+</div>
+
+<div id="outline-container-orgccd5ecb" class="outline-3">
+<h3 id="orgccd5ecb"><span class="section-number-3">1.2</span> E-mail</h3>
+<div class="outline-text-3" id="text-1-2">
+<p>
+For other questions feel free to write directly to <a href="mailto:pjotr.public821@thebird.nl">Pjotr Prins</a>.
+</p>
+</div>
+</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 2020-08-22 Sat 05:03</small>.
+</div>
+</body>
+</html>
diff --git a/doc/web/contact.org b/doc/web/contact.org
new file mode 100644
index 0000000..f410cee
--- /dev/null
+++ b/doc/web/contact.org
@@ -0,0 +1,20 @@
+#+TITLE: CONTACT
+#+AUTHOR: Pjotr Prins
+
+* CONTACT and SUPPORT
+
+COVID-19 PubSeq was created by a group of [[https://github.com/arvados/bh20-seq-resource/graphs/contributors][bioinformaticians]] and
+software developers working at leading institutes (see sponsors
+below). You can talk with us directly on a [[https://gitter.im/arvados/pubseq?utm_source=share-link&utm_medium=link&utm_campaign=share-link][gitter channel]]. We are open
+to improving work flows and analysis.
+
+** Professional support
+
+To use COVID-19 PubSeq solutions for professional purposes you can
+contact [[mailto:info@curii.com][Curii]], the creators of [[https://arvados.org/][Arvados]], directly.
+
+COVID-19 is built on Arvados using CWL workflows.
+
+** E-mail
+
+For other questions feel free to write directly to [[mailto:pjotr.public821@thebird.nl][Pjotr Prins]].
generated by cgit v1.2.3 (git 2.44.0) at 2024-05-19 11:59:49 +0000