Edits

author: Pjotr Prins 2020-05-24 11:28:09 -0500
committer: Pjotr Prins 2020-05-24 11:28:09 -0500
commit: 17c698f29742cbd24bdbf79e613a0124fce20316 (patch)
tree: 8d41340a3414b5c096ec0cbc611b0bdcd5988960 /doc/web
parent: e4738edf99cb96214db066079adae021c25bc059 (diff)
download: bh20-seq-resource-17c698f29742cbd24bdbf79e613a0124fce20316.tar.gz
bh20-seq-resource-17c698f29742cbd24bdbf79e613a0124fce20316.tar.lz
bh20-seq-resource-17c698f29742cbd24bdbf79e613a0124fce20316.zip
3 files changed, 78 insertions, 51 deletions
diff --git a/doc/web/about.html b/doc/web/about.html
index 1f8b1a1..ca0d952 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>
-<!-- 2020-05-24 Sun 10:27 -->
+<!-- 2020-05-24 Sun 11:24 -->
 <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>
@@ -247,26 +247,26 @@ for the JavaScript code in this tag.
 <h2>Table of Contents</h2>
 <div id="text-table-of-contents">
 <ul>
-<li><a href="#org4fc5d3e">1. What is the 'public sequence resource' about?</a></li>
-<li><a href="#orga424b3d">2. Who created the public sequence resource?</a></li>
-<li><a href="#org250dbae">3. How does the public sequence resource compare to other data resources?</a></li>
-<li><a href="#orgd065057">4. Why should I upload my data here?</a></li>
-<li><a href="#org5f94b02">5. Why should I not upload by data here?</a></li>
-<li><a href="#orgbaaaeaf">6. How does the public sequence resource work?</a></li>
-<li><a href="#org68363cb">7. Is this about open data?</a></li>
-<li><a href="#orgb6aaf34">8. Is this about free software?</a></li>
-<li><a href="#orga01eab2">9. How do I upload raw data?</a></li>
-<li><a href="#org57f1ee0">10. How do I change metadata?</a></li>
-<li><a href="#org5585441">11. How do I change the work flows?</a></li>
-<li><a href="#orgc51ee58">12. How do I change the source code?</a></li>
-<li><a href="#org79c6c9b">13. How do I deal with private data and privacy?</a></li>
-<li><a href="#org8ed8b69">14. Who are the sponsors?</a></li>
+<li><a href="#orgc702afb">1. What is the 'public sequence resource' about?</a></li>
+<li><a href="#org757df7a">2. Who created the public sequence resource?</a></li>
+<li><a href="#orgbcdc47e">3. How does the public sequence resource compare to other data resources?</a></li>
+<li><a href="#org9a5b80c">4. Why should I upload my data here?</a></li>
+<li><a href="#orge7b928b">5. Why should I not upload by data here?</a></li>
+<li><a href="#org095184f">6. How does the public sequence resource work?</a></li>
+<li><a href="#org562edc8">7. Is this about open data?</a></li>
+<li><a href="#org9dab2c1">8. Is this about free software?</a></li>
+<li><a href="#org71012a1">9. How do I upload raw data?</a></li>
+<li><a href="#orgd1586af">10. How do I change metadata?</a></li>
+<li><a href="#org6de2b89">11. How do I change the work flows?</a></li>
+<li><a href="#org276e949">12. How do I change the source code?</a></li>
+<li><a href="#org3fb1663">13. How do I deal with private data and privacy?</a></li>
+<li><a href="#org4741f67">14. Who are the sponsors?</a></li>
 </ul>
 </div>
 </div>
 
-<div id="outline-container-org4fc5d3e" class="outline-2">
-<h2 id="org4fc5d3e"><span class="section-number-2">1</span> What is the 'public sequence resource' about?</h2>
+<div id="outline-container-orgc702afb" class="outline-2">
+<h2 id="orgc702afb"><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
@@ -277,25 +277,29 @@ sequence comparison and protein prediction.
 </div>
 </div>
 
-<div id="outline-container-orga424b3d" class="outline-2">
-<h2 id="orga424b3d"><span class="section-number-2">2</span> Who created the public sequence resource?</h2>
+<div id="outline-container-org757df7a" class="outline-2">
+<h2 id="org757df7a"><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
+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), Michael Crusoe (Common
-Workflow Language) and Thomas Liener (consultant, formerly EBI). But
-as this is a free software initiative the project represents major
-work by hundreds of software developers and ontology and data
+Workflow Language), Thomas Liener (consultant, formerly EBI) 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-org250dbae" class="outline-2">
-<h2 id="org250dbae"><span class="section-number-2">3</span> How does the public sequence resource compare to other data resources?</h2>
+<div id="outline-container-orgbcdc47e" class="outline-2">
+<h2 id="orgbcdc47e"><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
@@ -314,8 +318,8 @@ public resources, including GISAID.
 </div>
 </div>
 
-<div id="outline-container-orgd065057" class="outline-2">
-<h2 id="orgd065057"><span class="section-number-2">4</span> Why should I upload my data here?</h2>
+<div id="outline-container-org9a5b80c" class="outline-2">
+<h2 id="org9a5b80c"><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
@@ -329,6 +333,9 @@ for bulk uploads</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>
 </ol>
 
 <p>
@@ -340,8 +347,8 @@ multiple resources.
 </div>
 </div>
 
-<div id="outline-container-org5f94b02" class="outline-2">
-<h2 id="org5f94b02"><span class="section-number-2">5</span> Why should I not upload by data here?</h2>
+<div id="outline-container-orge7b928b" class="outline-2">
+<h2 id="orge7b928b"><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 is no good reason not to upload your data here!
@@ -354,8 +361,8 @@ data once and make the process smooth.
 </div>
 </div>
 
-<div id="outline-container-orgbaaaeaf" class="outline-2">
-<h2 id="orgbaaaeaf"><span class="section-number-2">6</span> How does the public sequence resource work?</h2>
+<div id="outline-container-org095184f" class="outline-2">
+<h2 id="org095184f"><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
@@ -366,8 +373,8 @@ using workflows from the High Performance Open Biology Lab defined
 </div>
 </div>
 
-<div id="outline-container-org68363cb" class="outline-2">
-<h2 id="org68363cb"><span class="section-number-2">7</span> Is this about open data?</h2>
+<div id="outline-container-org562edc8" class="outline-2">
+<h2 id="org562edc8"><span class="section-number-2">7</span> Is this about open data?</h2>
 <div class="outline-text-2" id="text-7">
 <p>
 All data is published under a <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons 4.0 attribution license</a>
@@ -377,8 +384,8 @@ data and store it for further processing.
 </div>
 </div>
 
-<div id="outline-container-orgb6aaf34" class="outline-2">
-<h2 id="orgb6aaf34"><span class="section-number-2">8</span> Is this about free software?</h2>
+<div id="outline-container-org9dab2c1" class="outline-2">
+<h2 id="org9dab2c1"><span class="section-number-2">8</span> Is this about free software?</h2>
 <div class="outline-text-2" id="text-8">
 <p>
 Absolutely. Free software allows for fully reproducible pipelines. You
@@ -387,8 +394,8 @@ can take our workflows and data and run it elsewhere!
 </div>
 </div>
 
-<div id="outline-container-orga01eab2" class="outline-2">
-<h2 id="orga01eab2"><span class="section-number-2">9</span> How do I upload raw data?</h2>
+<div id="outline-container-org71012a1" class="outline-2">
+<h2 id="org71012a1"><span class="section-number-2">9</span> How do I upload raw data?</h2>
 <div class="outline-text-2" id="text-9">
 <p>
 We are preparing raw sequence data pipelines (fastq and BAM). The
@@ -403,8 +410,8 @@ assembly variations into consideration. This is all work in progress.
 </div>
 </div>
 
-<div id="outline-container-org57f1ee0" class="outline-2">
-<h2 id="org57f1ee0"><span class="section-number-2">10</span> How do I change metadata?</h2>
+<div id="outline-container-orgd1586af" class="outline-2">
+<h2 id="orgd1586af"><span class="section-number-2">10</span> How do I change metadata?</h2>
 <div class="outline-text-2" id="text-10">
 <p>
 See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a>!
@@ -412,8 +419,8 @@ See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork
 </div>
 </div>
 
-<div id="outline-container-org5585441" class="outline-2">
-<h2 id="org5585441"><span class="section-number-2">11</span> How do I change the work flows?</h2>
+<div id="outline-container-org6de2b89" class="outline-2">
+<h2 id="org6de2b89"><span class="section-number-2">11</span> How do I change the work flows?</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>!
@@ -421,8 +428,8 @@ See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork
 </div>
 </div>
 
-<div id="outline-container-orgc51ee58" class="outline-2">
-<h2 id="orgc51ee58"><span class="section-number-2">12</span> How do I change the source code?</h2>
+<div id="outline-container-org276e949" class="outline-2">
+<h2 id="org276e949"><span class="section-number-2">12</span> How do I change the source code?</h2>
 <div class="outline-text-2" id="text-12">
 <p>
 Go to our <a href="https://github.com/arvados/bh20-seq-resource">source code repositories</a>, fork/clone the repository, change
@@ -432,20 +439,20 @@ many PRs we already merged.
 </div>
 </div>
 
-<div id="outline-container-org79c6c9b" class="outline-2">
-<h2 id="org79c6c9b"><span class="section-number-2">13</span> How do I deal with private data and privacy?</h2>
+<div id="outline-container-org3fb1663" class="outline-2">
+<h2 id="org3fb1663"><span class="section-number-2">13</span> How do I deal with private data and privacy?</h2>
 <div class="outline-text-2" id="text-13">
 <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>. Contact Pjotr Prins if you want to work on this.
+<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-org8ed8b69" class="outline-2">
-<h2 id="org8ed8b69"><span class="section-number-2">14</span> Who are the sponsors?</h2>
+<div id="outline-container-org4741f67" class="outline-2">
+<h2 id="org4741f67"><span class="section-number-2">14</span> Who are the sponsors?</h2>
 <div class="outline-text-2" id="text-14">
 <p>
 The main sponsors are listed in the footer. In addition to the time
@@ -456,7 +463,7 @@ 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 2020-05-24 Sun 10:26</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 2020-05-24 Sun 11:24</small>.
 </div>
 </body>
 </html>
diff --git a/doc/web/about.org b/doc/web/about.org
index 26b675d..497b1b4 100644
--- a/doc/web/about.org
+++ b/doc/web/about.org
@@ -130,7 +130,7 @@ many PRs we already merged.
 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
-[[https://redcap-covid19.elixir-luxembourg.org/redcap/][REDCap]]. Contact Pjotr Prins if you want to work on this.
+[[https://redcap-covid19.elixir-luxembourg.org/redcap/][REDCap]]. See the relevant [[https://github.com/arvados/bh20-seq-resource/issues/21][tracker]] for more information and contributing.
 
 * Who are the sponsors?
 
diff --git a/doc/web/download.org b/doc/web/download.org
index 498b132..c48b6d8 100644
--- a/doc/web/download.org
+++ b/doc/web/download.org
@@ -11,6 +11,10 @@
    - [[#pangenome-browser-format][Pangenome Browser format]]
  - [[#log-of-workflow-output][Log of workflow output]]
  - [[#all-files][All files]]
+ - [[#planned][Planned]]
+   - [[#raw-sequence-data][Raw sequence data]]
+   - [[#multiple-sequence-alignment-msa][Multiple Sequence Alignment (MSA)]]
+   - [[#phylogenetic-tree][Phylogenetic tree]]
 
 * FASTA files
 
@@ -67,3 +71,19 @@ Including in below link is a log file of the last workflow runs.
 * All files
 
 https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/
+
+* Planned
+
+We are planning the add the following output (see also
+
+** Raw sequence data
+
+See [[https://github.com/arvados/bh20-seq-resource/issues/16][fastq tracker]] and [[https://github.com/arvados/bh20-seq-resource/issues/63][BAM tracker]].
+
+** Multiple Sequence Alignment (MSA)
+
+See [[https://github.com/arvados/bh20-seq-resource/issues/11][MSA tracker]].
+
+** Phylogenetic tree
+
+See [[https://github.com/arvados/bh20-seq-resource/issues/43][Phylo tracker]].
author	Pjotr Prins	2020-05-24 11:28:09 -0500
committer	Pjotr Prins	2020-05-24 11:28:09 -0500
commit	17c698f29742cbd24bdbf79e613a0124fce20316 (patch)
tree	8d41340a3414b5c096ec0cbc611b0bdcd5988960 /doc/web
parent	e4738edf99cb96214db066079adae021c25bc059 (diff)
download	bh20-seq-resource-17c698f29742cbd24bdbf79e613a0124fce20316.tar.gz bh20-seq-resource-17c698f29742cbd24bdbf79e613a0124fce20316.tar.lz bh20-seq-resource-17c698f29742cbd24bdbf79e613a0124fce20316.zip