Display About/FAQ

author: Pjotr Prins 2020-05-24 10:31:24 -0500
committer: Pjotr Prins 2020-05-24 10:31:24 -0500
commit: c3bbd48601cdb4bec510db72bd2296724874f4f3 (patch)
tree: b61ca5b473cc30aa971264994697c70c06f20c56 /doc
parent: a3c37de9105a784a8f73d3925269c847108baa17 (diff)
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diff --git a/doc/blog/using-covid-19-pubseq-part1.org b/doc/blog/using-covid-19-pubseq-part1.org
index 8d3dae5..b1edbad 100644
--- a/doc/blog/using-covid-19-pubseq-part1.org
+++ b/doc/blog/using-covid-19-pubseq-part1.org
@@ -11,7 +11,7 @@ most importantly, providing standardised workflows that get triggered
 on upload, so that results are immediately available in standardised
 data formats.
 
-* Table of Contents                                                     :TOC:
+* Table of Contents                                                     :TOC:noexport:
  - [[#what-does-this-mean][What does this mean?]]
  - [[#fetch-sequence-data][Fetch sequence data]]
  - [[#predicates][Predicates]]
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+<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="#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>
+</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 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-orga424b3d" class="outline-2">
+<h2 id="orga424b3d"><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), 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
+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 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!
+</p>
+
+<p>
+Importantly: all data is published under the <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons 4.0
+attribution 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, including GISAID.
+</p>
+</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 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 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>
+</ol>
+
+<p>
+Finally, if you upload your data here we have workflows that output
+formatted data suitable for uploading to EBI resources (and soon
+others). Uploading your data here get your data ready for upload to
+multiple resources.
+</p>
+</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 class="outline-text-2" id="text-5">
+<p>
+Funny question.  There is no good reason not to upload your data here!
+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. We recommend uploading to
+EBI and NCBI resources. Use our data conversion tools to only enter
+data once and make the process smooth.
+</p>
+</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 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-org68363cb" class="outline-2">
+<h2 id="org68363cb"><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>
+(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-orgb6aaf34" class="outline-2">
+<h2 id="orgb6aaf34"><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
+can take our workflows and data and run it elsewhere!
+</p>
+</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 class="outline-text-2" id="text-9">
+<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-org57f1ee0" class="outline-2">
+<h2 id="org57f1ee0"><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>!
+</p>
+</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 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-orgc51ee58" class="outline-2">
+<h2 id="orgc51ee58"><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
+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-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 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.
+</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 class="outline-text-2" id="text-14">
+<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 2020-05-24 Sun 10:26</small>.
+</div>
+</body>
+</html>
diff --git a/doc/web/about.org b/doc/web/about.org
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+#+TITLE: About/FAQ
+#+AUTHOR: Pjotr Prins
+
+* Table of Contents                                                     :TOC:noexport:
+ - [[#what-is-the-public-sequence-resource-about][What is the 'public sequence resource' about?]]
+ - [[#who-created-the-public-sequence-resource][Who created the public sequence resource?]]
+ - [[#how-does-the-public-sequence-resource-compare-to-other-data-resources][How does the public sequence resource compare to other data resources?]]
+ - [[#why-should-i-upload-my-data-here][Why should I upload my data here?]]
+ - [[#why-should-i-not-upload-by-data-here][Why should I not upload by data here?]]
+ - [[#how-does-the-public-sequence-resource-work][How does the public sequence resource work?]]
+ - [[#is-this-about-open-data][Is this about open data?]]
+ - [[#is-this-about-free-software][Is this about free software?]]
+ - [[#how-do-i-upload-raw-data][How do I upload raw data?]]
+ - [[#how-do-i-change-metadata][How do I change metadata?]]
+ - [[#how-do-i-change-the-work-flows][How do I change the work flows?]]
+ - [[#how-do-i-change-the-source-code][How do I change the source code?]]
+ - [[#how-do-i-deal-with-private-data-and-privacy][How do I deal with private data and privacy?]]
+ - [[#who-are-the-sponsors][Who are the sponsors?]]
+
+* What is the 'public sequence resource' about?
+
+The *public sequence resource* 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.
+
+* 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
+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
+wrangling experts. Thank you everyone!
+
+* How does the public sequence resource compare to other data resources?
+
+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!
+
+Importantly: all data is published under the [[https://creativecommons.org/licenses/by/4.0/][Creative Commons 4.0
+attribution license]] 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, including GISAID.
+
+* Why should I upload my data here?
+
+1. We champion truly shareable data without licensing restrictions - with proper
+   attribution
+2. We provide full metadata support using state-of-the-art ontology's
+2. We provide a web-based sequence uploader and a command-line version
+   for bulk uploads
+3. We provide a live SPARQL end-point for all metadata
+2. We provide free data analysis and sequence comparison triggered on data upload
+4. We provide free downloads of all computed output
+3. There is no need to set up pipelines and/or compute clusters
+4. All workflows get triggered on uploading a new sequence
+4. When someone (you?) improves the software/workflows and everyone benefits
+
+Finally, if you upload your data here we have workflows that output
+formatted data suitable for uploading to EBI resources (and soon
+others). Uploading your data here get your data ready for upload to
+multiple resources.
+
+* Why should I not upload by data here?
+
+Funny question.  There is no good reason not to upload your data here!
+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. We recommend uploading to
+EBI and NCBI resources. Use our data conversion tools to only enter
+data once and make the process smooth.
+
+* How does the public sequence resource work?
+
+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
+[[https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate][here]].
+
+* Is this about open data?
+
+All data is published under a [[https://creativecommons.org/licenses/by/4.0/][Creative Commons 4.0 attribution license]]
+(CC-BY-4.0). You can download the raw and published (GFA/RDF/FASTA)
+data and store it for further processing.
+
+* Is this about free software?
+
+Absolutely. Free software allows for fully reproducible pipelines. You
+can take our workflows and data and run it elsewhere!
+
+* How do I upload raw data?
+
+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.
+
+* How do I change metadata?
+
+See the [[http://covid19.genenetwork.org/blog]]!
+
+* How do I change the work flows?
+
+See the [[http://covid19.genenetwork.org/blog]]!
+
+* How do I change the source code?
+
+Go to our [[https://github.com/arvados/bh20-seq-resource][source code repositories]], fork/clone the repository, change
+something and submit a [[https://github.com/arvados/bh20-seq-resource/pulls][pull request]] (PR). That easy! Check out how
+many PRs we already merged.
+
+* How do I deal with private data and privacy?
+
+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.
+
+* Who are the sponsors?
+
+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.
author	Pjotr Prins	2020-05-24 10:31:24 -0500
committer	Pjotr Prins	2020-05-24 10:31:24 -0500
commit	c3bbd48601cdb4bec510db72bd2296724874f4f3 (patch)
tree	b61ca5b473cc30aa971264994697c70c06f20c56 /doc
parent	a3c37de9105a784a8f73d3925269c847108baa17 (diff)
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