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<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>
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