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diff --git a/doc/web/about.html b/doc/web/about.html index cf718e7..bad4bb1 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> -<!-- 2020-05-27 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&utm_medium=link&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> </body> </html> diff --git a/doc/web/about.org b/doc/web/about.org index bb49c2a..8e535dc 100644 --- a/doc/web/about.org +++ b/doc/web/about.org @@ -8,6 +8,7 @@ - [[#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?]] + - [[#who-uses-the-public-sequence-resource][Who uses the public sequence resource?]] - [[#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?]] @@ -69,6 +70,7 @@ public resources, including GISAID. 4. Your data gets automatically integrated with the Swiss Institure of Bioinformatics COVID-19 knowledge base https://covid-19-sparql.expasy.org/ (Elixir Switzerland) +4. Your data will be used to develop drug targets Finally, if you upload your data here we have workflows that output formatted data suitable for uploading to EBI resources (and soon @@ -96,6 +98,14 @@ 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]]. +* Who uses the public sequence resource? + +The Swiss Institute of Bioinformatics has included this data in +https://covid-19-sparql.expasy.org/ and made it part of [[https://www.uniprot.org/][Uniprot]]. + +[[https://uthsc.edu][UTHSC]] and [[https://www.ornl.gov/news/ornl-fight-against-covid-19][ORNL]] use COVID-19 PubSeq data for protein prediction and +drug development. + * Is this about open data? All data is published under a [[https://creativecommons.org/licenses/by/4.0/][Creative Commons 4.0 attribution license]] |