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Diffstat (limited to 'doc/web/about.html')
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diff --git a/doc/web/about.html b/doc/web/about.html index c971a4e..2d1f51d 100644 --- a/doc/web/about.html +++ b/doc/web/about.html @@ -1,964 +1,649 @@ <?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"> +"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <head> - <!-- 2020-07-18 Sat 03:27 --> - <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> - <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; 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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> +<!-- 2020-08-24 Mon 03:12 --> +<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> +<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; 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} + 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; } + .equation-container { + display: table; + text-align: center; + width: 100%; + } + .equation { + vertical-align: middle; + } + .equation-label { + display: table-cell; + text-align: right; + vertical-align: middle; + } + .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) 2012-2020 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">About/FAQ</h1> - <div id="table-of-contents"> - <h2>Table of Contents</h2> - <div id="text-table-of-contents"> - <ul> - <li><a href="#org0db9061">1. What is the 'public sequence resource' about?</a></li> - <li><a href="#org983877d">2. Who created the public sequence resource?</a></li> - <li><a href="#org83093c3">3. How does the public sequence resource compare to other data resources?</a> - </li> - <li><a href="#org9b31fd4">4. Why should I upload my data here?</a></li> - <li><a href="#org4e92cb5">5. Why should I not upload by data here?</a></li> - <li><a href="#orgdfe72f6">6. How does the public sequence resource work?</a></li> - <li><a href="#orgd0c5abb">7. Who uses the public sequence resource?</a></li> - <li><a href="#org56f4a54">8. How can I contribute?</a></li> - <li><a href="#org2240ef7">9. Is this about open data?</a></li> - <li><a href="#orgbb655e0">10. Is this about free software?</a></li> - <li><a href="#org4e779f4">11. How do I upload raw data?</a></li> - <li><a href="#org83f6b7b">12. How do I change metadata?</a></li> - <li><a href="#org1bc6dab">13. How do I change the work flows?</a></li> - <li><a href="#org1140d62">14. How do I change the source code?</a></li> - <li><a href="#orge182714">15. Should I choose CC-BY or CC0?</a></li> - <li><a href="#orgf4a692b">16. How do I deal with private data and privacy?</a></li> - <li><a href="#org7757574">17. How do I communicate with you?</a></li> - <li><a href="#org194006f">18. Who are the sponsors?</a></li> - </ul> - </div> - </div> - - <div id="outline-container-org0db9061" class="outline-2"> - <h2 id="org0db9061"><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> - <p> - We were at the <strong>Bioinformatics Community Conference 2020</strong>! Have a look at the - <a href="https://bcc2020.sched.com/event/coLw">video talk</a></li> - (<a href="https://drive.google.com/file/d/1skXHwVKM_gl73-_4giYIOQ1IlC5X5uBo/view?usp=sharing">alternative link</a>) - and the <a href="https://drive.google.com/file/d/1vyEgfvSqhM9yIwWZ6Iys-QxhxtVxPSdp/view?usp=sharing">poster</a>. - </p> - </div> - </div> - - <div id="outline-container-org983877d" class="outline-2"> - <h2 id="org983877d"><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), Andrea Guarracino - (University of Rome Tor Vergata), Michael Crusoe (Common Workflow - Language), Thomas Liener (consultant, formerly EBI), Erik Garrison - (UCSC) 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-org83093c3" class="outline-2"> - <h2 id="org83093c3"><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! Sequences from GenBank, EBI/ENA and - others are regularly added to PubSeq. We encourage people to everyone - to submit on PubSeq because of its superior live tooling and metadata - support (see the next question). - </p> - - <p> - Importantly: all data is published under either the <a - href="https://creativecommons.org/licenses/by/4.0/">Creative Commons - 4.0 attribution license</a> or the <a - href="https://creativecommons.org/share-your-work/public-domain/cc0/">CC0 “No Rights Reserved” - 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, - such as GISAID. - </p> - </div> - </div> - - <div id="outline-container-org9b31fd4" class="outline-2"> - <h2 id="org9b31fd4"><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 do real work for you, with this <a - href="https://workbench.lugli.arvadosapi.com/container_requests/lugli-xvhdp-bhhk4nxx1lch5od">link</a> - you can see the last - run took 5.5 hours! - </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> - <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> - Finally, if you upload your data here we have workflows that output - formatted data suitable for <a - href="http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part6">uploading to EBI - resources</a> (and soon - others). Uploading your data here get your data ready for upload to - multiple resources. - </p> - </div> - </div> - - <div id="outline-container-org4e92cb5" class="outline-2"> - <h2 id="org4e92cb5"><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 - and make it available to the widest audience possible. - </p> - - <p> - 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. - </p> - - <p> - We recommend uploading to EBI and NCBI resources using our data - conversion tools. It means you only enter data once and make the - process smooth. You can also use our command line data uploader - for bulk uploads! - </p> - </div> - </div> - - <div id="outline-container-orgdfe72f6" class="outline-2"> - <h2 id="orgdfe72f6"><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-orgd0c5abb" class="outline-2"> - <h2 id="orgd0c5abb"><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> - The Pantograph <a href="https://graph-genome.github.io/">viewer</a> uses PubSeq data for their - visualisations. - </p> - - <p> - <a href="https://uthsc.edu">UTHSC</a> (USA), <a href="https://www.esr.cri.nz/">ESR</a> (New Zealand) and - <a href="https://www.ornl.gov/news/ornl-fight-against-covid-19">ORNL</a> (USA) use COVID-19 PubSeq data - for monitoring, protein prediction and drug development. - </p> - </div> - </div> - - <div id="outline-container-org56f4a54" class="outline-2"> - <h2 id="org56f4a54"><span class="section-number-2">8</span> How can I contribute?</h2> - <div class="outline-text-2" id="text-8"> - <p> - You can contribute by submitting sequences, updating metadata, submit - issues on our issue tracker, and more importantly add functionality. - See 'How do I change the source code' below. Read through our online - documentation at <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a> - as a starting - point. - </p> - </div> - </div> - - <div id="outline-container-org2240ef7" class="outline-2"> - <h2 id="org2240ef7"><span class="section-number-2">9</span> Is this about open data?</h2> - <div class="outline-text-2" id="text-9"> - <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-orgbb655e0" class="outline-2"> - <h2 id="orgbb655e0"><span class="section-number-2">10</span> Is this about free software?</h2> - <div class="outline-text-2" id="text-10"> - <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-org4e779f4" class="outline-2"> - <h2 id="org4e779f4"><span class="section-number-2">11</span> How do I upload raw data?</h2> - <div class="outline-text-2" id="text-11"> - <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-org83f6b7b" class="outline-2"> - <h2 id="org83f6b7b"><span class="section-number-2">12</span> How do I change metadata?</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-org1bc6dab" class="outline-2"> - <h2 id="org1bc6dab"><span class="section-number-2">13</span> How do I change the work flows?</h2> - <div class="outline-text-2" id="text-13"> - <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 - <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a> on workflows. - </p> - </div> - </div> - - <div id="outline-container-org1140d62" class="outline-2"> - <h2 id="org1140d62"><span class="section-number-2">14</span> How do I change the source code?</h2> - <div class="outline-text-2" id="text-14"> - <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-orge182714" class="outline-2"> - <h2 id="orge182714"><span class="section-number-2">15</span> Should I choose CC-BY or CC0?</h2> - <div class="outline-text-2" id="text-15"> - <p> - Restrictive data licenses are hampering data sharing and reproducible - research. CC0 is the preferred license because it gives researchers - the most freedom. Since we provide metadata there is no reason for - others not to honour your work. We also provide CC-BY as an option - because we know people like the attribution clause. - </p> - - <p> - In all honesty: we prefer both data and software to be free. - </p> - </div> - </div> - - <div id="outline-container-orgf4a692b" class="outline-2"> - <h2 id="orgf4a692b"><span class="section-number-2">16</span> How do I deal with private data and privacy?</h2> - <div class="outline-text-2" id="text-16"> - <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>. 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-org7757574" class="outline-2"> - <h2 id="org7757574"><span class="section-number-2">17</span> How do I communicate with you?</h2> - <div class="outline-text-2" id="text-17"> - <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-org194006f" class="outline-2"> - <h2 id="org194006f"><span class="section-number-2">18</span> Who are the sponsors?</h2> - <div class="outline-text-2" id="text-18"> - <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> +<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="#orge0f47ff">1. What is the 'public sequence resource' about?</a></li> +<li><a href="#orgdf364dc">2. Presentations</a></li> +<li><a href="#org5fc8f04">3. Who created the public sequence resource?</a></li> +<li><a href="#org6f93b70">4. How does the public sequence resource compare to other data resources?</a></li> +<li><a href="#org8e3181a">5. Why should I upload my data here?</a></li> +<li><a href="#orgdf83b8b">6. Why should I not upload by data here?</a></li> +<li><a href="#org99d5e54">7. How does the public sequence resource work?</a></li> +<li><a href="#org8eac95c">8. Who uses the public sequence resource?</a></li> +<li><a href="#orgd5907cf">9. How can I contribute?</a></li> +<li><a href="#orgef93e3d">10. Is this about open data?</a></li> +<li><a href="#orgab39a73">11. Is this about free software?</a></li> +<li><a href="#orgad533ff">12. How do I upload raw data?</a></li> +<li><a href="#org4ca5ce9">13. How do I change metadata?</a></li> +<li><a href="#org2af2c45">14. How do I change the work flows?</a></li> +<li><a href="#org6a3ff30">15. How do I change the source code?</a></li> +<li><a href="#org3bdaa46">16. Should I choose CC-BY or CC0?</a></li> +<li><a href="#orge4cdab7">17. Are there also variant in the RDF databases?</a></li> +<li><a href="#org8a56c4c">18. How do I deal with private data and privacy?</a></li> +<li><a href="#orgf3ba61a">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="#orgc693d03">20. Does PubSeq support only SARS-CoV-2 data?</a></li> +<li><a href="#org927057f">21. How do I communicate with you?</a></li> +<li><a href="#orgb05122d">22. Citing PubSeq</a></li> +<li><a href="#org16a19a4">23. Who are the sponsors?</a></li> +</ul> +</div> +</div> + +<div id="outline-container-orge0f47ff" class="outline-2"> +<h2 id="orge0f47ff"><span class="section-number-2">1</span> What is the 'public sequence resource' about?</h2> +<div class="outline-text-2" id="text-1"> +<p> +PubSeq, 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> + +<p> +Just to avoid the notion that PubSeq is a biorepository: it is far +more than that. We are not competing with the likes of GenBank, +EBI/ENA and GISAID - in fact, PubSeq sources much of the data from +those and they get ours. +</p> + +<p> +There is no conflict of posting data to multiple repositories. +</p> + +<p> +It is better to view PubSeq as an <b>open precision medicine initiative</b> that +allows for early detection of new variants and strains; very valuable +for both testing and treatment. We have live analysis work flows that +run on uploading a new sequence. Contributing sequences helps the +overall detection. At this moment the output is limited. We will soon +add interactive discovery tools. Uploading data from a sequencer will +give researchers all information they want in 5 hours <b>without any +bioinformatics knowledge</b>. We may even provide workflows that take +data straight from the sequencer. In fact, you get very little out of +existing biorepositories, in our opinion, unless you have solid +bioinformatics support. And even then there is the question about +comparing data that was created using different technologies and +workflows. How do you deal with that? +</p> + +<p> +With PubSeq we are in a position to reanalyse that data from raw +material when new insights arise. It is likely that COVID19 will be +around for another year at least. After that we should prepare for +the next pandemic. PubSeq is meant for that. We take the long view and +it will only get more powerful. Who knows: maybe the live analysis +part of PubSeq will be an approach that other biorepositories will +follow. +</p> +</div> +</div> + +<div id="outline-container-orgdf364dc" class="outline-2"> +<h2 id="orgdf364dc"><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 +link</a>) and the <a href="https://drive.google.com/file/d/1vyEgfvSqhM9yIwWZ6Iys-QxhxtVxPSdp/view?usp=sharing">poster</a>. +</p> +</div> +</div> + +<div id="outline-container-org5fc8f04" class="outline-2"> +<h2 id="org5fc8f04"><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 +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), Andrea Guarracino +(University of Rome Tor Vergata), Michael Crusoe (Common Workflow +Language), Thomas Liener (consultant, formerly EBI), Erik Garrison +(UCSC) 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-org6f93b70" class="outline-2"> +<h2 id="org6f93b70"><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 +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! Sequences from GenBank, EBI/ENA and +others are regularly added to PubSeq. We encourage people to everyone +to submit on PubSeq because of its superior live tooling and metadata +support (see the next question). +</p> + +<p> +Importantly: all data is published under either the <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons +4.0 attribution license</a> or the <a href="https://creativecommons.org/share-your-work/public-domain/cc0/">CC0 “No Rights Reserved” 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, +such as GISAID. +</p> +</div> +</div> + +<div id="outline-container-org8e3181a" class="outline-2"> +<h2 id="org8e3181a"><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 +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 do real work for you, with this <a href="https://workbench.lugli.arvadosapi.com/container_requests/lugli-xvhdp-bhhk4nxx1lch5od">link</a> you can see the last +run took 5.5 hours!</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> +<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> +Finally, if you upload your data here we have workflows that output +formatted data suitable for <a href="http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part6">uploading to EBI resources</a> (and soon +others). Uploading your data here get your data ready for upload to +multiple resources. +</p> +</div> +</div> + +<div id="outline-container-orgdf83b8b" class="outline-2"> +<h2 id="orgdf83b8b"><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 +and make it available to the widest audience possible. +</p> + +<p> +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. +</p> + +<p> +We recommend uploading to EBI and NCBI resources using our data +conversion tools. It means you only enter data once and make the +process smooth. You can also use our command line data uploader +for bulk uploads! +</p> +</div> +</div> + +<div id="outline-container-org99d5e54" class="outline-2"> +<h2 id="org99d5e54"><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 +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-org8eac95c" class="outline-2"> +<h2 id="org8eac95c"><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 +<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> +The Pantograph <a href="https://graph-genome.github.io/">viewer</a> uses PubSeq data for their visualisations. +</p> + +<p> +<a href="https://uthsc.edu">UTHSC</a> (USA), <a href="https://www.esr.cri.nz/">ESR</a> (New Zealand) and <a href="https://www.ornl.gov/news/ornl-fight-against-covid-19">ORNL</a> (USA) use COVID-19 PubSeq data +for monitoring, protein prediction and drug development. +</p> +</div> +</div> + +<div id="outline-container-orgd5907cf" class="outline-2"> +<h2 id="orgd5907cf"><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 +issues on our issue tracker, and more importantly add functionality. +See 'How do I change the source code' below. Read through our online +documentation at <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a> as a starting +point. +</p> +</div> +</div> + +<div id="outline-container-orgef93e3d" class="outline-2"> +<h2 id="orgef93e3d"><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> +(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-orgab39a73" class="outline-2"> +<h2 id="orgab39a73"><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 +can take our workflows and data and run it elsewhere! +</p> +</div> +</div> + +<div id="outline-container-orgad533ff" class="outline-2"> +<h2 id="orgad533ff"><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 +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-org4ca5ce9" class="outline-2"> +<h2 id="org4ca5ce9"><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>! +</p> +</div> +</div> + +<div id="outline-container-org2af2c45" class="outline-2"> +<h2 id="org2af2c45"><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 +<a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a> on workflows. +</p> +</div> +</div> + +<div id="outline-container-org6a3ff30" class="outline-2"> +<h2 id="org6a3ff30"><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 +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-org3bdaa46" class="outline-2"> +<h2 id="org3bdaa46"><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 +research. CC0 is the preferred license because it gives researchers +the most freedom. Since we provide metadata there is no reason for +others not to honour your work. We also provide CC-BY as an option +because we know people like the attribution clause. +</p> + +<p> +In all honesty: we prefer both data and software to be free. +</p> +</div> +</div> + +<div id="outline-container-orge4cdab7" class="outline-2"> +<h2 id="orge4cdab7"><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. +</p> + +<p> +We are also writing tools to generate VCF files directly from the pangenome. +</p> +</div> +</div> + +<div id="outline-container-org8a56c4c" class="outline-2"> +<h2 id="org8a56c4c"><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 +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>. 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-orgf3ba61a" class="outline-2"> +<h2 id="orgf3ba61a"><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. +</p> +</div> +</div> + +<div id="outline-container-orgc693d03" class="outline-2"> +<h2 id="orgc693d03"><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. +</p> +</div> +</div> + + +<div id="outline-container-org927057f" class="outline-2"> +<h2 id="org927057f"><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&utm_medium=link&utm_campaign=share-link">gitter channel</a> you can join. See also <a href="./contact">contact</a>. +</p> +</div> +</div> + +<div id="outline-container-orgb05122d" class="outline-2"> +<h2 id="orgb05122d"><span class="section-number-2">22</span> Citing PubSeq</h2> +<div class="outline-text-2" id="text-22"> +<p> +We have two publications in the works. Until we have a DOI please cite +PubSeq in the following way: +</p> + +<p> +We made use of the COVID-19 public sequence (PubSeq) resources hosted +at <a href="http://covid19.genenetwork.org/">http://covid19.genenetwork.org/</a>. +</p> +</div> +</div> + + +<div id="outline-container-org16a19a4" class="outline-2"> +<h2 id="org16a19a4"><span class="section-number-2">23</span> Who are the sponsors?</h2> +<div class="outline-text-2" id="text-23"> +<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 2020-07-18 Sat 03:27</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 2020-08-24 Mon 03:12</small>. </div> </body> </html> |