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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]] diff --git a/doc/web/about.html b/doc/web/about.html new file mode 100644 index 0000000..1f8b1a1 --- /dev/null +++ b/doc/web/about.html @@ -0,0 +1,462 @@ +<?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"> +<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> +<head> +<!-- 2020-05-24 Sun 10:27 --> +<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; 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+ 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="#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 new file mode 100644 index 0000000..fc9d1ff --- /dev/null +++ b/doc/web/about.org @@ -0,0 +1,134 @@ +#+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. |