diff options
Diffstat (limited to 'doc/web')
| -rw-r--r-- | doc/web/about.html | 169 | ||||
| -rw-r--r-- | doc/web/about.org | 26 |
2 files changed, 119 insertions, 76 deletions
diff --git a/doc/web/about.html b/doc/web/about.html index 9b16c92..dfd4252 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> -<!-- 2020-07-12 Sun 06:29 --> +<!-- 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> @@ -161,6 +161,19 @@ .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; @@ -185,7 +198,7 @@ @licstart The following is the entire license notice for the JavaScript code in this tag. -Copyright (C) 2012-2018 Free Software Foundation, Inc. +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 @@ -234,29 +247,30 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#orgac6ad8b">1. What is the 'public sequence resource' about?</a></li> -<li><a href="#org0c21c2e">2. Who created the public sequence resource?</a></li> -<li><a href="#org3fb8cb3">3. How does the public sequence resource compare to other data resources?</a></li> -<li><a href="#org6cd9ea2">4. Why should I upload my data here?</a></li> -<li><a href="#org0b6e3fb">5. Why should I not upload by data here?</a></li> -<li><a href="#org3eb3a4e">6. How does the public sequence resource work?</a></li> -<li><a href="#org7a397f5">7. Who uses the public sequence resource?</a></li> -<li><a href="#org92cb008">8. Is this about open data?</a></li> -<li><a href="#org232d6fa">9. Is this about free software?</a></li> -<li><a href="#orgd93869f">10. How do I upload raw data?</a></li> -<li><a href="#org88e8b0a">11. How do I change metadata?</a></li> -<li><a href="#orgd04b8f8">12. How do I change the work flows?</a></li> -<li><a href="#org5d1ee05">13. How do I change the source code?</a></li> -<li><a href="#orgae6461b">14. Should I choose CC-BY or CC0?</a></li> -<li><a href="#org3ea90a9">15. How do I deal with private data and privacy?</a></li> -<li><a href="#org7ff7106">16. How do I communicate with you?</a></li> -<li><a href="#org9566fa7">17. Who are the sponsors?</a></li> +<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-orgac6ad8b" class="outline-2"> -<h2 id="orgac6ad8b"><span class="section-number-2">1</span> What is the 'public sequence resource' about?</h2> +<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 @@ -267,8 +281,8 @@ sequence comparison and protein prediction. </div> </div> -<div id="outline-container-org0c21c2e" class="outline-2"> -<h2 id="org0c21c2e"><span class="section-number-2">2</span> Who created the public sequence resource?</h2> +<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 @@ -289,14 +303,17 @@ wrangling experts. Thank you everyone! </div> </div> -<div id="outline-container-org3fb8cb3" class="outline-2"> -<h2 id="org3fb8cb3"><span class="section-number-2">3</span> How does the public sequence resource compare to other data resources?</h2> +<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! +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> @@ -305,13 +322,13 @@ Importantly: all data is published under either the <a href="https://creativecom 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. +such as GISAID. </p> </div> </div> -<div id="outline-container-org6cd9ea2" class="outline-2"> -<h2 id="org6cd9ea2"><span class="section-number-2">4</span> Why should I upload my data here?</h2> +<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 @@ -335,15 +352,15 @@ Bioinformatics COVID-19 knowledge base <p> Finally, if you upload your data here we have workflows that output -formatted data suitable for uploading to EBI resources (and soon +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-org0b6e3fb" class="outline-2"> -<h2 id="org0b6e3fb"><span class="section-number-2">5</span> Why should I not upload by data here?</h2> +<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 @@ -365,8 +382,8 @@ for bulk uploads! </div> </div> -<div id="outline-container-org3eb3a4e" class="outline-2"> -<h2 id="org3eb3a4e"><span class="section-number-2">6</span> How does the public sequence resource work?</h2> +<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 @@ -377,8 +394,8 @@ using workflows from the High Performance Open Biology Lab defined </div> </div> -<div id="outline-container-org7a397f5" class="outline-2"> -<h2 id="org7a397f5"><span class="section-number-2">7</span> Who uses the public sequence resource?</h2> +<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 @@ -390,16 +407,29 @@ The Pantograph <a href="https://graph-genome.github.io/">viewer</a> uses PubSeq </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. +<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-org92cb008" class="outline-2"> -<h2 id="org92cb008"><span class="section-number-2">8</span> Is this about open data?</h2> +<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. @@ -407,9 +437,9 @@ data and store it for further processing. </div> </div> -<div id="outline-container-org232d6fa" class="outline-2"> -<h2 id="org232d6fa"><span class="section-number-2">9</span> Is this about free software?</h2> -<div class="outline-text-2" id="text-9"> +<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! @@ -417,9 +447,9 @@ can take our workflows and data and run it elsewhere! </div> </div> -<div id="outline-container-orgd93869f" class="outline-2"> -<h2 id="orgd93869f"><span class="section-number-2">10</span> How do I upload raw data?</h2> -<div class="outline-text-2" id="text-10"> +<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 @@ -433,27 +463,28 @@ assembly variations into consideration. This is all work in progress. </div> </div> -<div id="outline-container-org88e8b0a" class="outline-2"> -<h2 id="org88e8b0a"><span class="section-number-2">11</span> How do I change metadata?</h2> -<div class="outline-text-2" id="text-11"> +<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-orgd04b8f8" class="outline-2"> -<h2 id="orgd04b8f8"><span class="section-number-2">12</span> How do I change the work flows?</h2> -<div class="outline-text-2" id="text-12"> +<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> -See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork.org/blog</a>! +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-org5d1ee05" class="outline-2"> -<h2 id="org5d1ee05"><span class="section-number-2">13</span> How do I change the source code?</h2> -<div class="outline-text-2" id="text-13"> +<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 @@ -462,9 +493,9 @@ many PRs we already merged. </div> </div> -<div id="outline-container-orgae6461b" class="outline-2"> -<h2 id="orgae6461b"><span class="section-number-2">14</span> Should I choose CC-BY or CC0?</h2> -<div class="outline-text-2" id="text-14"> +<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 @@ -479,9 +510,9 @@ In all honesty: we prefer both data and software to be free. </div> </div> -<div id="outline-container-org3ea90a9" class="outline-2"> -<h2 id="org3ea90a9"><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"> +<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 @@ -491,18 +522,18 @@ plan to combine identifiers with clinical data stored securely at </div> </div> -<div id="outline-container-org7ff7106" class="outline-2"> -<h2 id="org7ff7106"><span class="section-number-2">16</span> How do I communicate with you?</h2> -<div class="outline-text-2" id="text-16"> +<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-org9566fa7" class="outline-2"> -<h2 id="org9566fa7"><span class="section-number-2">17</span> Who are the sponsors?</h2> -<div class="outline-text-2" id="text-17"> +<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 @@ -512,7 +543,7 @@ 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 2020-07-12 Sun 04:54</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 2020-07-18 Sat 03:27</small>. </div> </body> </html> diff --git a/doc/web/about.org b/doc/web/about.org index 1949e2d..39fb667 100644 --- a/doc/web/about.org +++ b/doc/web/about.org @@ -9,6 +9,7 @@ - [[#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?]] + - [[#how-can-i-contribute][How can I contribute?]] - [[#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?]] @@ -47,14 +48,17 @@ wrangling experts. Thank you everyone! 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! +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). Importantly: all data is published under either the [[https://creativecommons.org/licenses/by/4.0/][Creative Commons 4.0 attribution license]] or the [[https://creativecommons.org/share-your-work/public-domain/cc0/][CC0 “No Rights Reserved” 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. +such as GISAID. * Why should I upload my data here? @@ -77,7 +81,7 @@ including GISAID. 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 +formatted data suitable for [[http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part6][uploading to EBI resources]] (and soon others). Uploading your data here get your data ready for upload to multiple resources. @@ -109,8 +113,16 @@ https://covid-19-sparql.expasy.org/ and made it part of [[https://www.uniprot.or The Pantograph [[https://graph-genome.github.io/][viewer]] uses PubSeq data for their visualisations. -[[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. +[[https://uthsc.edu][UTHSC]] (USA), [[https://www.esr.cri.nz/][ESR]] (New Zealand) and [[https://www.ornl.gov/news/ornl-fight-against-covid-19][ORNL]] (USA) use COVID-19 PubSeq data +for monitoring, protein prediction and drug development. + +* How can I contribute? + +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 http://covid19.genenetwork.org/blog as a starting +point. * Is this about open data? @@ -140,8 +152,8 @@ See the [[http://covid19.genenetwork.org/blog]]! * How do I change the work flows? -Workflows are on [[https://github.com/arvados/bh20-seq-resource/tree/master/workflows][github]] and can be modified. See also the -[[[[http://covid19.genenetwork.org/blog]]][workflow blog]]. +Workflows are on [[https://github.com/arvados/bh20-seq-resource/tree/master/workflows][github]] and can be modified. See also the BLOG +[[http://covid19.genenetwork.org/blog]] on workflows. * How do I change the source code? |