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diff --git a/doc/web/about.html b/doc/web/about.html index f6d1761..aa12851 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> -<!-- 2020-08-22 Sat 04:42 --> +<!-- 2020-08-23 Sun 04:26 --> <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 @@ -234,46 +247,83 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#org43f5d1e">1. What is the 'public sequence resource' about?</a></li> -<li><a href="#org706e720">2. Presentations</a></li> -<li><a href="#orge3b0114">3. Who created the public sequence resource?</a></li> -<li><a href="#org6b86244">4. How does the public sequence resource compare to other data resources?</a></li> -<li><a href="#org1030148">5. Why should I upload my data here?</a></li> -<li><a href="#orgdf90c2c">6. Why should I not upload by data here?</a></li> -<li><a href="#org3294b2e">7. How does the public sequence resource work?</a></li> -<li><a href="#orgfca20f4">8. Who uses the public sequence resource?</a></li> -<li><a href="#org0f602e3">9. How can I contribute?</a></li> -<li><a href="#org441ff7c">10. Is this about open data?</a></li> -<li><a href="#org42ceb37">11. Is this about free software?</a></li> -<li><a href="#org1c3275d">12. How do I upload raw data?</a></li> -<li><a href="#org7cb05f2">13. How do I change metadata?</a></li> -<li><a href="#org875e3c9">14. How do I change the work flows?</a></li> -<li><a href="#orgf485768">15. How do I change the source code?</a></li> -<li><a href="#orgae7cb27">16. Should I choose CC-BY or CC0?</a></li> -<li><a href="#org765d1a7">17. Are there also variant in the RDF databases? *</a></li> -<li><a href="#org66263d5">18. How do I deal with private data and privacy?</a></li> -<li><a href="#org6cd833b">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="#orge8f395f">20. Does PubSeq support only SARS-CoV-2 data? *</a></li> -<li><a href="#org8f5ae93">21. How do I communicate with you?</a></li> -<li><a href="#org15ea9a8">22. Who are the sponsors?</a></li> +<li><a href="#orgb53cfc4">1. What is the 'public sequence resource' about?</a></li> +<li><a href="#orgadbe833">2. Presentations</a></li> +<li><a href="#org6341702">3. Who created the public sequence resource?</a></li> +<li><a href="#orgf4727de">4. How does the public sequence resource compare to other data resources?</a></li> +<li><a href="#org7628c20">5. Why should I upload my data here?</a></li> +<li><a href="#org1d5608f">6. Why should I not upload by data here?</a></li> +<li><a href="#org247f60a">7. How does the public sequence resource work?</a></li> +<li><a href="#org08f84bf">8. Who uses the public sequence resource?</a></li> +<li><a href="#org3789965">9. How can I contribute?</a></li> +<li><a href="#orge01d432">10. Is this about open data?</a></li> +<li><a href="#org75db52c">11. Is this about free software?</a></li> +<li><a href="#org2334a85">12. How do I upload raw data?</a></li> +<li><a href="#org888f62f">13. How do I change metadata?</a></li> +<li><a href="#org13f3dcb">14. How do I change the work flows?</a></li> +<li><a href="#orga445ffc">15. How do I change the source code?</a></li> +<li><a href="#org35ec40a">16. Should I choose CC-BY or CC0?</a></li> +<li><a href="#org2ed95f2">17. Are there also variant in the RDF databases? *</a></li> +<li><a href="#org6e0f616">18. How do I deal with private data and privacy?</a></li> +<li><a href="#org4484eb1">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="#org22adb98">20. Does PubSeq support only SARS-CoV-2 data? *</a></li> +<li><a href="#org85ba0ed">21. How do I communicate with you?</a></li> +<li><a href="#orgd7bf178">22. Who are the sponsors?</a></li> </ul> </div> </div> -<div id="outline-container-org43f5d1e" class="outline-2"> -<h2 id="org43f5d1e"><span class="section-number-2">1</span> What is the 'public sequence resource' about?</h2> +<div id="outline-container-orgb53cfc4" class="outline-2"> +<h2 id="orgb53cfc4"><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. +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-org706e720" class="outline-2"> -<h2 id="org706e720"><span class="section-number-2">2</span> Presentations</h2> +<div id="outline-container-orgadbe833" class="outline-2"> +<h2 id="orgadbe833"><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 @@ -282,8 +332,8 @@ link</a>) and the <a href="https://drive.google.com/file/d/1vyEgfvSqhM9yIwWZ6Iys </div> </div> -<div id="outline-container-orge3b0114" class="outline-2"> -<h2 id="orge3b0114"><span class="section-number-2">3</span> Who created the public sequence resource?</h2> +<div id="outline-container-org6341702" class="outline-2"> +<h2 id="org6341702"><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 @@ -304,8 +354,8 @@ wrangling experts. Thank you everyone! </div> </div> -<div id="outline-container-org6b86244" class="outline-2"> -<h2 id="org6b86244"><span class="section-number-2">4</span> How does the public sequence resource compare to other data resources?</h2> +<div id="outline-container-orgf4727de" class="outline-2"> +<h2 id="orgf4727de"><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 @@ -328,8 +378,8 @@ such as GISAID. </div> </div> -<div id="outline-container-org1030148" class="outline-2"> -<h2 id="org1030148"><span class="section-number-2">5</span> Why should I upload my data here?</h2> +<div id="outline-container-org7628c20" class="outline-2"> +<h2 id="org7628c20"><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 @@ -360,8 +410,8 @@ multiple resources. </div> </div> -<div id="outline-container-orgdf90c2c" class="outline-2"> -<h2 id="orgdf90c2c"><span class="section-number-2">6</span> Why should I not upload by data here?</h2> +<div id="outline-container-org1d5608f" class="outline-2"> +<h2 id="org1d5608f"><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 @@ -383,8 +433,8 @@ for bulk uploads! </div> </div> -<div id="outline-container-org3294b2e" class="outline-2"> -<h2 id="org3294b2e"><span class="section-number-2">7</span> How does the public sequence resource work?</h2> +<div id="outline-container-org247f60a" class="outline-2"> +<h2 id="org247f60a"><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 @@ -395,8 +445,8 @@ using workflows from the High Performance Open Biology Lab defined </div> </div> -<div id="outline-container-orgfca20f4" class="outline-2"> -<h2 id="orgfca20f4"><span class="section-number-2">8</span> Who uses the public sequence resource?</h2> +<div id="outline-container-org08f84bf" class="outline-2"> +<h2 id="org08f84bf"><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 @@ -414,8 +464,8 @@ for monitoring, protein prediction and drug development. </div> </div> -<div id="outline-container-org0f602e3" class="outline-2"> -<h2 id="org0f602e3"><span class="section-number-2">9</span> How can I contribute?</h2> +<div id="outline-container-org3789965" class="outline-2"> +<h2 id="org3789965"><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 @@ -427,8 +477,8 @@ point. </div> </div> -<div id="outline-container-org441ff7c" class="outline-2"> -<h2 id="org441ff7c"><span class="section-number-2">10</span> Is this about open data?</h2> +<div id="outline-container-orge01d432" class="outline-2"> +<h2 id="orge01d432"><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> @@ -438,8 +488,8 @@ data and store it for further processing. </div> </div> -<div id="outline-container-org42ceb37" class="outline-2"> -<h2 id="org42ceb37"><span class="section-number-2">11</span> Is this about free software?</h2> +<div id="outline-container-org75db52c" class="outline-2"> +<h2 id="org75db52c"><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 @@ -448,8 +498,8 @@ can take our workflows and data and run it elsewhere! </div> </div> -<div id="outline-container-org1c3275d" class="outline-2"> -<h2 id="org1c3275d"><span class="section-number-2">12</span> How do I upload raw data?</h2> +<div id="outline-container-org2334a85" class="outline-2"> +<h2 id="org2334a85"><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 @@ -464,8 +514,8 @@ assembly variations into consideration. This is all work in progress. </div> </div> -<div id="outline-container-org7cb05f2" class="outline-2"> -<h2 id="org7cb05f2"><span class="section-number-2">13</span> How do I change metadata?</h2> +<div id="outline-container-org888f62f" class="outline-2"> +<h2 id="org888f62f"><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>! @@ -473,8 +523,8 @@ See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork </div> </div> -<div id="outline-container-org875e3c9" class="outline-2"> -<h2 id="org875e3c9"><span class="section-number-2">14</span> How do I change the work flows?</h2> +<div id="outline-container-org13f3dcb" class="outline-2"> +<h2 id="org13f3dcb"><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 @@ -483,8 +533,8 @@ Workflows are on <a href="https://github.com/arvados/bh20-seq-resource/tree/mast </div> </div> -<div id="outline-container-orgf485768" class="outline-2"> -<h2 id="orgf485768"><span class="section-number-2">15</span> How do I change the source code?</h2> +<div id="outline-container-orga445ffc" class="outline-2"> +<h2 id="orga445ffc"><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 @@ -494,8 +544,8 @@ many PRs we already merged. </div> </div> -<div id="outline-container-orgae7cb27" class="outline-2"> -<h2 id="orgae7cb27"><span class="section-number-2">16</span> Should I choose CC-BY or CC0?</h2> +<div id="outline-container-org35ec40a" class="outline-2"> +<h2 id="org35ec40a"><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 @@ -511,8 +561,8 @@ In all honesty: we prefer both data and software to be free. </div> </div> -<div id="outline-container-org765d1a7" class="outline-2"> -<h2 id="org765d1a7"><span class="section-number-2">17</span> Are there also variant in the RDF databases? *</h2> +<div id="outline-container-org2ed95f2" class="outline-2"> +<h2 id="org2ed95f2"><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. @@ -524,8 +574,8 @@ We are also writing tools to generate VCF files directly from the pangenome. </div> </div> -<div id="outline-container-org66263d5" class="outline-2"> -<h2 id="org66263d5"><span class="section-number-2">18</span> How do I deal with private data and privacy?</h2> +<div id="outline-container-org6e0f616" class="outline-2"> +<h2 id="org6e0f616"><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 @@ -536,8 +586,8 @@ plan to combine identifiers with clinical data stored securely at </div> </div> -<div id="outline-container-org6cd833b" class="outline-2"> -<h2 id="org6cd833b"><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 id="outline-container-org4484eb1" class="outline-2"> +<h2 id="org4484eb1"><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. @@ -545,8 +595,8 @@ We are planning to remove reads that match the human reference. </div> </div> -<div id="outline-container-orge8f395f" class="outline-2"> -<h2 id="orge8f395f"><span class="section-number-2">20</span> Does PubSeq support only SARS-CoV-2 data? *</h2> +<div id="outline-container-org22adb98" class="outline-2"> +<h2 id="org22adb98"><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. @@ -555,8 +605,8 @@ To date, PubSeq is a resource specific to SARS-CoV-2, but we are designing it to </div> -<div id="outline-container-org8f5ae93" class="outline-2"> -<h2 id="org8f5ae93"><span class="section-number-2">21</span> How do I communicate with you?</h2> +<div id="outline-container-org85ba0ed" class="outline-2"> +<h2 id="org85ba0ed"><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>. @@ -564,8 +614,8 @@ We use a <a href="https://gitter.im/arvados/pubseq?utm_source=share-link&utm </div> </div> -<div id="outline-container-org15ea9a8" class="outline-2"> -<h2 id="org15ea9a8"><span class="section-number-2">22</span> Who are the sponsors?</h2> +<div id="outline-container-orgd7bf178" class="outline-2"> +<h2 id="orgd7bf178"><span class="section-number-2">22</span> Who are the sponsors?</h2> <div class="outline-text-2" id="text-22"> <p> The main sponsors are listed in the footer. In addition to the time @@ -576,7 +626,7 @@ 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 2020-08-22 Sat 04:42</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 2020-08-23 Sun 04:26</small>. </div> </body> </html> |