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| author | Pjotr Prins | 2020-08-24 09:12:31 +0100 |
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| committer | Pjotr Prins | 2020-08-24 09:12:31 +0100 |
| commit | fe1402f898e3673aba725df62109df5bb2d8eef4 (patch) | |
| tree | 5815b6b08b10768f743f460ffcbd7c588a8ea273 /doc/web/about.html | |
| parent | 9a1ed60533e03830eac6d8e719d522a0b171dc67 (diff) | |
| download | bh20-seq-resource-fe1402f898e3673aba725df62109df5bb2d8eef4.tar.gz bh20-seq-resource-fe1402f898e3673aba725df62109df5bb2d8eef4.tar.lz bh20-seq-resource-fe1402f898e3673aba725df62109df5bb2d8eef4.zip | |
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| -rw-r--r-- | doc/web/about.html | 153 |
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diff --git a/doc/web/about.html b/doc/web/about.html index aa12851..2d1f51d 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> -<!-- 2020-08-23 Sun 04:26 --> +<!-- 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> @@ -247,34 +247,35 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<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> +<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-orgb53cfc4" class="outline-2"> -<h2 id="orgb53cfc4"><span class="section-number-2">1</span> What is the 'public sequence resource' about?</h2> +<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 @@ -322,8 +323,8 @@ follow. </div> </div> -<div id="outline-container-orgadbe833" class="outline-2"> -<h2 id="orgadbe833"><span class="section-number-2">2</span> Presentations</h2> +<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 @@ -332,8 +333,8 @@ link</a>) and the <a href="https://drive.google.com/file/d/1vyEgfvSqhM9yIwWZ6Iys </div> </div> -<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 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 @@ -354,8 +355,8 @@ wrangling experts. Thank you everyone! </div> </div> -<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 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 @@ -378,8 +379,8 @@ such as GISAID. </div> </div> -<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 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 @@ -410,8 +411,8 @@ multiple resources. </div> </div> -<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 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 @@ -433,8 +434,8 @@ for bulk uploads! </div> </div> -<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 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 @@ -445,8 +446,8 @@ using workflows from the High Performance Open Biology Lab defined </div> </div> -<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 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 @@ -464,8 +465,8 @@ for monitoring, protein prediction and drug development. </div> </div> -<div id="outline-container-org3789965" class="outline-2"> -<h2 id="org3789965"><span class="section-number-2">9</span> How can I contribute?</h2> +<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 @@ -477,8 +478,8 @@ point. </div> </div> -<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 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> @@ -488,8 +489,8 @@ data and store it for further processing. </div> </div> -<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 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 @@ -498,8 +499,8 @@ can take our workflows and data and run it elsewhere! </div> </div> -<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 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 @@ -514,8 +515,8 @@ assembly variations into consideration. This is all work in progress. </div> </div> -<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 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>! @@ -523,8 +524,8 @@ See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork </div> </div> -<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 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 @@ -533,8 +534,8 @@ Workflows are on <a href="https://github.com/arvados/bh20-seq-resource/tree/mast </div> </div> -<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 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 @@ -544,8 +545,8 @@ many PRs we already merged. </div> </div> -<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 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 @@ -561,8 +562,8 @@ In all honesty: we prefer both data and software to be free. </div> </div> -<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 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. @@ -574,8 +575,8 @@ We are also writing tools to generate VCF files directly from the pangenome. </div> </div> -<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 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 @@ -586,8 +587,8 @@ plan to combine identifiers with clinical data stored securely at </div> </div> -<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 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. @@ -595,8 +596,8 @@ We are planning to remove reads that match the human reference. </div> </div> -<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 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. @@ -605,8 +606,8 @@ To date, PubSeq is a resource specific to SARS-CoV-2, but we are designing it to </div> -<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 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>. @@ -614,10 +615,26 @@ We use a <a href="https://gitter.im/arvados/pubseq?utm_source=share-link&utm </div> </div> -<div id="outline-container-orgd7bf178" class="outline-2"> -<h2 id="orgd7bf178"><span class="section-number-2">22</span> Who are the sponsors?</h2> +<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. @@ -626,7 +643,7 @@ 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 2020-08-23 Sun 04:26</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> |