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diff --git a/doc/web/about.html b/doc/web/about.html index bad4bb1..c907e6c 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> -<!-- 2020-05-28 Thu 08:40 --> +<!-- 2020-05-29 Fri 08:27 --> <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> @@ -247,29 +247,29 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#org43f7738">1. What is the 'public sequence resource' about?</a></li> -<li><a href="#orgde86ccd">2. Who created the public sequence resource?</a></li> -<li><a href="#orgdd37e45">3. How does the public sequence resource compare to other data resources?</a></li> -<li><a href="#org9edb5aa">4. Why should I upload my data here?</a></li> -<li><a href="#orgfbf8cae">5. Why should I not upload by data here?</a></li> -<li><a href="#org847ae99">6. How does the public sequence resource work?</a></li> -<li><a href="#orgf5b82cd">7. Who uses the public sequence resource?</a></li> -<li><a href="#orgb98ff9a">8. Is this about open data?</a></li> -<li><a href="#org1bd01df">9. Is this about free software?</a></li> -<li><a href="#org9b933c4">10. How do I upload raw data?</a></li> -<li><a href="#org3425b34">11. How do I change metadata?</a></li> -<li><a href="#org7ef551b">12. How do I change the work flows?</a></li> -<li><a href="#org2bdd0eb">13. How do I change the source code?</a></li> -<li><a href="#org0468035">14. Should I choose CC-BY or CC0?</a></li> -<li><a href="#org246712c">15. How do I deal with private data and privacy?</a></li> -<li><a href="#org29eb659">16. How do I communicate with you?</a></li> -<li><a href="#orgce9d1ee">17. Who are the sponsors?</a></li> +<li><a href="#org783b5e9">1. What is the 'public sequence resource' about?</a></li> +<li><a href="#org2c0bcfd">2. Who created the public sequence resource?</a></li> +<li><a href="#org34070d3">3. How does the public sequence resource compare to other data resources?</a></li> +<li><a href="#org64a9493">4. Why should I upload my data here?</a></li> +<li><a href="#orgf898e7f">5. Why should I not upload by data here?</a></li> +<li><a href="#org828e164">6. How does the public sequence resource work?</a></li> +<li><a href="#org7b0d03f">7. Who uses the public sequence resource?</a></li> +<li><a href="#org31aaf23">8. Is this about open data?</a></li> +<li><a href="#orgb376b6c">9. Is this about free software?</a></li> +<li><a href="#orgf19cd96">10. How do I upload raw data?</a></li> +<li><a href="#orgebfed00">11. How do I change metadata?</a></li> +<li><a href="#orge2aecf8">12. How do I change the work flows?</a></li> +<li><a href="#orgd45b3bc">13. How do I change the source code?</a></li> +<li><a href="#org2bb9455">14. Should I choose CC-BY or CC0?</a></li> +<li><a href="#org62bf23f">15. How do I deal with private data and privacy?</a></li> +<li><a href="#org40c6da0">16. How do I communicate with you?</a></li> +<li><a href="#org1f27c44">17. Who are the sponsors?</a></li> </ul> </div> </div> -<div id="outline-container-org43f7738" class="outline-2"> -<h2 id="org43f7738"><span class="section-number-2">1</span> What is the 'public sequence resource' about?</h2> +<div id="outline-container-org783b5e9" class="outline-2"> +<h2 id="org783b5e9"><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 @@ -280,8 +280,8 @@ sequence comparison and protein prediction. </div> </div> -<div id="outline-container-orgde86ccd" class="outline-2"> -<h2 id="orgde86ccd"><span class="section-number-2">2</span> Who created the public sequence resource?</h2> +<div id="outline-container-org2c0bcfd" class="outline-2"> +<h2 id="org2c0bcfd"><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 @@ -301,8 +301,8 @@ wrangling experts. Thank you everyone! </div> </div> -<div id="outline-container-orgdd37e45" class="outline-2"> -<h2 id="orgdd37e45"><span class="section-number-2">3</span> How does the public sequence resource compare to other data resources?</h2> +<div id="outline-container-org34070d3" class="outline-2"> +<h2 id="org34070d3"><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 @@ -321,8 +321,8 @@ public resources, including GISAID. </div> </div> -<div id="outline-container-org9edb5aa" class="outline-2"> -<h2 id="org9edb5aa"><span class="section-number-2">4</span> Why should I upload my data here?</h2> +<div id="outline-container-org64a9493" class="outline-2"> +<h2 id="org64a9493"><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 @@ -332,6 +332,8 @@ attribution</li> 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> @@ -351,8 +353,8 @@ multiple resources. </div> </div> -<div id="outline-container-orgfbf8cae" class="outline-2"> -<h2 id="orgfbf8cae"><span class="section-number-2">5</span> Why should I not upload by data here?</h2> +<div id="outline-container-orgf898e7f" class="outline-2"> +<h2 id="orgf898e7f"><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 @@ -374,8 +376,8 @@ for bulk uploads! </div> </div> -<div id="outline-container-org847ae99" class="outline-2"> -<h2 id="org847ae99"><span class="section-number-2">6</span> How does the public sequence resource work?</h2> +<div id="outline-container-org828e164" class="outline-2"> +<h2 id="org828e164"><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 @@ -386,8 +388,8 @@ using workflows from the High Performance Open Biology Lab defined </div> </div> -<div id="outline-container-orgf5b82cd" class="outline-2"> -<h2 id="orgf5b82cd"><span class="section-number-2">7</span> Who uses the public sequence resource?</h2> +<div id="outline-container-org7b0d03f" class="outline-2"> +<h2 id="org7b0d03f"><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 @@ -401,8 +403,8 @@ drug development. </div> </div> -<div id="outline-container-orgb98ff9a" class="outline-2"> -<h2 id="orgb98ff9a"><span class="section-number-2">8</span> Is this about open data?</h2> +<div id="outline-container-org31aaf23" class="outline-2"> +<h2 id="org31aaf23"><span class="section-number-2">8</span> Is this about open data?</h2> <div class="outline-text-2" id="text-8"> <p> All data is published under a <a href="https://creativecommons.org/licenses/by/4.0/">Creative Commons 4.0 attribution license</a> @@ -412,8 +414,8 @@ data and store it for further processing. </div> </div> -<div id="outline-container-org1bd01df" class="outline-2"> -<h2 id="org1bd01df"><span class="section-number-2">9</span> Is this about free software?</h2> +<div id="outline-container-orgb376b6c" class="outline-2"> +<h2 id="orgb376b6c"><span class="section-number-2">9</span> Is this about free software?</h2> <div class="outline-text-2" id="text-9"> <p> Absolutely. Free software allows for fully reproducible pipelines. You @@ -422,8 +424,8 @@ can take our workflows and data and run it elsewhere! </div> </div> -<div id="outline-container-org9b933c4" class="outline-2"> -<h2 id="org9b933c4"><span class="section-number-2">10</span> How do I upload raw data?</h2> +<div id="outline-container-orgf19cd96" class="outline-2"> +<h2 id="orgf19cd96"><span class="section-number-2">10</span> How do I upload raw data?</h2> <div class="outline-text-2" id="text-10"> <p> We are preparing raw sequence data pipelines (fastq and BAM). The @@ -438,8 +440,8 @@ assembly variations into consideration. This is all work in progress. </div> </div> -<div id="outline-container-org3425b34" class="outline-2"> -<h2 id="org3425b34"><span class="section-number-2">11</span> How do I change metadata?</h2> +<div id="outline-container-orgebfed00" class="outline-2"> +<h2 id="orgebfed00"><span class="section-number-2">11</span> How do I change metadata?</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>! @@ -447,8 +449,8 @@ See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork </div> </div> -<div id="outline-container-org7ef551b" class="outline-2"> -<h2 id="org7ef551b"><span class="section-number-2">12</span> How do I change the work flows?</h2> +<div id="outline-container-orge2aecf8" class="outline-2"> +<h2 id="orge2aecf8"><span class="section-number-2">12</span> How do I change the work flows?</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>! @@ -456,8 +458,8 @@ See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork </div> </div> -<div id="outline-container-org2bdd0eb" class="outline-2"> -<h2 id="org2bdd0eb"><span class="section-number-2">13</span> How do I change the source code?</h2> +<div id="outline-container-orgd45b3bc" class="outline-2"> +<h2 id="orgd45b3bc"><span class="section-number-2">13</span> How do I change the source code?</h2> <div class="outline-text-2" id="text-13"> <p> Go to our <a href="https://github.com/arvados/bh20-seq-resource">source code repositories</a>, fork/clone the repository, change @@ -467,8 +469,8 @@ many PRs we already merged. </div> </div> -<div id="outline-container-org0468035" class="outline-2"> -<h2 id="org0468035"><span class="section-number-2">14</span> Should I choose CC-BY or CC0?</h2> +<div id="outline-container-org2bb9455" class="outline-2"> +<h2 id="org2bb9455"><span class="section-number-2">14</span> Should I choose CC-BY or CC0?</h2> <div class="outline-text-2" id="text-14"> <p> Restrictive data licenses are hampering data sharing and reproducible @@ -484,8 +486,8 @@ In all honesty: we prefer both data and software to be free. </div> </div> -<div id="outline-container-org246712c" class="outline-2"> -<h2 id="org246712c"><span class="section-number-2">15</span> How do I deal with private data and privacy?</h2> +<div id="outline-container-org62bf23f" class="outline-2"> +<h2 id="org62bf23f"><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"> <p> A public sequence resource is about public data. Metadata can refer to @@ -496,8 +498,8 @@ plan to combine identifiers with clinical data stored securely at </div> </div> -<div id="outline-container-org29eb659" class="outline-2"> -<h2 id="org29eb659"><span class="section-number-2">16</span> How do I communicate with you?</h2> +<div id="outline-container-org40c6da0" class="outline-2"> +<h2 id="org40c6da0"><span class="section-number-2">16</span> How do I communicate with you?</h2> <div class="outline-text-2" id="text-16"> <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. @@ -505,8 +507,8 @@ We use a <a href="https://gitter.im/arvados/pubseq?utm_source=share-link&utm </div> </div> -<div id="outline-container-orgce9d1ee" class="outline-2"> -<h2 id="orgce9d1ee"><span class="section-number-2">17</span> Who are the sponsors?</h2> +<div id="outline-container-org1f27c44" class="outline-2"> +<h2 id="org1f27c44"><span class="section-number-2">17</span> Who are the sponsors?</h2> <div class="outline-text-2" id="text-17"> <p> The main sponsors are listed in the footer. In addition to the time @@ -517,7 +519,7 @@ 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 2020-05-28 Thu 08:40</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 2020-05-29 Fri 08:26</small>. </div> </body> </html> |