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diff --git a/doc/web/about.html b/doc/web/about.html index ca0d952..cf718e7 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> -<!-- 2020-05-24 Sun 11:24 --> +<!-- 2020-05-27 Wed 07:08 --> <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> @@ -247,26 +247,28 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#orgc702afb">1. What is the 'public sequence resource' about?</a></li> -<li><a href="#org757df7a">2. Who created the public sequence resource?</a></li> -<li><a href="#orgbcdc47e">3. How does the public sequence resource compare to other data resources?</a></li> -<li><a href="#org9a5b80c">4. Why should I upload my data here?</a></li> -<li><a href="#orge7b928b">5. Why should I not upload by data here?</a></li> -<li><a href="#org095184f">6. How does the public sequence resource work?</a></li> -<li><a href="#org562edc8">7. Is this about open data?</a></li> -<li><a href="#org9dab2c1">8. Is this about free software?</a></li> -<li><a href="#org71012a1">9. How do I upload raw data?</a></li> -<li><a href="#orgd1586af">10. How do I change metadata?</a></li> -<li><a href="#org6de2b89">11. How do I change the work flows?</a></li> -<li><a href="#org276e949">12. How do I change the source code?</a></li> -<li><a href="#org3fb1663">13. How do I deal with private data and privacy?</a></li> -<li><a href="#org4741f67">14. Who are the sponsors?</a></li> +<li><a href="#org2fe6bec">1. What is the 'public sequence resource' about?</a></li> +<li><a href="#org9946c6e">2. Who created the public sequence resource?</a></li> +<li><a href="#org947d1d7">3. How does the public sequence resource compare to other data resources?</a></li> +<li><a href="#org84cfcc3">4. Why should I upload my data here?</a></li> +<li><a href="#orgf0aeec4">5. Why should I not upload by data here?</a></li> +<li><a href="#orgdfa56b7">6. How does the public sequence resource work?</a></li> +<li><a href="#org18d42bb">7. Is this about open data?</a></li> +<li><a href="#orge4f73e2">8. Is this about free software?</a></li> +<li><a href="#org2329f25">9. How do I upload raw data?</a></li> +<li><a href="#org0a77739">10. How do I change metadata?</a></li> +<li><a href="#orgc390505">11. How do I change the work flows?</a></li> +<li><a href="#org22e65a5">12. How do I change the source code?</a></li> +<li><a href="#org414bffe">13. Should I choose CC-BY or CC0?</a></li> +<li><a href="#orga36bf3d">14. How do I deal with private data and privacy?</a></li> +<li><a href="#org9f4676e">15. How do I communicate with you?</a></li> +<li><a href="#org9bb4341">16. Who are the sponsors?</a></li> </ul> </div> </div> -<div id="outline-container-orgc702afb" class="outline-2"> -<h2 id="orgc702afb"><span class="section-number-2">1</span> What is the 'public sequence resource' about?</h2> +<div id="outline-container-org2fe6bec" class="outline-2"> +<h2 id="org2fe6bec"><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 @@ -277,8 +279,8 @@ sequence comparison and protein prediction. </div> </div> -<div id="outline-container-org757df7a" class="outline-2"> -<h2 id="org757df7a"><span class="section-number-2">2</span> Who created the public sequence resource?</h2> +<div id="outline-container-org9946c6e" class="outline-2"> +<h2 id="org9946c6e"><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 @@ -298,8 +300,8 @@ wrangling experts. Thank you everyone! </div> </div> -<div id="outline-container-orgbcdc47e" class="outline-2"> -<h2 id="orgbcdc47e"><span class="section-number-2">3</span> How does the public sequence resource compare to other data resources?</h2> +<div id="outline-container-org947d1d7" class="outline-2"> +<h2 id="org947d1d7"><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 @@ -318,8 +320,8 @@ public resources, including GISAID. </div> </div> -<div id="outline-container-org9a5b80c" class="outline-2"> -<h2 id="org9a5b80c"><span class="section-number-2">4</span> Why should I upload my data here?</h2> +<div id="outline-container-org84cfcc3" class="outline-2"> +<h2 id="org84cfcc3"><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 @@ -347,22 +349,31 @@ multiple resources. </div> </div> -<div id="outline-container-orge7b928b" class="outline-2"> -<h2 id="orge7b928b"><span class="section-number-2">5</span> Why should I not upload by data here?</h2> +<div id="outline-container-orgf0aeec4" class="outline-2"> +<h2 id="orgf0aeec4"><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! +Funny question. There are only good reasons to upload your data here +and make it available to the widest audience possible. +</p> + +<p> 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. +uploading your data to multiple resources. +</p> + +<p> +We recommend uploading to EBI and NCBI resources using our data +conversion tools. It means you only enter data once and make the +process smooth. You can also use our command line data uploader +for bulk uploads! </p> </div> </div> -<div id="outline-container-org095184f" class="outline-2"> -<h2 id="org095184f"><span class="section-number-2">6</span> How does the public sequence resource work?</h2> +<div id="outline-container-orgdfa56b7" class="outline-2"> +<h2 id="orgdfa56b7"><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 @@ -373,8 +384,8 @@ using workflows from the High Performance Open Biology Lab defined </div> </div> -<div id="outline-container-org562edc8" class="outline-2"> -<h2 id="org562edc8"><span class="section-number-2">7</span> Is this about open data?</h2> +<div id="outline-container-org18d42bb" class="outline-2"> +<h2 id="org18d42bb"><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> @@ -384,8 +395,8 @@ data and store it for further processing. </div> </div> -<div id="outline-container-org9dab2c1" class="outline-2"> -<h2 id="org9dab2c1"><span class="section-number-2">8</span> Is this about free software?</h2> +<div id="outline-container-orge4f73e2" class="outline-2"> +<h2 id="orge4f73e2"><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 @@ -394,8 +405,8 @@ can take our workflows and data and run it elsewhere! </div> </div> -<div id="outline-container-org71012a1" class="outline-2"> -<h2 id="org71012a1"><span class="section-number-2">9</span> How do I upload raw data?</h2> +<div id="outline-container-org2329f25" class="outline-2"> +<h2 id="org2329f25"><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 @@ -410,8 +421,8 @@ assembly variations into consideration. This is all work in progress. </div> </div> -<div id="outline-container-orgd1586af" class="outline-2"> -<h2 id="orgd1586af"><span class="section-number-2">10</span> How do I change metadata?</h2> +<div id="outline-container-org0a77739" class="outline-2"> +<h2 id="org0a77739"><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>! @@ -419,8 +430,8 @@ See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork </div> </div> -<div id="outline-container-org6de2b89" class="outline-2"> -<h2 id="org6de2b89"><span class="section-number-2">11</span> How do I change the work flows?</h2> +<div id="outline-container-orgc390505" class="outline-2"> +<h2 id="orgc390505"><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>! @@ -428,8 +439,8 @@ See the <a href="http://covid19.genenetwork.org/blog">http://covid19.genenetwork </div> </div> -<div id="outline-container-org276e949" class="outline-2"> -<h2 id="org276e949"><span class="section-number-2">12</span> How do I change the source code?</h2> +<div id="outline-container-org22e65a5" class="outline-2"> +<h2 id="org22e65a5"><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 @@ -439,10 +450,27 @@ many PRs we already merged. </div> </div> -<div id="outline-container-org3fb1663" class="outline-2"> -<h2 id="org3fb1663"><span class="section-number-2">13</span> How do I deal with private data and privacy?</h2> +<div id="outline-container-org414bffe" class="outline-2"> +<h2 id="org414bffe"><span class="section-number-2">13</span> Should I choose CC-BY or CC0?</h2> <div class="outline-text-2" id="text-13"> <p> +Restrictive data licenses are hampering data sharing and reproducible +research. CC0 is the preferred license because it gives researchers +the most freedom. Since we provide metadata there is no reason for +others not to honour your work. We also provide CC-BY as an option +because we know people like the attribution clause. +</p> + +<p> +In all honesty: we prefer both data and software to be free. +</p> +</div> +</div> + +<div id="outline-container-orga36bf3d" class="outline-2"> +<h2 id="orga36bf3d"><span class="section-number-2">14</span> How do I deal with private data and privacy?</h2> +<div class="outline-text-2" id="text-14"> +<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 @@ -451,9 +479,18 @@ plan to combine identifiers with clinical data stored securely at </div> </div> -<div id="outline-container-org4741f67" class="outline-2"> -<h2 id="org4741f67"><span class="section-number-2">14</span> Who are the sponsors?</h2> -<div class="outline-text-2" id="text-14"> +<div id="outline-container-org9f4676e" class="outline-2"> +<h2 id="org9f4676e"><span class="section-number-2">15</span> How do I communicate with you?</h2> +<div class="outline-text-2" id="text-15"> +<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-org9bb4341" class="outline-2"> +<h2 id="org9bb4341"><span class="section-number-2">16</span> Who are the sponsors?</h2> +<div class="outline-text-2" id="text-16"> <p> The main sponsors are listed in the footer. In addition to the time generously donated by many contributors we also acknowledge Amazon AWS @@ -463,7 +500,7 @@ 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 2020-05-24 Sun 11:24</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 2020-05-27 Wed 07:08</small>. </div> </body> </html> diff --git a/doc/web/about.org b/doc/web/about.org index f343eb2..bb49c2a 100644 --- a/doc/web/about.org +++ b/doc/web/about.org @@ -14,7 +14,9 @@ - [[#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?]] + - [[#should-i-choose-cc-by-or-cc0][Should I choose CC-BY or CC0?]] - [[#how-do-i-deal-with-private-data-and-privacy][How do I deal with private data and privacy?]] + - [[#how-do-i-communicate-with-you][How do I communicate with you?]] - [[#who-are-the-sponsors][Who are the sponsors?]] * What is the 'public sequence resource' about? @@ -130,6 +132,16 @@ Go to our [[https://github.com/arvados/bh20-seq-resource][source code repositori 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. +* Should I choose CC-BY or CC0? + +Restrictive data licenses are hampering data sharing and reproducible +research. CC0 is the preferred license because it gives researchers +the most freedom. Since we provide metadata there is no reason for +others not to honour your work. We also provide CC-BY as an option +because we know people like the attribution clause. + +In all honesty: we prefer both data and software to be free. + * How do I deal with private data and privacy? A public sequence resource is about public data. Metadata can refer to @@ -137,6 +149,10 @@ 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]]. See the relevant [[https://github.com/arvados/bh20-seq-resource/issues/21][tracker]] for more information and contributing. +* How do I communicate with you? + +We use a [[https://gitter.im/arvados/pubseq?utm_source=share-link&utm_medium=link&utm_campaign=share-link][gitter channel]] you can join. + * Who are the sponsors? The main sponsors are listed in the footer. In addition to the time |