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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> diff --git a/doc/web/about.org b/doc/web/about.org index 1b7bda1..d8d7f73 100644 --- a/doc/web/about.org +++ b/doc/web/about.org @@ -18,11 +18,12 @@ - [[#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?]] - - [[#are-there-also-variant-in-the-rdf-databases-][Are there also variant in the RDF databases? *]] + - [[#are-there-also-variant-in-the-rdf-databases][Are there also variant in the RDF databases?]] - [[#how-do-i-deal-with-private-data-and-privacy][How do I deal with private data and privacy?]] - [[#do-you-have-any-checks-or-concerns-if-human-sequence-accidentally-submitted-to-your-service-as-part-of-a-fastq-][Do you have any checks or concerns if human sequence accidentally submitted to your service as part of a fastq? *]] - - [[#does-pubseq-support-only-sars-cov-2-data-][Does PubSeq support only SARS-CoV-2 data? *]] + - [[#does-pubseq-support-only-sars-cov-2-data][Does PubSeq support only SARS-CoV-2 data?]] - [[#how-do-i-communicate-with-you][How do I communicate with you?]] + - [[#citing-pubseq][Citing PubSeq]] - [[#who-are-the-sponsors][Who are the sponsors?]] * What is the 'public sequence resource' about? @@ -209,7 +210,7 @@ because we know people like the attribution clause. In all honesty: we prefer both data and software to be free. -* Are there also variant in the RDF databases? * +* Are there also variant in the RDF databases? We do output a RDF file with the pangenome built in, and you can parse it because it has variants implicitly. @@ -226,7 +227,7 @@ plan to combine identifiers with clinical data stored securely at We are planning to remove reads that match the human reference. -* Does PubSeq support only SARS-CoV-2 data? * +* Does PubSeq support only SARS-CoV-2 data? 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. @@ -235,6 +236,15 @@ To date, PubSeq is a resource specific to SARS-CoV-2, but we are designing it to We use a [[https://gitter.im/arvados/pubseq?utm_source=share-link&utm_medium=link&utm_campaign=share-link][gitter channel]] you can join. See also [[./contact][contact]]. +* Citing PubSeq + +We have two publications in the works. Until we have a DOI please cite +PubSeq in the following way: + +We made use of the COVID-19 public sequence (PubSeq) resources hosted +at http://covid19.genenetwork.org/. + + * Who are the sponsors? The main sponsors are listed in the footer. In addition to the time diff --git a/doc/web/download.html b/doc/web/download.html index 1d196a0..998c87b 100644 --- a/doc/web/download.html +++ b/doc/web/download.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> -<!-- 2020-06-12 Fri 04:41 --> +<!-- 2020-08-24 Mon 03:08 --> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1" /> <title>Download</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="#orgcd3d82f">1. Workflow runs</a></li> -<li><a href="#org9aff936">2. FASTA files</a></li> -<li><a href="#orgc3e953c">3. Metadata</a></li> -<li><a href="#orgc9c55c4">4. Pangenome</a> +<li><a href="#orgc7d7db3">1. Workflow runs</a></li> +<li><a href="#org3b6bb40">2. FASTA files</a></li> +<li><a href="#orgef20a06">3. Metadata</a></li> +<li><a href="#orgaabb9da">4. Pangenome</a> <ul> -<li><a href="#org82c3ce9">4.1. Pangenome GFA format</a></li> -<li><a href="#orgf63e9f7">4.2. Pangenome in ODGI format</a></li> -<li><a href="#org8faf32f">4.3. Pangenome RDF format</a></li> -<li><a href="#org0c452f6">4.4. Pangenome Browser format</a></li> +<li><a href="#org1171db3">4.1. Pangenome GFA format</a></li> +<li><a href="#orgfc74439">4.2. Pangenome in ODGI format</a></li> +<li><a href="#orge6bb923">4.3. Pangenome RDF format</a></li> +<li><a href="#org5978f5c">4.4. Pangenome Browser format</a></li> </ul> </li> -<li><a href="#org4707094">5. Log of workflow output</a></li> -<li><a href="#orgd4d8f91">6. All files</a></li> -<li><a href="#org237b3cf">7. Planned</a> +<li><a href="#orgae23127">5. Log of workflow output</a></li> +<li><a href="#org88613e5">6. All files</a></li> +<li><a href="#org97e0327">7. Planned</a> <ul> -<li><a href="#org66e03ac">7.1. Raw sequence data</a></li> -<li><a href="#orgdfae1b9">7.2. Multiple Sequence Alignment (MSA)</a></li> -<li><a href="#orgaedc43e">7.3. Phylogenetic tree</a></li> -<li><a href="#org19a6a11">7.4. Protein prediction</a></li> +<li><a href="#org35758f9">7.1. Raw sequence data</a></li> +<li><a href="#orgab1c848">7.2. Multiple Sequence Alignment (MSA)</a></li> +<li><a href="#orgadb7ade">7.3. Phylogenetic tree</a></li> +<li><a href="#org3ec62c4">7.4. Protein prediction</a></li> </ul> </li> -<li><a href="#org49778b7">8. Source code</a></li> +<li><a href="#orga430457">8. Source code</a></li> +<li><a href="#org768f91e">9. Citing PubSeq</a></li> </ul> </div> </div> -<div id="outline-container-orgcd3d82f" class="outline-2"> -<h2 id="orgcd3d82f"><span class="section-number-2">1</span> Workflow runs</h2> +<div id="outline-container-orgc7d7db3" class="outline-2"> +<h2 id="orgc7d7db3"><span class="section-number-2">1</span> Workflow runs</h2> <div class="outline-text-2" id="text-1"> <p> The last runs can be viewed <a href="https://workbench.lugli.arvadosapi.com/projects/lugli-j7d0g-y4k4uswcqi3ku56#Subprojects">here</a>. If you click on a run you can see @@ -285,8 +286,8 @@ is listed under <code>Data collections</code>. All current data is listed </div> </div> -<div id="outline-container-org9aff936" class="outline-2"> -<h2 id="org9aff936"><span class="section-number-2">2</span> FASTA files</h2> +<div id="outline-container-org3b6bb40" class="outline-2"> +<h2 id="org3b6bb40"><span class="section-number-2">2</span> FASTA files</h2> <div class="outline-text-2" id="text-2"> <p> The <b>public sequence resource</b> provides all uploaded sequences as @@ -296,8 +297,8 @@ also provide a single file <a href="https://collections.lugli.arvadosapi.com/c=l </div> </div> -<div id="outline-container-orgc3e953c" class="outline-2"> -<h2 id="orgc3e953c"><span class="section-number-2">3</span> Metadata</h2> +<div id="outline-container-orgef20a06" class="outline-2"> +<h2 id="orgef20a06"><span class="section-number-2">3</span> Metadata</h2> <div class="outline-text-2" id="text-3"> <p> Metadata can be downloaded as <a href="https://www.w3.org/TR/turtle/">Turtle RDF</a> as a <a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/mergedmetadata.ttl">mergedmetadat.ttl</a> which @@ -319,8 +320,8 @@ graph can be downloaded from below Pangenome RDF format. </div> </div> -<div id="outline-container-orgc9c55c4" class="outline-2"> -<h2 id="orgc9c55c4"><span class="section-number-2">4</span> Pangenome</h2> +<div id="outline-container-orgaabb9da" class="outline-2"> +<h2 id="orgaabb9da"><span class="section-number-2">4</span> Pangenome</h2> <div class="outline-text-2" id="text-4"> <p> Pangenome data is made available in multiple guises. Variation graphs @@ -328,8 +329,8 @@ Pangenome data is made available in multiple guises. Variation graphs </p> </div> -<div id="outline-container-org82c3ce9" class="outline-3"> -<h3 id="org82c3ce9"><span class="section-number-3">4.1</span> Pangenome GFA format</h3> +<div id="outline-container-org1171db3" class="outline-3"> +<h3 id="org1171db3"><span class="section-number-3">4.1</span> Pangenome GFA format</h3> <div class="outline-text-3" id="text-4-1"> <p> <a href="https://github.com/GFA-spec/GFA-spec">GFA</a> is a standard for graphical fragment assembly and consumed @@ -338,8 +339,8 @@ by tools such as <a href="https://github.com/vgteam/vg">vgtools</a>. </div> </div> -<div id="outline-container-orgf63e9f7" class="outline-3"> -<h3 id="orgf63e9f7"><span class="section-number-3">4.2</span> Pangenome in ODGI format</h3> +<div id="outline-container-orgfc74439" class="outline-3"> +<h3 id="orgfc74439"><span class="section-number-3">4.2</span> Pangenome in ODGI format</h3> <div class="outline-text-3" id="text-4-2"> <p> <a href="https://github.com/vgteam/odgi">ODGI</a> is a format that supports an optimised dynamic genome/graph @@ -348,8 +349,8 @@ implementation. </div> </div> -<div id="outline-container-org8faf32f" class="outline-3"> -<h3 id="org8faf32f"><span class="section-number-3">4.3</span> Pangenome RDF format</h3> +<div id="outline-container-orge6bb923" class="outline-3"> +<h3 id="orge6bb923"><span class="section-number-3">4.3</span> Pangenome RDF format</h3> <div class="outline-text-3" id="text-4-3"> <p> An RDF file that includes the sequences themselves in a variation @@ -360,8 +361,8 @@ graph can be downloaded from </div> -<div id="outline-container-org0c452f6" class="outline-3"> -<h3 id="org0c452f6"><span class="section-number-3">4.4</span> Pangenome Browser format</h3> +<div id="outline-container-org5978f5c" class="outline-3"> +<h3 id="org5978f5c"><span class="section-number-3">4.4</span> Pangenome Browser format</h3> <div class="outline-text-3" id="text-4-4"> <p> The many JSON files that are named as @@ -372,8 +373,8 @@ Pangenome browser. </div> </div> -<div id="outline-container-org4707094" class="outline-2"> -<h2 id="org4707094"><span class="section-number-2">5</span> Log of workflow output</h2> +<div id="outline-container-orgae23127" class="outline-2"> +<h2 id="orgae23127"><span class="section-number-2">5</span> Log of workflow output</h2> <div class="outline-text-2" id="text-5"> <p> Including in below link is a log file of the last workflow runs. @@ -381,8 +382,8 @@ Including in below link is a log file of the last workflow runs. </div> </div> -<div id="outline-container-orgd4d8f91" class="outline-2"> -<h2 id="orgd4d8f91"><span class="section-number-2">6</span> All files</h2> +<div id="outline-container-org88613e5" class="outline-2"> +<h2 id="org88613e5"><span class="section-number-2">6</span> All files</h2> <div class="outline-text-2" id="text-6"> <p> <a href="https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/">https://collections.lugli.arvadosapi.com/c=lugli-4zz18-z513nlpqm03hpca/</a> @@ -390,16 +391,16 @@ Including in below link is a log file of the last workflow runs. </div> </div> -<div id="outline-container-org237b3cf" class="outline-2"> -<h2 id="org237b3cf"><span class="section-number-2">7</span> Planned</h2> +<div id="outline-container-org97e0327" class="outline-2"> +<h2 id="org97e0327"><span class="section-number-2">7</span> Planned</h2> <div class="outline-text-2" id="text-7"> <p> We are planning the add the following output (see also </p> </div> -<div id="outline-container-org66e03ac" class="outline-3"> -<h3 id="org66e03ac"><span class="section-number-3">7.1</span> Raw sequence data</h3> +<div id="outline-container-org35758f9" class="outline-3"> +<h3 id="org35758f9"><span class="section-number-3">7.1</span> Raw sequence data</h3> <div class="outline-text-3" id="text-7-1"> <p> See <a href="https://github.com/arvados/bh20-seq-resource/issues/16">fastq tracker</a> and <a href="https://github.com/arvados/bh20-seq-resource/issues/63">BAM tracker</a>. @@ -407,8 +408,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/16">fastq track </div> </div> -<div id="outline-container-orgdfae1b9" class="outline-3"> -<h3 id="orgdfae1b9"><span class="section-number-3">7.2</span> Multiple Sequence Alignment (MSA)</h3> +<div id="outline-container-orgab1c848" class="outline-3"> +<h3 id="orgab1c848"><span class="section-number-3">7.2</span> Multiple Sequence Alignment (MSA)</h3> <div class="outline-text-3" id="text-7-2"> <p> See <a href="https://github.com/arvados/bh20-seq-resource/issues/11">MSA tracker</a>. @@ -416,8 +417,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/11">MSA tracker </div> </div> -<div id="outline-container-orgaedc43e" class="outline-3"> -<h3 id="orgaedc43e"><span class="section-number-3">7.3</span> Phylogenetic tree</h3> +<div id="outline-container-orgadb7ade" class="outline-3"> +<h3 id="orgadb7ade"><span class="section-number-3">7.3</span> Phylogenetic tree</h3> <div class="outline-text-3" id="text-7-3"> <p> See <a href="https://github.com/arvados/bh20-seq-resource/issues/43">Phylo tracker</a>. @@ -425,8 +426,8 @@ See <a href="https://github.com/arvados/bh20-seq-resource/issues/43">Phylo track </div> </div> -<div id="outline-container-org19a6a11" class="outline-3"> -<h3 id="org19a6a11"><span class="section-number-3">7.4</span> Protein prediction</h3> +<div id="outline-container-org3ec62c4" class="outline-3"> +<h3 id="org3ec62c4"><span class="section-number-3">7.4</span> Protein prediction</h3> <div class="outline-text-3" id="text-7-4"> <p> We aim to make protein predictions available. @@ -435,8 +436,8 @@ We aim to make protein predictions available. </div> </div> -<div id="outline-container-org49778b7" class="outline-2"> -<h2 id="org49778b7"><span class="section-number-2">8</span> Source code</h2> +<div id="outline-container-orga430457" class="outline-2"> +<h2 id="orga430457"><span class="section-number-2">8</span> Source code</h2> <div class="outline-text-2" id="text-8"> <p> All source code for this website and tooling is available @@ -445,9 +446,18 @@ from </p> </div> </div> + +<div id="outline-container-org768f91e" class="outline-2"> +<h2 id="org768f91e"><span class="section-number-2">9</span> Citing PubSeq</h2> +<div class="outline-text-2" id="text-9"> +<p> +See the <a href="./about">FAQ</a>. +</p> +</div> +</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 2020-06-12 Fri 04:41</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 03:07</small>. </div> </body> </html> diff --git a/doc/web/download.org b/doc/web/download.org index 7614c60..a3f1949 100644 --- a/doc/web/download.org +++ b/doc/web/download.org @@ -18,6 +18,7 @@ - [[#phylogenetic-tree][Phylogenetic tree]] - [[#protein-prediction][Protein prediction]] - [[#source-code][Source code]] + - [[#citing-pubseq][Citing PubSeq]] * Workflow runs @@ -107,3 +108,7 @@ We aim to make protein predictions available. All source code for this website and tooling is available from https://github.com/arvados/bh20-seq-resource + +* Citing PubSeq + +See the [[./about][FAQ]]. |