From e5f0990f97b8316ea618f0831b6858dde92afaed Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 27 May 2020 07:36:27 -0500 Subject: Wiring up blog entries --- doc/blog/using-covid-19-pubseq-part1.org | 7 + doc/blog/using-covid-19-pubseq-part2.org | 16 ++ doc/blog/using-covid-19-pubseq-part3.html | 286 ++++++++++++++++++++++++++++++ doc/blog/using-covid-19-pubseq-part3.org | 30 ++++ 4 files changed, 339 insertions(+) create mode 100644 doc/blog/using-covid-19-pubseq-part3.html (limited to 'doc/blog') diff --git a/doc/blog/using-covid-19-pubseq-part1.org b/doc/blog/using-covid-19-pubseq-part1.org index b1edbad..5a749d6 100644 --- a/doc/blog/using-covid-19-pubseq-part1.org +++ b/doc/blog/using-covid-19-pubseq-part1.org @@ -1,5 +1,12 @@ #+TITLE: COVID-19 PubSeq (part 1) #+AUTHOR: Pjotr Prins +# C-c C-e h h publish +# C-c ! insert date (use . for active agenda, C-u C-c ! for date, C-u C-c . for time) +# C-c C-t task rotate +# RSS_IMAGE_URL: http://xxxx.xxxx.free.fr/rss_icon.png + +#+HTML_LINK_HOME: http://covid19.genenetwork.org +#+HTML_HEAD: As part of the COVID-19 Biohackathon 2020 we formed a working group to create a COVID-19 Public Sequence Resource (COVID-19 PubSeq) for diff --git a/doc/blog/using-covid-19-pubseq-part2.org b/doc/blog/using-covid-19-pubseq-part2.org index d61bf42..d2a1cbc 100644 --- a/doc/blog/using-covid-19-pubseq-part2.org +++ b/doc/blog/using-covid-19-pubseq-part2.org @@ -8,6 +8,22 @@ #+HTML_LINK_HOME: http://covid19.genenetwork.org #+HTML_HEAD: +As part of the COVID-19 Biohackathon 2020 we formed a working group to +create a COVID-19 Public Sequence Resource (COVID-19 PubSeq) for +Corona virus sequences. The general idea is to create a repository +that has a low barrier to entry for uploading sequence data using best +practices. I.e., data published with a creative commons 4.0 (CC-4.0) +license with metadata using state-of-the art standards and, perhaps +most importantly, providing standardised workflows that get triggered +on upload, so that results are immediately available in standardised +data formats. + +* Table of Contents :TOC:noexport: + - [[#finding-output-of-workflows][Finding output of workflows]] + - [[#introduction][Introduction]] + - [[#the-arvados-file-interface][The Arvados file interface]] + - [[#using-the-arvados-api][Using the Arvados API]] + * Finding output of workflows As part of the COVID-19 Biohackathon 2020 we formed a working group to diff --git a/doc/blog/using-covid-19-pubseq-part3.html b/doc/blog/using-covid-19-pubseq-part3.html new file mode 100644 index 0000000..94d5a2e --- /dev/null +++ b/doc/blog/using-covid-19-pubseq-part3.html @@ -0,0 +1,286 @@ + + + + + + + +COVID-19 PubSeq Uploading Data (part 3) + + + + + + + +
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COVID-19 PubSeq Uploading Data (part 3)

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Table of Contents

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1 Uploading Data

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+Work in progress! +

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+As part of the COVID-19 Biohackathon 2020 we formed a working group to +create a COVID-19 Public Sequence Resource (COVID-19 PubSeq) for +Corona virus sequences. The general idea is to create a repository +that has a low barrier to entry for uploading sequence data using best +practices. I.e., data published with a creative commons 4.0 (CC-4.0) +license with metadata using state-of-the art standards and, perhaps +most importantly, providing standardised workflows that get triggered +on upload, so that results are immediately available in standardised +data formats. +

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2 What does this mean?

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Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-05-27 Wed 07:27. +
+ + diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org index c147ba3..d088f78 100644 --- a/doc/blog/using-covid-19-pubseq-part3.org +++ b/doc/blog/using-covid-19-pubseq-part3.org @@ -1,2 +1,32 @@ +#+TITLE: COVID-19 PubSeq Uploading Data (part 3) +#+AUTHOR: Pjotr Prins +# C-c C-e h h publish +# C-c ! insert date (use . for active agenda, C-u C-c ! for date, C-u C-c . for time) +# C-c C-t task rotate +# RSS_IMAGE_URL: http://xxxx.xxxx.free.fr/rss_icon.png + +#+HTML_HEAD: + +* Uploading Data + /Work in progress!/ +As part of the COVID-19 Biohackathon 2020 we formed a working group to +create a COVID-19 Public Sequence Resource (COVID-19 PubSeq) for +Corona virus sequences. The general idea is to create a repository +that has a low barrier to entry for uploading sequence data using best +practices. I.e., data published with a creative commons 4.0 (CC-4.0) +license with metadata using state-of-the art standards and, perhaps +most importantly, providing standardised workflows that get triggered +on upload, so that results are immediately available in standardised +data formats. + +* Table of Contents :TOC:noexport: + - [[#uploading-data][Uploading Data]] + - [[#table-of-contents][Table of Contents]] + - [[#what-does-this-mean][What does this mean?]] + +* Table of Contents :TOC:noexport: + - [[#what-does-this-mean][What does this mean?]] + +* What does this mean? -- cgit v1.2.3