From d12a580db8146f8ebc511119698e63e3a5de0147 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 28 May 2020 08:42:05 -0500 Subject: Added Who uses the public sequence resource? to the FAQ --- doc/web/about.html | 135 ++++++++++++++++++++++++++++++----------------------- 1 file changed, 76 insertions(+), 59 deletions(-) (limited to 'doc/web/about.html') diff --git a/doc/web/about.html b/doc/web/about.html index cf718e7..bad4bb1 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"> - + About/FAQ @@ -247,28 +247,29 @@ for the JavaScript code in this tag.

Table of Contents

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1 What is the 'public sequence resource' about?

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1 What is the 'public sequence resource' about?

The public sequence resource aims to provide a generic and useful @@ -279,8 +280,8 @@ sequence comparison and protein prediction.

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2 Who created the public sequence resource?

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2 Who created the public sequence resource?

The public sequence resource is an initiative by bioinformatics and @@ -300,8 +301,8 @@ wrangling experts. Thank you everyone!

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3 How does the public sequence resource compare to other data resources?

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3 How does the public sequence resource compare to other data resources?

The short version is that we use state-of-the-art practices in @@ -320,8 +321,8 @@ public resources, including GISAID.

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4 Why should I upload my data here?

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4 Why should I upload my data here?

  1. We champion truly shareable data without licensing restrictions - with proper @@ -338,6 +339,7 @@ for bulk uploads
  2. Your data gets automatically integrated with the Swiss Institure of Bioinformatics COVID-19 knowledge base https://covid-19-sparql.expasy.org/ (Elixir Switzerland)
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  3. Your data will be used to develop drug targets

@@ -349,8 +351,8 @@ multiple resources.

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5 Why should I not upload by data here?

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5 Why should I not upload by data here?

Funny question. There are only good reasons to upload your data here @@ -372,8 +374,8 @@ for bulk uploads!

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6 How does the public sequence resource work?

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6 How does the public sequence resource work?

On uploading a sequence with metadata it will automatically be @@ -384,10 +386,25 @@ using workflows from the High Performance Open Biology Lab defined

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7 Is this about open data?

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7 Who uses the public sequence resource?

+The Swiss Institute of Bioinformatics has included this data in +https://covid-19-sparql.expasy.org/ and made it part of Uniprot. +

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+UTHSC and ORNL use COVID-19 PubSeq data for protein prediction and +drug development. +

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8 Is this about open data?

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All data is published under a Creative Commons 4.0 attribution license (CC-BY-4.0). You can download the raw and published (GFA/RDF/FASTA) data and store it for further processing. @@ -395,9 +412,9 @@ data and store it for further processing.

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8 Is this about free software?

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9 Is this about free software?

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Absolutely. Free software allows for fully reproducible pipelines. You can take our workflows and data and run it elsewhere! @@ -405,9 +422,9 @@ can take our workflows and data and run it elsewhere!

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9 How do I upload raw data?

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10 How do I upload raw data?

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We are preparing raw sequence data pipelines (fastq and BAM). The reason is that we want the best data possible for downstream analysis @@ -421,27 +438,27 @@ assembly variations into consideration. This is all work in progress.

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10 How do I change metadata?

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11 How do I change metadata?

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See the http://covid19.genenetwork.org/blog!

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11 How do I change the work flows?

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12 How do I change the work flows?

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See the http://covid19.genenetwork.org/blog!

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12 How do I change the source code?

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13 How do I change the source code?

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Go to our source code repositories, fork/clone the repository, change something and submit a pull request (PR). That easy! Check out how @@ -450,9 +467,9 @@ many PRs we already merged.

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13 Should I choose CC-BY or CC0?

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14 Should I choose CC-BY or CC0?

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Restrictive data licenses are hampering data sharing and reproducible research. CC0 is the preferred license because it gives researchers @@ -467,9 +484,9 @@ In all honesty: we prefer both data and software to be free.

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14 How do I deal with private data and privacy?

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15 How do I deal with private data and privacy?

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A public sequence resource is about public data. Metadata can refer to private data. You can use your own (anonymous) identifiers. We also @@ -479,18 +496,18 @@ plan to combine identifiers with clinical data stored securely at

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15 How do I communicate with you?

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16 How do I communicate with you?

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We use a gitter channel you can join.

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16 Who are the sponsors?

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17 Who are the sponsors?

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The main sponsors are listed in the footer. In addition to the time generously donated by many contributors we also acknowledge Amazon AWS @@ -500,7 +517,7 @@ for donating COVID-19 related compute time.

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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 07:08. +
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-05-28 Thu 08:40.
-- cgit v1.2.3