From cab2f4ca70c08d9f44442ba01bdfa5639017084b Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sat, 22 Aug 2020 11:04:56 +0100 Subject: Repositioning content --- doc/web/about.html | 138 ++++++++++++------------- doc/web/about.org | 2 +- doc/web/contact.html | 286 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/web/contact.org | 20 ++++ 4 files changed, 376 insertions(+), 70 deletions(-) create mode 100644 doc/web/contact.html create mode 100644 doc/web/contact.org (limited to 'doc') diff --git a/doc/web/about.html b/doc/web/about.html index a4ab186..f6d1761 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 @@ -234,34 +234,34 @@ 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 @@ -272,8 +272,8 @@ sequence comparison and protein prediction.

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2 Presentations

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2 Presentations

We presented at the BOSC 2020 Have a look at the video (alternative @@ -282,8 +282,8 @@ link) and the -

3 Who created the public sequence resource?

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

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

The short version is that we use state-of-the-art practices in @@ -328,8 +328,8 @@ such as GISAID.

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5 Why should I upload my data here?

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5 Why should I upload my data here?

  1. We champion truly shareable data without licensing restrictions - with proper @@ -360,8 +360,8 @@ multiple resources.
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6 Why should I not upload by data here?

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6 Why should I not upload by data here?

Funny question. There are only good reasons to upload your data here @@ -383,8 +383,8 @@ for bulk uploads!

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7 How does the public sequence resource work?

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7 How does the public sequence resource work?

On uploading a sequence with metadata it will automatically be @@ -395,8 +395,8 @@ using workflows from the High Performance Open Biology Lab defined

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8 Who uses the public sequence resource?

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8 Who uses the public sequence resource?

The Swiss Institute of Bioinformatics has included this data in @@ -414,8 +414,8 @@ for monitoring, protein prediction and drug development.

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9 How can I contribute?

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9 How can I contribute?

You can contribute by submitting sequences, updating metadata, submit @@ -427,8 +427,8 @@ point.

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10 Is this about open data?

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10 Is this about open data?

All data is published under a Creative Commons 4.0 attribution license @@ -438,8 +438,8 @@ data and store it for further processing.

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11 Is this about free software?

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11 Is this about free software?

Absolutely. Free software allows for fully reproducible pipelines. You @@ -448,8 +448,8 @@ can take our workflows and data and run it elsewhere!

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12 How do I upload raw data?

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12 How do I upload raw data?

We are preparing raw sequence data pipelines (fastq and BAM). The @@ -464,8 +464,8 @@ assembly variations into consideration. This is all work in progress.

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13 How do I change metadata?

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13 How do I change metadata?

See the http://covid19.genenetwork.org/blog! @@ -473,8 +473,8 @@ See the http://covid19.genenetwork

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14 How do I change the work flows?

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14 How do I change the work flows?

Workflows are on github and can be modified. See also the BLOG @@ -483,8 +483,8 @@ Workflows are on -

15 How do I change the source code?

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15 How do I change the source code?

Go to our source code repositories, fork/clone the repository, change @@ -494,8 +494,8 @@ many PRs we already merged.

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16 Should I choose CC-BY or CC0?

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16 Should I choose CC-BY or CC0?

Restrictive data licenses are hampering data sharing and reproducible @@ -511,8 +511,8 @@ In all honesty: we prefer both data and software to be free.

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17 Are there also variant in the RDF databases? *

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17 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. @@ -524,8 +524,8 @@ We are also writing tools to generate VCF files directly from the pangenome.

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18 How do I deal with private data and privacy?

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18 How do I deal with private data and privacy?

A public sequence resource is about public data. Metadata can refer to @@ -536,8 +536,8 @@ plan to combine identifiers with clinical data stored securely at

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19 Do you have any checks or concerns if human sequence accidentally submitted to your service as part of a fastq? *

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19 Do you have any checks or concerns if human sequence accidentally submitted to your service as part of a fastq? *

We are planning to remove reads that match the human reference. @@ -545,8 +545,8 @@ We are planning to remove reads that match the human reference.

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20 Does PubSeq support only SARS-CoV-2 data? *

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20 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. @@ -555,17 +555,17 @@ To date, PubSeq is a resource specific to SARS-CoV-2, but we are designing it to

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21 How do I communicate with you?

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21 How do I communicate with you?

-We use a gitter channel you can join. +We use a gitter channel you can join. See also contact.

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22 Who are the sponsors?

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22 Who are the sponsors?

The main sponsors are listed in the footer. In addition to the time @@ -576,7 +576,7 @@ 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 2020-08-22 Sat 03:48. +
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-08-22 Sat 04:42.
diff --git a/doc/web/about.org b/doc/web/about.org index 5f864e9..efd914f 100644 --- a/doc/web/about.org +++ b/doc/web/about.org @@ -204,7 +204,7 @@ To date, PubSeq is a resource specific to SARS-CoV-2, but we are designing it to * 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. +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]]. * Who are the sponsors? diff --git a/doc/web/contact.html b/doc/web/contact.html new file mode 100644 index 0000000..8372743 --- /dev/null +++ b/doc/web/contact.html @@ -0,0 +1,286 @@ + + + + + + + +CONTACT + + + + + + +
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CONTACT

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Table of Contents

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1 CONTACT and SUPPORT

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+COVID-19 PubSeq was created by a group of bioinformaticians and +software developers working at leading institutes (see sponsors +below). You can talk with us directly on a gitter channel. We are open +to improving work flows and analysis. +

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1.1 Professional support

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+To use COVID-19 PubSeq solutions for professional purposes you can +contact Curii, the creators of Arvados, directly. +

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+COVID-19 is built on Arvados using CWL workflows. +

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1.2 E-mail

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+For other questions feel free to write directly to Pjotr Prins. +

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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 2020-08-22 Sat 05:03. +
+ + diff --git a/doc/web/contact.org b/doc/web/contact.org new file mode 100644 index 0000000..f410cee --- /dev/null +++ b/doc/web/contact.org @@ -0,0 +1,20 @@ +#+TITLE: CONTACT +#+AUTHOR: Pjotr Prins + +* CONTACT and SUPPORT + +COVID-19 PubSeq was created by a group of [[https://github.com/arvados/bh20-seq-resource/graphs/contributors][bioinformaticians]] and +software developers working at leading institutes (see sponsors +below). You can talk with us directly on a [[https://gitter.im/arvados/pubseq?utm_source=share-link&utm_medium=link&utm_campaign=share-link][gitter channel]]. We are open +to improving work flows and analysis. + +** Professional support + +To use COVID-19 PubSeq solutions for professional purposes you can +contact [[mailto:info@curii.com][Curii]], the creators of [[https://arvados.org/][Arvados]], directly. + +COVID-19 is built on Arvados using CWL workflows. + +** E-mail + +For other questions feel free to write directly to [[mailto:pjotr.public821@thebird.nl][Pjotr Prins]]. -- cgit v1.2.3