From 9b0f79d557cfe370d09ff76fbc41c4ffd9f16f12 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Mon, 16 Nov 2020 10:42:55 +0000 Subject: About page --- doc/web/about.html | 206 +++++++++++++++++++++++------------------------------ 1 file changed, 91 insertions(+), 115 deletions(-) diff --git a/doc/web/about.html b/doc/web/about.html index 2d1f51d..81aed4d 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 @@ -40,7 +40,7 @@ } pre.src { position: relative; - overflow: visible; + overflow: auto; padding-top: 1.2em; } pre.src:before { @@ -194,50 +194,26 @@ /*]]>*/--> @@ -247,35 +223,35 @@ 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?

PubSeq, the public sequence resource, aims to provide a generic and @@ -323,8 +299,8 @@ follow.

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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 @@ -333,8 +309,8 @@ 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 @@ -379,8 +355,8 @@ 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 @@ -411,8 +387,8 @@ 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 @@ -434,8 +410,8 @@ 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 @@ -446,8 +422,8 @@ 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 @@ -465,8 +441,8 @@ 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 @@ -478,8 +454,8 @@ 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 @@ -489,8 +465,8 @@ 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 @@ -499,8 +475,8 @@ 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 @@ -515,8 +491,8 @@ 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! @@ -524,8 +500,8 @@ 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 @@ -534,8 +510,8 @@ 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 @@ -545,8 +521,8 @@ 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 @@ -562,8 +538,8 @@ 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. @@ -575,8 +551,8 @@ 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 @@ -587,8 +563,8 @@ 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. @@ -596,8 +572,8 @@ 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. @@ -606,8 +582,8 @@ 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 Contact: how do I communicate with you?

We use a gitter channel you can join. See also contact. @@ -615,8 +591,8 @@ We use a -

22 Citing PubSeq

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22 Citing PubSeq

We have two publications in the works. Until we have a DOI please cite @@ -631,8 +607,8 @@ at http://covid19.genenetwork.org/

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23 Who are the sponsors?

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23 Who are the sponsors?

The main sponsors are listed in the footer. In addition to the time @@ -643,7 +619,7 @@ 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 2020-08-24 Mon 03:12. +
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-11-16 Mon 04:42.
-- cgit v1.2.3