From fe1402f898e3673aba725df62109df5bb2d8eef4 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Mon, 24 Aug 2020 09:12:31 +0100 Subject: Images --- doc/web/about.html | 153 +++++++++++++++++++++++++++++------------------------ 1 file changed, 85 insertions(+), 68 deletions(-) (limited to 'doc/web/about.html') 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"> - + About/FAQ @@ -247,34 +247,35 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 What is the 'public sequence resource' about?

+
+

1 What is the 'public sequence resource' about?

PubSeq, the public sequence resource, aims to provide a generic and @@ -322,8 +323,8 @@ follow.

-
-

2 Presentations

+
+

2 Presentations

We presented at the BOSC 2020 Have a look at the video (alternative @@ -332,8 +333,8 @@ link) and the -

3 Who created the public sequence resource?

+ -
-

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

+
+

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 @@ -378,8 +379,8 @@ such as GISAID.

-
-

5 Why should I upload my data here?

+
+

5 Why should I upload my data here?

  1. We champion truly shareable data without licensing restrictions - with proper @@ -410,8 +411,8 @@ multiple resources.
-
-

6 Why should I not upload by data here?

+
+

6 Why should I not upload by data here?

Funny question. There are only good reasons to upload your data here @@ -433,8 +434,8 @@ for bulk uploads!

-
-

7 How does the public sequence resource work?

+
+

7 How does the public sequence resource work?

On uploading a sequence with metadata it will automatically be @@ -445,8 +446,8 @@ using workflows from the High Performance Open Biology Lab defined

-
-

8 Who uses the public sequence resource?

+
+

8 Who uses the public sequence resource?

The Swiss Institute of Bioinformatics has included this data in @@ -464,8 +465,8 @@ for monitoring, protein prediction and drug development.

-
-

9 How can I contribute?

+
+

9 How can I contribute?

You can contribute by submitting sequences, updating metadata, submit @@ -477,8 +478,8 @@ point.

-
-

10 Is this about open data?

+
+

10 Is this about open data?

All data is published under a Creative Commons 4.0 attribution license @@ -488,8 +489,8 @@ data and store it for further processing.

-
-

11 Is this about free software?

+
+

11 Is this about free software?

Absolutely. Free software allows for fully reproducible pipelines. You @@ -498,8 +499,8 @@ can take our workflows and data and run it elsewhere!

-
-

12 How do I upload raw data?

+
+

12 How do I upload raw data?

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.

-
-

13 How do I change metadata?

+
+

13 How do I change metadata?

See the http://covid19.genenetwork.org/blog! @@ -523,8 +524,8 @@ See the http://covid19.genenetwork

-
-

14 How do I change the work flows?

+
+

14 How do I change the work flows?

Workflows are on github and can be modified. See also the BLOG @@ -533,8 +534,8 @@ Workflows are on -

15 How do I change the source code?

+
+

15 How do I change the source code?

Go to our source code repositories, fork/clone the repository, change @@ -544,8 +545,8 @@ many PRs we already merged.

-
-

16 Should I choose CC-BY or CC0?

+
+

16 Should I choose CC-BY or CC0?

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.

-
-

17 Are there also variant in the RDF databases? *

+
+

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. @@ -574,8 +575,8 @@ We are also writing tools to generate VCF files directly from the pangenome.

-
-

18 How do I deal with private data and privacy?

+
+

18 How do I deal with private data and privacy?

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

-
-

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

+
+

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. @@ -595,8 +596,8 @@ We are planning to remove reads that match the human reference.

-
-

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

+
+

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. @@ -605,8 +606,8 @@ To date, PubSeq is a resource specific to SARS-CoV-2, but we are designing it to

-
-

21 How do I communicate with you?

+
+

21 How do I communicate with you?

We use a gitter channel you can join. See also contact. @@ -614,10 +615,26 @@ We use a -

22 Who are the sponsors?

+ + + +
+

23 Who are the sponsors?

+
+

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.

-
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-08-23 Sun 04:26. +
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.
-- cgit v1.2.3