From fe8129b37d8b6787920a21f9961316747b62fb30 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sat, 18 Jul 2020 09:28:03 +0100 Subject: Updating stylesheets and about page after receiving feedback. --- doc/web/about.html | 169 +++++++++++++++++++++++++++++++---------------------- doc/web/about.org | 26 ++++++--- 2 files changed, 119 insertions(+), 76 deletions(-) (limited to 'doc') diff --git a/doc/web/about.html b/doc/web/about.html index 9b16c92..dfd4252 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">
- +The public sequence resource aims to provide a generic and useful @@ -267,8 +281,8 @@ sequence comparison and protein prediction.
The public sequence resource is an initiative by bioinformatics and @@ -289,14 +303,17 @@ wrangling experts. Thank you everyone!
The short version is that we use state-of-the-art practices in bioinformatics using agile methods. Unlike the resources from large institutes we can improve things on a dime and anyone can contribute -to building out this resource! +to building out this resource! Sequences from GenBank, EBI/ENA and +others are regularly added to PubSeq. We encourage people to everyone +to submit on PubSeq because of its superior live tooling and metadata +support (see the next question).
@@ -305,13 +322,13 @@ Importantly: all data is published under either the
-
Finally, if you upload your data here we have workflows that output
-formatted data suitable for uploading to EBI resources (and soon
+formatted data suitable for uploading to EBI resources (and soon
others). Uploading your data here get your data ready for upload to
multiple resources.
Funny question. There are only good reasons to upload your data here
@@ -365,8 +382,8 @@ for bulk uploads!
On uploading a sequence with metadata it will automatically be
@@ -377,8 +394,8 @@ using workflows from the High Performance Open Biology Lab defined
The Swiss Institute of Bioinformatics has included this data in
@@ -390,16 +407,29 @@ The Pantograph viewer uses PubSeq
-UTHSC and ORNL use COVID-19 PubSeq data for protein prediction and
-drug development.
+UTHSC (USA), ESR (New Zealand) and ORNL (USA) use COVID-19 PubSeq data
+for monitoring, protein prediction and drug development.
+You can contribute by submitting sequences, updating metadata, submit
+issues on our issue tracker, and more importantly add functionality.
+See 'How do I change the source code' below. Read through our online
+documentation at http://covid19.genenetwork.org/blog as a starting
+point.
+
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.
@@ -407,9 +437,9 @@ data and store it for further processing.
Absolutely. Free software allows for fully reproducible pipelines. You
can take our workflows and data and run it elsewhere!
@@ -417,9 +447,9 @@ can take our workflows and data and run it elsewhere!
We are preparing raw sequence data pipelines (fastq and BAM). The
reason is that we want the best data possible for downstream analysis
@@ -433,27 +463,28 @@ assembly variations into consideration. This is all work in progress.
See the http://covid19.genenetwork.org/blog!
-See the http://covid19.genenetwork.org/blog!
+Workflows are on github and can be modified. See also the BLOG
+http://covid19.genenetwork.org/blog on workflows.
Go to our source code repositories, fork/clone the repository, change
something and submit a pull request (PR). That easy! Check out how
@@ -462,9 +493,9 @@ many PRs we already merged.
Restrictive data licenses are hampering data sharing and reproducible
research. CC0 is the preferred license because it gives researchers
@@ -479,9 +510,9 @@ In all honesty: we prefer both data and software to be free.
A public sequence resource is about public data. Metadata can refer to
private data. You can use your own (anonymous) identifiers. We also
@@ -491,18 +522,18 @@ plan to combine identifiers with clinical data stored securely at
We use a gitter channel you can join.
The main sponsors are listed in the footer. In addition to the time
generously donated by many contributors we also acknowledge Amazon AWS
@@ -512,7 +543,7 @@ for donating COVID-19 related compute time.
4 Why should I upload my data here?
+4 Why should I upload my data here?
5 Why should I not upload by data here?
+5 Why should I not upload by data here?
6 How does the public sequence resource work?
+6 How does the public sequence resource work?
7 Who uses the public sequence resource?
+7 Who uses the public sequence resource?
8 Is this about open data?
+8 How can I contribute?
9 Is this about open data?
+9 Is this about free software?
-10 Is this about free software?
+10 How do I upload raw data?
-11 How do I upload raw data?
+11 How do I change metadata?
-12 How do I change metadata?
+12 How do I change the work flows?
-13 How do I change the work flows?
+13 How do I change the source code?
-14 How do I change the source code?
+14 Should I choose CC-BY or CC0?
-15 Should I choose CC-BY or CC0?
+15 How do I deal with private data and privacy?
-16 How do I deal with private data and privacy?
+16 How do I communicate with you?
-17 How do I communicate with you?
+17 Who are the sponsors?
-18 Who are the sponsors?
+
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-07-12 Sun 04:54.
+
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-07-18 Sat 03:27.