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. --- bh20simplewebuploader/main.py | 8 +- bh20simplewebuploader/static/blog.css | 2 +- bh20simplewebuploader/static/main.css | 13 ++- bh20simplewebuploader/templates/footer.html | 4 +- doc/web/about.html | 169 ++++++++++++++++------------ doc/web/about.org | 26 +++-- 6 files changed, 141 insertions(+), 81 deletions(-) diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 206f884..2c360e1 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -459,7 +459,11 @@ def edit_button(url,text="Edit text!"): return '

'+text+'

' def get_html_body(fn,source="https://github.com/arvados/bh20-seq-resource/tree/master/doc"): - buf = edit_button(source) + """ + This function gets the HTML generated from org-mode exports, strips + headers and footers and surrounds it with a blog section. + """ + buf = '
'+edit_button(source) in_body = False begin_body = re.compile(r"",re.IGNORECASE) end_body = re.compile(r"(|.*=\"postamble\")",re.IGNORECASE) @@ -471,7 +475,7 @@ def get_html_body(fn,source="https://github.com/arvados/bh20-seq-resource/tree/m buf += line elif begin_body.match(line): in_body = True - buf += edit_button(source) + buf += edit_button(source)+'
' return buf @app.route('/download') diff --git a/bh20simplewebuploader/static/blog.css b/bh20simplewebuploader/static/blog.css index 3ee8c44..a9e83a4 100644 --- a/bh20simplewebuploader/static/blog.css +++ b/bh20simplewebuploader/static/blog.css @@ -7,7 +7,7 @@ h1,h2 { font-family: Lucida Sans Typewriter,Lucida Console,monaco,Bitstream Vera h2 { color: black; } h3,h4 { color: black; margin:0; } code { color: darkblue; } -body {font-family: Palatino, 'Palatino Linotype', serif; color:black; background-color:white; font-size: large } +body {font-family: Palatino, 'Palatino Linotype', serif; color:black; background-color:white; font-size: large; padding: 10px; } div.verbatim { margin: 30px; color: black; background-color: white; border-style:outset; font-family: palatino font, monospace; font-size:80%; font-weight:bold; } diff --git a/bh20simplewebuploader/static/main.css b/bh20simplewebuploader/static/main.css index 6e651a4..2f547ad 100644 --- a/bh20simplewebuploader/static/main.css +++ b/bh20simplewebuploader/static/main.css @@ -8,7 +8,6 @@ body { margin: 0; } - h1, h2, h3, h4 { font-family: 'Inter', sans-serif; color: #008066; @@ -186,6 +185,10 @@ span.dropt:hover {text-decoration: none; background: #ffffff; z-index: 6; } text-align: left; } +.about a { + color: #008066; +} + .about p { // font-weight: 300; color: #505050; @@ -344,6 +347,14 @@ footer { } } +.blog { + margin: 10px; +} + +.blog h2 { + color: black; +} + .blog-table { display: table; width: 100%; diff --git a/bh20simplewebuploader/templates/footer.html b/bh20simplewebuploader/templates/footer.html index f84cef5..26ea82a 100644 --- a/bh20simplewebuploader/templates/footer.html +++ b/bh20simplewebuploader/templates/footer.html @@ -42,7 +42,9 @@
- Source code · Powered by Common Workflow Language & Arvados; Made for COVID-19-BH20 + + COVID-19 PubSeq · + Contribute · Powered by Common Workflow Language & Arvados · Made for COVID-19-BH20
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"> - + About/FAQ @@ -161,6 +161,19 @@ .footdef { margin-bottom: 1em; } .figure { padding: 1em; } .figure p { text-align: center; } + .equation-container { + display: table; + text-align: center; + width: 100%; + } + .equation { + vertical-align: middle; + } + .equation-label { + display: table-cell; + text-align: right; + vertical-align: middle; + } .inlinetask { padding: 10px; border: 2px solid gray; @@ -185,7 +198,7 @@ @licstart The following is the entire license notice for the JavaScript code in this tag. -Copyright (C) 2012-2018 Free Software Foundation, Inc. +Copyright (C) 2012-2020 Free Software Foundation, Inc. The JavaScript code in this tag is free software: you can redistribute it and/or modify it under the terms of the GNU @@ -234,29 +247,30 @@ 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?

The public sequence resource aims to provide a generic and useful @@ -267,8 +281,8 @@ sequence comparison and protein prediction.

-
-

2 Who created the public sequence resource?

+
+

2 Who created the public sequence resource?

The public sequence resource is an initiative by bioinformatics and @@ -289,14 +303,17 @@ wrangling experts. Thank you everyone!

-
-

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

+
+

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 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 -

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?

Funny question. There are only good reasons to upload your data here @@ -365,8 +382,8 @@ for bulk uploads!

-
-

6 How does the public sequence resource work?

+
+

6 How does the public sequence resource work?

On uploading a sequence with metadata it will automatically be @@ -377,8 +394,8 @@ using workflows from the High Performance Open Biology Lab defined

-
-

7 Who uses the public sequence resource?

+
+

7 Who uses the public sequence resource?

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.

-
-

8 Is this about open data?

+
+

8 How can I contribute?

+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. +

+
+
+ +
+

9 Is this about open data?

+
+

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.

-
-

9 Is this about free software?

-
+
+

10 Is this about free software?

+

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!

-
-

10 How do I upload raw data?

-
+
+

11 How do I upload raw data?

+

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.

-
-

11 How do I change metadata?

-
+
+

12 How do I change metadata?

+

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

-
-

12 How do I change the work flows?

-
+
+

13 How do I change the work flows?

+

-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.

-
-

13 How do I change the source code?

-
+
+

14 How do I change the source code?

+

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.

-
-

14 Should I choose CC-BY or CC0?

-
+
+

15 Should I choose CC-BY or CC0?

+

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.

-
-

15 How do I deal with private data and privacy?

-
+
+

16 How do I deal with private data and privacy?

+

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

-
-

16 How do I communicate with you?

-
+
+

17 How do I communicate with you?

+

We use a gitter channel you can join.

-
-

17 Who are the sponsors?

-
+
+

18 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 @@ -512,7 +543,7 @@ 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 2020-07-12 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.
diff --git a/doc/web/about.org b/doc/web/about.org index 1949e2d..39fb667 100644 --- a/doc/web/about.org +++ b/doc/web/about.org @@ -9,6 +9,7 @@ - [[#why-should-i-not-upload-by-data-here][Why should I not upload by data here?]] - [[#how-does-the-public-sequence-resource-work][How does the public sequence resource work?]] - [[#who-uses-the-public-sequence-resource][Who uses the public sequence resource?]] + - [[#how-can-i-contribute][How can I contribute?]] - [[#is-this-about-open-data][Is this about open data?]] - [[#is-this-about-free-software][Is this about free software?]] - [[#how-do-i-upload-raw-data][How do I upload raw data?]] @@ -47,14 +48,17 @@ 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). Importantly: all data is published under either the [[https://creativecommons.org/licenses/by/4.0/][Creative Commons 4.0 attribution license]] or the [[https://creativecommons.org/share-your-work/public-domain/cc0/][CC0 “No Rights Reserved” license]] which means it data can be published and workflows can run in public environments allowing for improved access for research and reproducible results. This contrasts with some other public resources, -including GISAID. +such as GISAID. * Why should I upload my data here? @@ -77,7 +81,7 @@ including GISAID. 4. Your data will be used to develop drug targets 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 [[http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part6][uploading to EBI resources]] (and soon others). Uploading your data here get your data ready for upload to multiple resources. @@ -109,8 +113,16 @@ https://covid-19-sparql.expasy.org/ and made it part of [[https://www.uniprot.or The Pantograph [[https://graph-genome.github.io/][viewer]] uses PubSeq data for their visualisations. -[[https://uthsc.edu][UTHSC]] and [[https://www.ornl.gov/news/ornl-fight-against-covid-19][ORNL]] use COVID-19 PubSeq data for protein prediction and -drug development. +[[https://uthsc.edu][UTHSC]] (USA), [[https://www.esr.cri.nz/][ESR]] (New Zealand) and [[https://www.ornl.gov/news/ornl-fight-against-covid-19][ORNL]] (USA) use COVID-19 PubSeq data +for monitoring, protein prediction and drug development. + +* How can I contribute? + +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. * Is this about open data? @@ -140,8 +152,8 @@ See the [[http://covid19.genenetwork.org/blog]]! * How do I change the work flows? -Workflows are on [[https://github.com/arvados/bh20-seq-resource/tree/master/workflows][github]] and can be modified. See also the -[[[[http://covid19.genenetwork.org/blog]]][workflow blog]]. +Workflows are on [[https://github.com/arvados/bh20-seq-resource/tree/master/workflows][github]] and can be modified. See also the BLOG +[[http://covid19.genenetwork.org/blog]] on workflows. * How do I change the source code? -- cgit v1.2.3