From c3bbd48601cdb4bec510db72bd2296724874f4f3 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sun, 24 May 2020 10:31:24 -0500 Subject: Display About/FAQ --- bh20simplewebuploader/main.py | 14 +- bh20simplewebuploader/templates/about.html | 4 +- bh20simplewebuploader/templates/form.html | 2 +- bh20simplewebuploader/templates/org-header.html | 293 +++++++++++++++ doc/blog/using-covid-19-pubseq-part1.org | 2 +- doc/web/about.html | 462 ++++++++++++++++++++++++ doc/web/about.org | 134 +++++++ 7 files changed, 906 insertions(+), 5 deletions(-) create mode 100644 bh20simplewebuploader/templates/org-header.html create mode 100644 doc/web/about.html create mode 100644 doc/web/about.org diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index a30d350..eb9a0f5 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -428,7 +428,19 @@ def blog_page(): @app.route('/about') def about_page(): - return render_template('about.html',menu='ABOUT') + buf = "" + in_body = False + begin_body = re.compile(r"",re.IGNORECASE) + end_body = re.compile(r"(|.*=\"postamble\")",re.IGNORECASE) + with open('doc/web/about.html') as f: + for line in f: + if end_body.match(line): + break + if in_body: + buf += line + elif begin_body.match(line): + in_body = True + return render_template('about.html',menu='ABOUT',embed=buf) ## Dynamic API functions starting here ## This is quick and dirty for now, just to get something out and demonstrate the queries diff --git a/bh20simplewebuploader/templates/about.html b/bh20simplewebuploader/templates/about.html index 286a211..07b6951 100644 --- a/bh20simplewebuploader/templates/about.html +++ b/bh20simplewebuploader/templates/about.html @@ -1,11 +1,11 @@ - {% include 'header.html' %} + {% include 'org-header.html' %} {% include 'banner.html' %} {% include 'menu.html' %} - WIP + {{ embed|safe }} {% include 'footer.html' %} diff --git a/bh20simplewebuploader/templates/form.html b/bh20simplewebuploader/templates/form.html index b1bbad2..3a1b03b 100644 --- a/bh20simplewebuploader/templates/form.html +++ b/bh20simplewebuploader/templates/form.html @@ -12,7 +12,7 @@ Upload your SARS-CoV-2 sequence (FASTA or FASTQ formats) with metadata (JSONLD) to the public sequence resource. The upload will trigger a recompute with all available sequences into a Pangenome available for - download! + download!

Your uploaded sequence will automatically be processed diff --git a/bh20simplewebuploader/templates/org-header.html b/bh20simplewebuploader/templates/org-header.html new file mode 100644 index 0000000..915bcb7 --- /dev/null +++ b/bh20simplewebuploader/templates/org-header.html @@ -0,0 +1,293 @@ + + + + + Web uploader for Public SARS-CoV-2 Sequence Resource + + + + + + + + + diff --git a/doc/blog/using-covid-19-pubseq-part1.org b/doc/blog/using-covid-19-pubseq-part1.org index 8d3dae5..b1edbad 100644 --- a/doc/blog/using-covid-19-pubseq-part1.org +++ b/doc/blog/using-covid-19-pubseq-part1.org @@ -11,7 +11,7 @@ most importantly, providing standardised workflows that get triggered on upload, so that results are immediately available in standardised data formats. -* Table of Contents :TOC: +* Table of Contents :TOC:noexport: - [[#what-does-this-mean][What does this mean?]] - [[#fetch-sequence-data][Fetch sequence data]] - [[#predicates][Predicates]] diff --git a/doc/web/about.html b/doc/web/about.html new file mode 100644 index 0000000..1f8b1a1 --- /dev/null +++ b/doc/web/about.html @@ -0,0 +1,462 @@ + + + + + + + +About/FAQ + + + + + + +

+

About/FAQ

+
+

Table of Contents

+
+ +
+
+ +
+

1 What is the 'public sequence resource' about?

+
+

+The public sequence resource aims to provide a generic and useful +resource for COVID-19 research. The focus is on providing the best +possible sequence data with associated metadata that can be used for +sequence comparison and protein prediction. +

+
+
+ +
+

2 Who created the public sequence resource?

+
+

+The public sequence resource is an initiative by bioinformatics and +ontology experts who want to create something agile and useful for +the wider research community. The initiative started at the COVID-19 +biohackathon in April 2020 and is ongoing. The main project drivers +are Pjotr Prins (UTHSC), Peter Amstutz (Curii), Michael Crusoe (Common +Workflow Language) and Thomas Liener (consultant, formerly EBI). But +as this is a free software initiative the project represents major +work by hundreds of software developers and ontology and data +wrangling experts. Thank you everyone! +

+
+
+ +
+

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! +

+ +

+Importantly: all data is published under the Creative Commons 4.0 +attribution 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. +

+
+
+ +
+

4 Why should I upload my data here?

+
+
    +
  1. We champion truly shareable data without licensing restrictions - with proper +attribution
    2. +
  2. We provide full metadata support using state-of-the-art ontology's
    3. +
  3. We provide a web-based sequence uploader and a command-line version +for bulk uploads
    4. +
  4. We provide a live SPARQL end-point for all metadata
    5. +
  5. We provide free data analysis and sequence comparison triggered on data upload
    6. +
  6. We provide free downloads of all computed output
    7. +
  7. There is no need to set up pipelines and/or compute clusters
    8. +
  8. All workflows get triggered on uploading a new sequence
    9. +
  9. When someone (you?) improves the software/workflows and everyone benefits
    10. +
+ +

+Finally, if you upload your data here we have workflows that output +formatted data suitable for uploading to EBI resources (and soon +others). Uploading your data here get your data ready for upload to +multiple resources. +

+
+
+ +
+

5 Why should I not upload by data here?

+
+

+Funny question. There is no good reason not to upload your data here! +In fact, you can upload your data here as well as to other +resources. It is your data after all. No one can prevent you from +uploading your data to multiple resources. We recommend uploading to +EBI and NCBI resources. Use our data conversion tools to only enter +data once and make the process smooth. +

+
+
+ +
+

6 How does the public sequence resource work?

+
+

+On uploading a sequence with metadata it will automatically be +processed and incorporated into the public pangenome with metadata +using workflows from the High Performance Open Biology Lab defined +here. +

+
+
+ +
+

7 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. +

+
+
+ +
+

8 Is this about free software?

+
+

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

+
+
+ +
+

9 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 +(including protein prediction and test development). The current +approach where people publish final sequences of SARS-CoV-2 is lacking +because it hides how this sequence was created. For reasons of +reproducible and improved results we want/need to work with the raw +sequence reads (both short reads and long reads) and take alternative +assembly variations into consideration. This is all work in progress. +

+
+
+ +
+

10 How do I change metadata?

+
+

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

+
+
+ +
+

11 How do I change the work flows?

+
+

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

+
+
+ +
+

12 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 +many PRs we already merged. +

+
+
+ +
+

13 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 +plan to combine identifiers with clinical data stored securely at +REDCap. Contact Pjotr Prins if you want to work on this. +

+
+
+ +
+

14 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. +

+
+
+
+
+
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-05-24 Sun 10:26. +
+ + diff --git a/doc/web/about.org b/doc/web/about.org new file mode 100644 index 0000000..fc9d1ff --- /dev/null +++ b/doc/web/about.org @@ -0,0 +1,134 @@ +#+TITLE: About/FAQ +#+AUTHOR: Pjotr Prins + +* Table of Contents :TOC:noexport: + - [[#what-is-the-public-sequence-resource-about][What is the 'public sequence resource' about?]] + - [[#who-created-the-public-sequence-resource][Who created the public sequence resource?]] + - [[#how-does-the-public-sequence-resource-compare-to-other-data-resources][How does the public sequence resource compare to other data resources?]] + - [[#why-should-i-upload-my-data-here][Why should I upload my data here?]] + - [[#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?]] + - [[#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?]] + - [[#how-do-i-change-metadata][How do I change metadata?]] + - [[#how-do-i-change-the-work-flows][How do I change the work flows?]] + - [[#how-do-i-change-the-source-code][How do I change the source code?]] + - [[#how-do-i-deal-with-private-data-and-privacy][How do I deal with private data and privacy?]] + - [[#who-are-the-sponsors][Who are the sponsors?]] + +* What is the 'public sequence resource' about? + +The *public sequence resource* aims to provide a generic and useful +resource for COVID-19 research. The focus is on providing the best +possible sequence data with associated metadata that can be used for +sequence comparison and protein prediction. + +* Who created the public sequence resource? + +The *public sequence resource* is an initiative by [[https://github.com/arvados/bh20-seq-resource/graphs/contributors][bioinformatics]] and +ontology experts who want to create something agile and useful for +the wider research community. The initiative started at the COVID-19 +biohackathon in April 2020 and is ongoing. The main project drivers +are Pjotr Prins (UTHSC), Peter Amstutz (Curii), Michael Crusoe (Common +Workflow Language) and Thomas Liener (consultant, formerly EBI). But +as this is a free software initiative the project represents major +work by hundreds of software developers and ontology and data +wrangling experts. Thank you everyone! + +* 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! + +Importantly: all data is published under the [[https://creativecommons.org/licenses/by/4.0/][Creative Commons 4.0 +attribution 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. + +* Why should I upload my data here? + +1. We champion truly shareable data without licensing restrictions - with proper + attribution +2. We provide full metadata support using state-of-the-art ontology's +2. We provide a web-based sequence uploader and a command-line version + for bulk uploads +3. We provide a live SPARQL end-point for all metadata +2. We provide free data analysis and sequence comparison triggered on data upload +4. We provide free downloads of all computed output +3. There is no need to set up pipelines and/or compute clusters +4. All workflows get triggered on uploading a new sequence +4. When someone (you?) improves the software/workflows and everyone benefits + +Finally, if you upload your data here we have workflows that output +formatted data suitable for uploading to EBI resources (and soon +others). Uploading your data here get your data ready for upload to +multiple resources. + +* Why should I not upload by data here? + +Funny question. There is no good reason not to upload your data here! +In fact, you can upload your data here as well as to other +resources. It is your data after all. No one can prevent you from +uploading your data to multiple resources. We recommend uploading to +EBI and NCBI resources. Use our data conversion tools to only enter +data once and make the process smooth. + +* How does the public sequence resource work? + +On uploading a sequence with metadata it will automatically be +processed and incorporated into the public pangenome with metadata +using workflows from the High Performance Open Biology Lab defined +[[https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate][here]]. + +* Is this about open data? + +All data is published under a [[https://creativecommons.org/licenses/by/4.0/][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. + +* Is this about free software? + +Absolutely. Free software allows for fully reproducible pipelines. You +can take our workflows and data and run it elsewhere! + +* 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 +(including protein prediction and test development). The current +approach where people publish final sequences of SARS-CoV-2 is lacking +because it hides how this sequence was created. For reasons of +reproducible and improved results we want/need to work with the raw +sequence reads (both short reads and long reads) and take alternative +assembly variations into consideration. This is all work in progress. + +* How do I change metadata? + +See the [[http://covid19.genenetwork.org/blog]]! + +* How do I change the work flows? + +See the [[http://covid19.genenetwork.org/blog]]! + +* How do I change the source code? + +Go to our [[https://github.com/arvados/bh20-seq-resource][source code repositories]], fork/clone the repository, change +something and submit a [[https://github.com/arvados/bh20-seq-resource/pulls][pull request]] (PR). That easy! Check out how +many PRs we already merged. + +* 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 +plan to combine identifiers with clinical data stored securely at +[[https://redcap-covid19.elixir-luxembourg.org/redcap/][REDCap]]. Contact Pjotr Prins if you want to work on this. + +* 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. -- cgit v1.2.3