From bf6d73b68ab685ff4ad18ca883171e0fef40bc87 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sun, 23 Aug 2020 10:41:03 +0100 Subject: Textual changes --- doc/web/about.html | 196 ++++++++++++++++++++++++++++++++------------------- doc/web/about.org | 37 ++++++++-- doc/web/contact.html | 68 ++++++++++++++---- doc/web/contact.org | 17 ++++- 4 files changed, 224 insertions(+), 94 deletions(-) (limited to 'doc/web') diff --git a/doc/web/about.html b/doc/web/about.html index f6d1761..aa12851 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 @@ -234,46 +247,83 @@ 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 -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. +PubSeq, 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. +

+ +

+Just to avoid the notion that PubSeq is a biorepository: it is far +more than that. We are not competing with the likes of GenBank, +EBI/ENA and GISAID - in fact, PubSeq sources much of the data from +those and they get ours. +

+ +

+There is no conflict of posting data to multiple repositories. +

+ +

+It is better to view PubSeq as an open precision medicine initiative that +allows for early detection of new variants and strains; very valuable +for both testing and treatment. We have live analysis work flows that +run on uploading a new sequence. Contributing sequences helps the +overall detection. At this moment the output is limited. We will soon +add interactive discovery tools. Uploading data from a sequencer will +give researchers all information they want in 5 hours without any +bioinformatics knowledge. We may even provide workflows that take +data straight from the sequencer. In fact, you get very little out of +existing biorepositories, in our opinion, unless you have solid +bioinformatics support. And even then there is the question about +comparing data that was created using different technologies and +workflows. How do you deal with that? +

+ +

+With PubSeq we are in a position to reanalyse that data from raw +material when new insights arise. It is likely that COVID19 will be +around for another year at least. After that we should prepare for +the next pandemic. PubSeq is meant for that. We take the long view and +it will only get more powerful. Who knows: maybe the live analysis +part of PubSeq will be an approach that other biorepositories will +follow.

-
-

2 Presentations

+
+

2 Presentations

We presented at the BOSC 2020 Have a look at the video (alternative @@ -282,8 +332,8 @@ 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 @@ -328,8 +378,8 @@ 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 @@ -360,8 +410,8 @@ 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 @@ -383,8 +433,8 @@ 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 @@ -395,8 +445,8 @@ 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 @@ -414,8 +464,8 @@ 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 @@ -427,8 +477,8 @@ 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 @@ -438,8 +488,8 @@ 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 @@ -448,8 +498,8 @@ 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 @@ -464,8 +514,8 @@ 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! @@ -473,8 +523,8 @@ 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 @@ -483,8 +533,8 @@ 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 @@ -494,8 +544,8 @@ 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 @@ -511,8 +561,8 @@ 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. @@ -524,8 +574,8 @@ 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 @@ -536,8 +586,8 @@ 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. @@ -545,8 +595,8 @@ 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. @@ -555,8 +605,8 @@ 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. @@ -564,8 +614,8 @@ We use a -

22 Who are the sponsors?

+
+

22 Who are the sponsors?

The main sponsors are listed in the footer. In addition to the time @@ -576,7 +626,7 @@ 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 2020-08-22 Sat 04:42. +
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.
diff --git a/doc/web/about.org b/doc/web/about.org index efd914f..1b7bda1 100644 --- a/doc/web/about.org +++ b/doc/web/about.org @@ -27,10 +27,39 @@ * 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. +PubSeq, 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. + +Just to avoid the notion that PubSeq is a biorepository: it is far +more than that. We are not competing with the likes of GenBank, +EBI/ENA and GISAID - in fact, PubSeq sources much of the data from +those and they get ours. + +There is no conflict of posting data to multiple repositories. + +It is better to view PubSeq as an *open precision medicine initiative* that +allows for early detection of new variants and strains; very valuable +for both testing and treatment. We have live analysis work flows that +run on uploading a new sequence. Contributing sequences helps the +overall detection. At this moment the output is limited. We will soon +add interactive discovery tools. Uploading data from a sequencer will +give researchers all information they want in 5 hours *without any +bioinformatics knowledge*. We may even provide workflows that take +data straight from the sequencer. In fact, you get very little out of +existing biorepositories, in our opinion, unless you have solid +bioinformatics support. And even then there is the question about +comparing data that was created using different technologies and +workflows. How do you deal with that? + +With PubSeq we are in a position to reanalyse that data from raw +material when new insights arise. It is likely that COVID19 will be +around for another year at least. After that we should prepare for +the next pandemic. PubSeq is meant for that. We take the long view and +it will only get more powerful. Who knows: maybe the live analysis +part of PubSeq will be an approach that other biorepositories will +follow. * Presentations diff --git a/doc/web/contact.html b/doc/web/contact.html index 1ce663e..792b654 100644 --- a/doc/web/contact.html +++ b/doc/web/contact.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + CONTACT @@ -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 @@ -234,18 +247,20 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 CONTACT and SUPPORT

+
+

1 CONTACT and SUPPORT

COVID-19 PubSeq was created by a group of bioinformaticians and @@ -256,12 +271,35 @@ work flows and analysis.

-
-

1.1 Professional support

+
+

1.1 Oxford Nanopore Analysis

+We run Oxford Nanopore ourselves. We aim to make it easy to analyse +Nanopore material using our free Cloud infrastructure. If you need +help in using the online workflows don't hesitate to contact us. +

+
+
+ +
+

1.2 Data from other sequencers

+
+

+We accept FASTA sequences of SARS-CoV-2. Simply upload them using the +web form and/or REST API. No sign-up required! If you have large scale +short read data and require support we can discuss that. We also run +Illumina sequencing in several places. +

+
+
+ +
+

1.3 Professional support

+
+

To use COVID-19 PubSeq solutions for professional purposes you can -contact Curii, the creators of Arvados, directly. +contact Boston based Curii, the creators of Arvados, directly.

@@ -270,18 +308,18 @@ COVID-19 is built on Arvados using CWL workflows.

-
-

1.2 E-mail

-
+
+

1.4 E-mail

+

-For other questions feel free to write directly to Pjotr Prins. +For questions feel free to write directly to Pjotr Prins.

-
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-08-22 Sat 05:09. +
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 04:35.
diff --git a/doc/web/contact.org b/doc/web/contact.org index 96a9bb6..2892b15 100644 --- a/doc/web/contact.org +++ b/doc/web/contact.org @@ -9,13 +9,26 @@ with the goal of making online analysis available to everyone. You can talk with us directly on a [[https://gitter.im/arvados/pubseq?utm_source=share-link&utm_medium=link&utm_campaign=share-link][gitter channel]]. We are open to improving work flows and analysis. +** Oxford Nanopore Analysis + +We run Oxford Nanopore ourselves. We aim to make it easy to analyse +Nanopore material using our *free* Cloud infrastructure. If you need +help in using the online workflows don't hesitate to contact us. + +** Data from other sequencers + +We accept FASTA sequences of SARS-CoV-2. Simply upload them using the +web form and/or REST API. No sign-up required! If you have large scale +short read data and require support we can discuss that. We also run +Illumina sequencing in several places. + ** Professional support To use COVID-19 PubSeq solutions for professional purposes you can -contact [[mailto:info@curii.com][Curii]], the creators of [[https://arvados.org/][Arvados]], directly. +contact Boston based [[mailto:info@curii.com][Curii]], the creators of [[https://arvados.org/][Arvados]], directly. COVID-19 is built on Arvados using CWL workflows. ** E-mail -For other questions feel free to write directly to [[mailto:pjotr.public821@thebird.nl][Pjotr Prins]]. +For questions feel free to write directly to [[mailto:pjotr.public821@thebird.nl][Pjotr Prins]]. -- cgit v1.2.3