Database contains public sequences!
+public sequences ready for download!
diff --git a/bh20simplewebuploader/templates/blurb.html b/bh20simplewebuploader/templates/blurb.html index 8b65afa..e58bf78 100644 --- a/bh20simplewebuploader/templates/blurb.html +++ b/bh20simplewebuploader/templates/blurb.html @@ -6,7 +6,15 @@ virus strains. PubSeq allows anyone to upload sequence material in the form of FASTA or fastq files with accompanying metadata through a web interface or REST API. - + ++ PubSeq accepts sequence material from all sources (notably in FASTA + format). PubSeq also provides specific workflows for Oxford Nanopore + analysis in FASTQ format. If you need help analysing FAST5 or FASTQ + data, feel free to contact us! Also for + commercial support and Cloud pipelines you can reach out to us. +
+COVID-19 PubSeq is also a repository for sequences with a low barrier to entry for uploading sequence data using best practices, including FAIR @@ -14,7 +22,8 @@ standards and, perhaps most importantly, providing standardised workflows that get triggered on upload, so that results are immediately available in standardised data formats. - +
+
Your uploaded sequence will automatically be processed and
incorporated into the public pangenome with metadata using worklows
from the High Performance Open Biology Lab
diff --git a/bh20simplewebuploader/templates/footer.html b/bh20simplewebuploader/templates/footer.html
index 3a405de..f78e8bf 100644
--- a/bh20simplewebuploader/templates/footer.html
+++ b/bh20simplewebuploader/templates/footer.html
@@ -19,7 +19,7 @@
-
diff --git a/bh20simplewebuploader/templates/home.html b/bh20simplewebuploader/templates/home.html
index bede611..367f6e2 100644
--- a/bh20simplewebuploader/templates/home.html
+++ b/bh20simplewebuploader/templates/home.html
@@ -8,40 +8,50 @@
- Make your sequence - data FAIR. 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! -
-- Your uploaded sequence will automatically be - processed and incorporated into the public - pangenome with metadata using worklows from - the High Performance Open Biology Lab - defined here. All - data is published under - a Creative - Commons license You can take the published - (GFA/RDF/FASTA) data and store it in a triple - store for further processing. Clinical - data can be stored - securely - at REDCap. -
-- Note that form fields contain - web ontology - URI's - for disambiguation - and machine readable metadata. For examples of - use, see the BLOG. -
+ ++ COVID-19 PubSeq is a free and open online + bioinformatics public sequence resource with + on-the-fly analysis of sequenced SARS-CoV-2 + samples that allows for a quick turnaround in + identification of new virus strains. PubSeq allows + anyone to upload sequence material in the form of + FASTA or fastq files with accompanying metadata + through the web interface or REST API. +
++ Make your sequence + data FAIR. Upload + your SARS-CoV-2 sequence (FASTA or FASTQ formats) + with simple metadata (JSONLD) to + the public sequence + resource. The upload will trigger a recompute + with all available sequences into a Pangenome + available for + download! +
++ Your uploaded sequence will automatically be + processed and incorporated into the public + pangenome with metadata using worklows from the + High Performance Open Biology Lab + defined here. All + data is published under + a Creative + Commons license You can take the published + (GFA/RDF/FASTA) data and store it in a triple + store for further processing. Clinical data can + be stored securely + at REDCap. +
++ Note that form fields contain + web ontology + URI's + for disambiguation + and machine readable metadata. For examples of + use, see the BLOG. +
The public sequence resource aims to provide a generic and useful @@ -272,8 +272,8 @@ sequence comparison and protein prediction.
We presented at the BOSC 2020 Have a look at the video (alternative
@@ -282,8 +282,8 @@ link) and the
-
The public sequence resource is an initiative by bioinformatics and
@@ -304,8 +304,8 @@ wrangling experts. Thank you everyone!
The short version is that we use state-of-the-art practices in
@@ -328,8 +328,8 @@ such as GISAID.
Funny question. There are only good reasons to upload your data here
@@ -383,8 +383,8 @@ for bulk uploads!
On uploading a sequence with metadata it will automatically be
@@ -395,8 +395,8 @@ using workflows from the High Performance Open Biology Lab defined
The Swiss Institute of Bioinformatics has included this data in
@@ -414,8 +414,8 @@ for monitoring, protein prediction and drug development.
You can contribute by submitting sequences, updating metadata, submit
@@ -427,8 +427,8 @@ point.
All data is published under a Creative Commons 4.0 attribution license
@@ -438,8 +438,8 @@ data and store it for further processing.
Absolutely. Free software allows for fully reproducible pipelines. You
@@ -448,8 +448,8 @@ can take our workflows and data and run it elsewhere!
We are preparing raw sequence data pipelines (fastq and BAM). The
@@ -464,8 +464,8 @@ assembly variations into consideration. This is all work in progress.
See the http://covid19.genenetwork.org/blog!
@@ -473,8 +473,8 @@ See the http://covid19.genenetwork
Workflows are on github and can be modified. See also the BLOG
@@ -483,8 +483,8 @@ Workflows are on
-
Go to our source code repositories, fork/clone the repository, change
@@ -494,8 +494,8 @@ many PRs we already merged.
Restrictive data licenses are hampering data sharing and reproducible
@@ -511,8 +511,8 @@ In all honesty: we prefer both data and software to be free.
We do output a RDF file with the pangenome built in, and you can parse it because it has variants implicitly.
@@ -524,8 +524,8 @@ We are also writing tools to generate VCF files directly from the pangenome.
A public sequence resource is about public data. Metadata can refer to
@@ -536,8 +536,8 @@ plan to combine identifiers with clinical data stored securely at
We are planning to remove reads that match the human reference.
@@ -545,8 +545,8 @@ We are planning to remove reads that match the human reference.
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.
@@ -555,17 +555,17 @@ To date, PubSeq is a resource specific to SARS-CoV-2, but we are designing it to
-We use a gitter channel you can join.
+We use a gitter channel you can join. See also contact.
The main sponsors are listed in the footer. In addition to the time
@@ -576,7 +576,7 @@ for donating COVID-19 related compute time.
+COVID-19 PubSeq was created by a group of bioinformaticians and
+software developers working at leading institutes (see sponsors
+below). You can talk with us directly on a gitter channel. We are open
+to improving work flows and analysis.
+
+For other questions feel free to write directly to Pjotr Prins.
+3 Who created the public sequence resource?
+
+
-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?
-5 Why should I upload my data here?
+
+
-5 Why should I upload my data here?
-6 Why should I not upload by data here?
+
+
-6 Why should I not upload by data here?
-7 How does the public sequence resource work?
+
+
-7 How does the public sequence resource work?
-8 Who uses the public sequence resource?
+
+
-8 Who uses the public sequence resource?
-9 How can I contribute?
+
+
-9 How can I contribute?
-10 Is this about open data?
+
+
-10 Is this about open data?
-11 Is this about free software?
+
+
-11 Is this about free software?
-12 How do I upload raw data?
+
+
-12 How do I upload raw data?
-13 How do I change metadata?
+
+
-13 How do I change metadata?
-14 How do I change the work flows?
+
+14 How do I change the work flows?
15 How do I change the source code?
+
+
-15 How do I change the source code?
-16 Should I choose CC-BY or CC0?
+
+
-16 Should I choose CC-BY or CC0?
-17 Are there also variant in the RDF databases? *
+
+
-17 Are there also variant in the RDF databases? *
-18 How do I deal with private data and privacy?
+
+
-18 How do I deal with private data and privacy?
-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? *
-20 Does PubSeq support only SARS-CoV-2 data? *
+
+20 Does PubSeq support only SARS-CoV-2 data? *
-
-21 How do I communicate with you?
+
+
-21 How do I communicate with you?
-22 Who are the sponsors?
+
+
22 Who are the sponsors?
-
diff --git a/doc/web/about.org b/doc/web/about.org
index 5f864e9..efd914f 100644
--- a/doc/web/about.org
+++ b/doc/web/about.org
@@ -204,7 +204,7 @@ To date, PubSeq is a resource specific to SARS-CoV-2, but we are designing it to
* How do I communicate with you?
-We use a [[https://gitter.im/arvados/pubseq?utm_source=share-link&utm_medium=link&utm_campaign=share-link][gitter channel]] you can join.
+We use a [[https://gitter.im/arvados/pubseq?utm_source=share-link&utm_medium=link&utm_campaign=share-link][gitter channel]] you can join. See also [[./contact][contact]].
* Who are the sponsors?
diff --git a/doc/web/contact.html b/doc/web/contact.html
new file mode 100644
index 0000000..8372743
--- /dev/null
+++ b/doc/web/contact.html
@@ -0,0 +1,286 @@
+
+
+
+
+
+
+
+
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 03:48.
+
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.
+
+CONTACT
+
+
+
+Table of Contents
+
+
+
+
+
+1 CONTACT and SUPPORT
+
+
+
+
+
+
+1.1 Professional support
+
+
+
+1.2 E-mail
+
+
+
+
+
+
diff --git a/doc/web/contact.org b/doc/web/contact.org
new file mode 100644
index 0000000..f410cee
--- /dev/null
+++ b/doc/web/contact.org
@@ -0,0 +1,20 @@
+#+TITLE: CONTACT
+#+AUTHOR: Pjotr Prins
+
+* CONTACT and SUPPORT
+
+COVID-19 PubSeq was created by a group of [[https://github.com/arvados/bh20-seq-resource/graphs/contributors][bioinformaticians]] and
+software developers working at leading institutes (see sponsors
+below). 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.
+
+** 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.
+
+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]].
--
cgit v1.2.3
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 05:03.
+