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-rw-r--r--bh20simplewebuploader/templates/banner.html2
-rw-r--r--bh20simplewebuploader/templates/blurb.html36
-rw-r--r--bh20simplewebuploader/templates/footer.html7
-rw-r--r--bh20simplewebuploader/templates/form.html6
-rw-r--r--bh20simplewebuploader/templates/home.html92
-rw-r--r--bh20simplewebuploader/templates/menu.html1
6 files changed, 92 insertions, 52 deletions
diff --git a/bh20simplewebuploader/templates/banner.html b/bh20simplewebuploader/templates/banner.html
index 8f2b09a..32db983 100644
--- a/bh20simplewebuploader/templates/banner.html
+++ b/bh20simplewebuploader/templates/banner.html
@@ -2,6 +2,6 @@
<div class="logo"><a href="http://covid-19.genenetwork.org/"><img src="static/image/coronasmallcomp.gif" width="150" title="COVID-19 image by Tyler Morgan-Wall"></a></div>
<h1>COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource</h1>
- <p>Database contains <span id="Counter"></span> public sequences!</p>
+ <p><span id="Counter"></span> public sequences ready for <a href="/download">download</a>!</p>
</section>
diff --git a/bh20simplewebuploader/templates/blurb.html b/bh20simplewebuploader/templates/blurb.html
index 067cc3b..ed4d1e9 100644
--- a/bh20simplewebuploader/templates/blurb.html
+++ b/bh20simplewebuploader/templates/blurb.html
@@ -1,13 +1,31 @@
<p>
- This is the COVID-19 Public Sequence Resource (COVID-19 PubSeq) for
- SARS-CoV-2 virus sequences. COVID-19 PubSeq is a repository for
- sequences with a low barrier to entry for uploading sequence data
- using best practices, including <a href="https://en.wikipedia.org/wiki/FAIR_data">FAIR data</a>. Data are published with
- metadata using state-of-the art standards
- and, perhaps most importantly, providing standardised workflows that
- get triggered on upload, so that results are immediately available
- in standardised data formats.
-
+ 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
+ a web interface or REST API.
+</p>
+<p>
+ Our goal is to help map the viral variants in this pandemic. Early
+ identification of variants helps with testing and treatments!
+ COVID-19 PubSeq accepts sequence material from all sources (notably
+ in FASTA format). In addition, PubSeq provides specific workflows
+ for Oxford Nanopore analysis in FAST5 and FASTQ format. If you have
+ an Oxford Nanopore and need (free) help analysing SARS-CoV-2 FAST5
+ or FASTQ data, feel free to <a href="/contact">contact us</a>! Also
+ for commercial support you can reach out.
+</p>
+<p>
+ COVID-19 PubSeq is also a repository for sequences with a low
+ barrier to entry for uploading sequence data using best practices,
+ including <a href="https://en.wikipedia.org/wiki/FAIR_data">FAIR
+ data</a>. Data are published with metadata using state-of-the art
+ standards and, perhaps most importantly, providing standardised
+ workflows that get triggered on upload, so that results are
+ immediately available in standardised data formats.
+</p>
+<p>
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 abf46c3..f78e8bf 100644
--- a/bh20simplewebuploader/templates/footer.html
+++ b/bh20simplewebuploader/templates/footer.html
@@ -15,12 +15,11 @@
</p>
</div>
- <div>
+ <div class="sponsors">
<a href="static/image/BCC2020_AndreaGuarracino_COVID19PubSeq_Poster.pdf">
- <img src=static/image/BCC2020_AndreaGuarracino_COVID19PubSeq_Poster.png" alt="BCC2020 Andrea Guarracino COVID19 PubSeq Poster"/>
+ <img src="static/image/BCC2020_AndreaGuarracino_COVID19PubSeq_Poster.png" alt="BCC2020 COVID19 PubSeq Poster"/>
</a>
- </div>
- <div class="sponsors">
+ <h3>OUR SPONSORS</h3>
<div class="sponsorimg">
<a href="https://github.com/virtual-biohackathons/covid-19-bh20">
<img src="static/image/covid19biohackathon.png"></a>
diff --git a/bh20simplewebuploader/templates/form.html b/bh20simplewebuploader/templates/form.html
index b9b3776..847545c 100644
--- a/bh20simplewebuploader/templates/form.html
+++ b/bh20simplewebuploader/templates/form.html
@@ -30,7 +30,9 @@
<input type="radio" id="metadata_upload" name="metadata_type" value="upload" onchange="setMode()" required>
<label for="metadata_upload">Upload metadata file</label>
<br>
- <small>Make sure the metadata has submitter attribution details.</small>
+ <small>Make sure the metadata has submitter attribution details.
+ Note that most fields in the form are optional.
+ </small>
<div id="metadata_upload_form_spot">
<div id="metadata_upload_form">
@@ -101,7 +103,7 @@
</div>
- <input class="submit" id="submit" onclick="on_submit_button()" type="submit" value="Add to Pangenome">
+<input class="submit" id="submit" onclick="on_submit_button()" type="submit" value="Add to Pangenome">
</form>
</section>
diff --git a/bh20simplewebuploader/templates/home.html b/bh20simplewebuploader/templates/home.html
index bede611..cfc3506 100644
--- a/bh20simplewebuploader/templates/home.html
+++ b/bh20simplewebuploader/templates/home.html
@@ -8,47 +8,67 @@
<section>
<div class="intro">
- <p>
- Make your sequence
- data <a href="https://en.wikipedia.org/wiki/FAIR_data">FAIR</a>. Upload
- your SARS-CoV-2 sequence (FASTA or FASTQ
- formats) with metadata (JSONLD) to
- the <a href="/about">public sequence
- resource</a>. The upload will trigger a
- recompute with all available sequences into a
- Pangenome available for
- <a href="/download">download</a>!
- </p>
- <p>
- 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 <a href="https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate">here</a>. All
- data is published under
- a <a href="https://creativecommons.org/licenses/by/4.0/">Creative
- Commons license</a> 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 <a href="https://redcap-covid19.elixir-luxembourg.org/redcap/">REDCap</a>.
- </p>
- <p>
- Note that form fields contain
- web <a href="https://en.wikipedia.org/wiki/Web_Ontology_Language">ontology
- URI's</a>
- for <a href="https://en.wikipedia.org/wiki/Wikipedia:Disambiguation">disambiguation</a>
- and machine readable metadata. For examples of
- use, see the <a href="/blog">BLOG</a>.
- </p>
- </div>
- </section>
+ <p>
+ COVID-19 PubSeq is a free and open online
+ bioinformatics public sequence resource with
+ on-the-fly analysis of
+ sequenced <a href="https://pubmed.ncbi.nlm.nih.gov/?term=sars-cov-2&sort=date">SARS-CoV-2</a>
+ 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 <a href="/upload">web interface</a>
+ or <a href="/apidoc">REST API</a>. For more
+ information see the <a href="/about">FAQ!</a>.
+ </p>
<section id="map_view" class="map">
<div id="mapid"></div>
</section>
+ <a href="https://projectredcap.org/"><img class="img-right" src="static/image/REDCap.png" /></a>
+ <p>
+ Make your sequence
+ data <a href="https://en.wikipedia.org/wiki/FAIR_data">FAIR</a>. Upload
+ your SARS-CoV-2 sequence (FASTA or FASTQ formats)
+ with simple metadata (JSONLD) to
+ the <a href="/about">public sequence
+ resource</a>. The upload will trigger a recompute
+ with all available sequences into a Pangenome
+ available for
+ <a href="/download">download</a>!
+ </p>
+ <p>
+ 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 <a href="https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate">here</a>. All
+ data is published under
+ a <a href="https://creativecommons.org/licenses/by/4.0/">Creative
+ Commons license</a> 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 <a href="https://redcap-covid19.elixir-luxembourg.org/redcap/">REDCap</a>.
+ </p>
+ <a href="https://nanoporetech.com/"><img class="img-right" src="static/image/oxford-nanopore2.jpg" /></a>
+ <p>
+ We give special attention to workflows for the <a href="https://nanoporetech.com/">Oxford Nanopore</a> - see <a href="https://pubmed.ncbi.nlm.nih.gov/?term=sars-cov-2+nanopore&sort=date">pubmed</a> - because it offers an affordable platform that is great
+ for SARS-CoV-2 sequencing.
+ </p>
+ <p>
+ Note that form fields contain
+ web <a href="https://en.wikipedia.org/wiki/Web_Ontology_Language">ontology
+ URI's</a>
+ for <a href="https://en.wikipedia.org/wiki/Wikipedia:Disambiguation">disambiguation</a>
+ and machine readable metadata. For examples of
+ use, see the <a href="/blog">BLOG</a>.
+ </p>
+ </div>
+ </section>
+
{% include 'footer.html' %}
diff --git a/bh20simplewebuploader/templates/menu.html b/bh20simplewebuploader/templates/menu.html
index d408171..5d5fdc8 100644
--- a/bh20simplewebuploader/templates/menu.html
+++ b/bh20simplewebuploader/templates/menu.html
@@ -8,6 +8,7 @@
<a href="/export" class="{{ 'active' if menu=='EXPORT' }}">EXPORT</a>
<a href="/blog" class="{{ 'active' if menu=='BLOG' }}">BLOG</a>
<a href="/about" class="{{ 'active' if menu=='ABOUT' }}">ABOUT</a>
+ <a href="/contact" class="{{ 'active' if menu=='CONTACT' }}">CONTACT</a>
<a href="javascript:void(0);" class="icon" onclick="myFunction()">
<i class="fa fa-bars"></i>
</a>