diff options
Diffstat (limited to 'bh20simplewebuploader/templates')
| -rw-r--r-- | bh20simplewebuploader/templates/banner.html | 2 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/blurb.html | 36 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/footer.html | 7 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/form.html | 6 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/home.html | 92 | ||||
| -rw-r--r-- | bh20simplewebuploader/templates/menu.html | 1 |
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> |