Commit 43323c05 authored by Vermaat's avatar Vermaat
Browse files

wip

parent aa6b1b71
- [ ] Page: HGVS checker
- [ ] Page: Variant liftover
- [ ] Page: dbSNP to HGVS
- [ ] Page: Generate HGVS
- [ ] Page: Syntax Checker
- [ ] Page: Reference File Loader
- [ ] Page: Back Translator
- [ ] Page: Name Generator
- [ ] Page: Webservices
- [ ] Page: Batch Jobs
- [ ] Page: About
- [ ] Image: HGVS checker (main image landing page)
- [ ] Image: Variant liftover
- [ ] Image: dbSNP to HGVS
- [ ] Image: Generate HGVS
- [ ] Image: Webservices
- [ ] Image: Batch jobs
- [ ] Logo (and favicon)
- [ ] Change gears pattern?
- [ ] Footer content
- [ ] Texts on many pages
- [ ] Better example inputs
- [ ] Move trac wiki content to documentation pages
- [ ] Announcements
- [ ] Links to other tools: Syntax Checker, Reference File Loader, Back
Translator, Name Generator
- [ ] Is the Name Generator obsolete?
- [ ] Styling: non-primary buttons as on Guile website?
- [ ] Styling: buttons font weight normal?
- [ ] Styling: responsiveness of forms (960px width is now hardcoded)
- [ ] Page titles
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Mutalyzer {{ mutalyzer_version }} &mdash; {{ page_title }}</title>
<meta charset="utf-8" />
<meta name="author" content="Mutalyzer contributors" />
<meta name="keywords" content="LUMC, Mutalyzer, HGVS, DNA, RNA, Proteins, Variants, Checker, Bioinformatics, Human Genetics, Genomics" />
<meta name="description" content="Mutalyzer is an HGVS variant nomenclature checker." />
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<script src="{{ url_for('static', filename='js/jquery.min.js') }}"></script>
<script src="{{ url_for('static', filename='js/bootstrap.min.js') }}"></script>
<script src="{{ url_for('static', filename='js/mailcheck.min.js') }}"></script>
<script src="{{ url_for('static', filename='js/interface.js') }}"></script>
<script src="{{ url_for('static', filename='js/generator.js') }}"></script>
<link href="//fonts.googleapis.com/css?family=Roboto:400,300,300italic,400italic,500,500italic,700,700italic"
rel="stylesheet" type="text/css">
<link rel="stylesheet" type="text/css" href="{{ url_for('static', filename='css/bootstrap.min.css') }}" >
<link rel="stylesheet" type="text/css" href="{{ url_for('static', filename='css/style.css') }}">
<!--[if lt IE 9]>
<script src="{{ url_for('static', filename='js/html5shiv.min.js') }}"></script>
<script src="{{ url_for('static', filename='js/respond.min.js') }}"></script>
<![endif]-->
<link rel="shortcut icon" href="{{ url_for('static', filename='images/favicon.ico') }}" type="image/x-icon">
<link rel="stylesheet" type="text/css" href="{{ url_for('static', filename='css/base.css') }}">
<title>Mutalyzer {{ mutalyzer_version }} &mdash; {{ page_title }}</title>
<link rel="shortcut icon" href="{{ url_for('static', filename='images/favicon.ico') }}" type="image/x-icon">
</head>
<body>
{# Fields are: view, view_args, id, caption, beginsubnav, endsubnav #}
{% set navigation_menu = [
('website.name_checker', {}, 'dna-tools', 'DNA tools', True, False),
('website.name_checker', {}, 'name-checker', 'Name Checker', False, False),
('website.syntax_checker', {}, 'syntax-checker', 'Syntax Checker', False, False),
('website.position_converter', {}, 'position-converter', 'Position Converter', False, False),
('website.snp_converter', {}, 'snp-converter', 'SNP Converter', False, False),
('website.name_generator', {}, 'name-generator', 'Name Generator', False, False),
('website.description_extractor', {}, 'description-extractor', 'Description Extractor', False, False),
('website.back_translator', {}, 'back-translator', 'Back Translator', False, False),
('website.reference_loader', {}, 'reference-loader', 'Reference File Loader', False, True),
('website.batch_jobs', {}, 'batch-jobs', 'Batch Jobs', True, False),
('website.batch_jobs', {'job_type': 'name-checker'}, 'batch-name-checker', 'Name Checker', False, False),
('website.batch_jobs', {'job_type': 'syntax-checker'}, 'batch-syntax-checker', 'Syntax Checker', False, False),
('website.batch_jobs', {'job_type': 'position-converter'}, 'batch-position-converter', 'Position Converter', False, False),
('website.batch_jobs', {'job_type': 'snp-converter'}, 'batch-snp-converter', 'SNP Converter', False, True),
('website.webservices', {}, 'webservices', 'Web Services', False, False),
] -%}
{% set active_page = active_page|default('home') -%}
<nav class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="background"></div>
<div class="container-fluid">
<!-- Brand and toggle get grouped for better mobile display -->
<div class="navbar-header">
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target="#mutalyzer-navbar-collapse-1">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="/">LUMC Mutalyzer</a>
</div>
<!-- Collect the nav links, forms, and other content for toggling -->
<div class="collapse navbar-collapse" id="mutalyzer-navbar-collapse-1">
<ul class="nav navbar-nav">
{% for view, view_args, id, caption, beginsubnav, endsubnav in navigation_menu %}
{% if beginsubnav %}
<li class="dropdown">
<a href="{{ url_for(view, **view_args) }}" class="dropdown-toggle{% if id == active_page %} active{% endif %}" data-toggle="dropdown">{{ caption }} <span class="caret"></span></a>
<ul class="dropdown-menu">
{% elif endsubnav %}
<li {% if id == active_page %} class="active"{% endif %}>
<a href="{{ url_for(view, **view_args) }}">{{ caption }}</a></ul></li>
{% else %}
<li {% if id == active_page %} class="active"{% endif %}>
<a href="{{ url_for(view, **view_args) }}">{{ caption }}</a>
</li>
{% endif %}
{% endfor %}
<li class="dropdown {% if id == active_page %} active{% endif %}">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">External links <span class="caret"></span></a>
<ul class="dropdown-menu">
<li class="menu{% if id == active_page %} active{% endif %}"><a href="http://www.genenames.org/guidelines.html"
target="new">Human Gene Nomenclature</a></li>
<li class="menu{% if id == active_page %} active{% endif %}"><a href="http://www.hgvs.org/mutnomen/"
target="new">HGVS Variation Nomenclature</a></li>
<li class="menu{% if id == active_page %} active{% endif %}"><a href="http://dx.doi.org/10.1002/humu.21427"
target="new">HGVS Nomenclature Extension Proposal</a></li>
<li class="menu{% if id == active_page %} active{% endif %}"><a href="http://www.lovd.nl/"target="new">LOVD</a></li>
</ul>
</li>
<li class="{% if active_page == 'about' %} active{% endif %}">
<a href="/about" >About</a>
</li>
<li class="dropdown {% if id == active_page %} active{% endif %}">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Help <span class="caret"></span></a>
<ul class="dropdown-menu">
<li>
<a href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/MutalyzerDocumentation" target="new">Documentation</a>
</li>
<li>
<a href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/MutalyzerFaq" target="new">FAQ</a>
</li>
<li>
<a href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/MutalyzerExercise" target="new">Exercise</a>
</li>
<li>
<a href="https://humgenprojects.lumc.nl/trac/mutalyzer" target="new">Feedback</a>
</li>
<li>
<a href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/MutalyzerDocumentation#Mailinglist:mutalyzer-announce" target="new">Mailing list</a>
</li>
<li>
<a href="https://github.com/mutalyzer/mutalyzer" target="new">Source code</a>
</li>
</ul>
</li>
<li>
<a href="mailto:mutalyzer@humgen.nl" target="new">Contact</a>
</li>
<body>
<header id="site-menu">
<h1><a id="branding" href="{{ url_for('website.homepage') }}"><span>Mutalyzer</span></a></h1>
<nav id="pages-box">
<h2>Menu: </h2>
<a class="page-link" href="{{ url_for('website.name_checker') }}">HGVS check</a>
<a class="page-link" href="{{ url_for('website.homepage') }}#tools">Tools</a>
<a class="page-link" href="/software/guile/learn/">Documentation</a>
<a class="page-link page-link-active" href="{{ url_for('website.about') }}">About</a>
</nav>
</header>
<main>
{% block content %}{% endblock %}
</main>
<footer class="site-footer noise-bg">
<div>
<h2>About this website</h2>
<p>This website is powered by GNU Guile and the <a href="http://git.savannah.gnu.org/cgit/guile/guile-web.git">source code</a> is under the <a href="http://www.gnu.org/licenses/agpl-3.0.html">GNU AGPL</a>.</p>
<p>Please use the <a href="https://lists.gnu.org/mailman/listinfo/guile-user/">mailing list</a> or the <a href="http://webchat.freenode.net/?nick=guile-guest.&amp;channels=%23guile">#guile</a> channel on Freenode for more information about GNU Guile and this website.</p>
</div>
<section>
<h3>Guile</h3>
<ul>
<li><a href="/software/guile/">Home</a></li>
<li><a href="/software/guile/download/">Download</a></li>
<li><a href="/software/guile/learn/">Learn</a></li>
<li><a href="/software/guile/libraries/">Libraries</a></li>
<li><a href="https://savannah.gnu.org/news/?group=guile">News</a></li>
<li><a href="/software/guile/community/">Community</a></li>
<li><a href="/software/guile/contribute/">Contribute</a></li>
</ul>
</div><!-- /.navbar-collapse -->
</div><!-- /.container-fluid -->
</nav>
<div class="container-fluid" >
<div class="row">
<div class="col-md-12">
{% if announcement%}
<div id="announcement" class="alert alert-info">
<p><strong>Announcement:</strong> {% if announcement.url %}<a href="{{ announcement.url }}">{% endif %}{{ announcement.body }}{% if announcement.url %}</a>{% endif %}</p>
</div>
{% endif %}
<!-- Main content -->
<div class="block block-shadow">
{% if page_title %}<h1>{{ page_title }}</h1>{% endif %}
{% block content %}{% endblock %}
</div>
</div>
</div>
<footer class="row">
<div class="col-md-4">
<p>
<strong>Mutalyzer {{ mutalyzer_version }}</strong>
<br>
<span class="text-muted">
{% if release %}
released on {{ release_date }}
{% else %}
development version
{% endif %}
</span>
</p>
</div>
<div class="col-md-4">
<p class="text-muted">HGVS nomenclature version {{ nomenclature_version }}</p>
</div>
<div class="col-md-4">
<img src="{{ url_for('static', filename='images/LUMC_24x24.png') }}" align="middle">
<p>&copy; {{ copyright_years[0] }}-{{ copyright_years[1] }} <a href="http://www.lumc.nl" target="new">LUMC</a></p>
</div>
</section>
<section>
<h3>Learn</h3>
<ul>
<li><a href="/software/guile/learn/#tutorials">Tutorials</a></li>
<li><a href="/software/guile/learn/#manuals">Reference manuals</a></li>
<li><a href="/software/guile/learn/#scheme-resources">Scheme resources</a></li>
<li><a href="/software/guile/learn/#bibliography">Suggested bibliography</a></li>
<li><a href="/software/guile/docs/faq/guile-faq.html">FAQ</a></li>
</ul>
</section>
<section>
<h3>Libraries</h3>
<ul>
<li><a href="/software/guile/libraries/#core">Core</a></li>
<li><a href="/software/guile/libraries/#gui">GUI</a></li>
<li><a href="/software/guile/libraries/#file-formats">File formats</a></li>
<li><a href="/software/guile/libraries/#networking">Networking</a></li>
<li><a href="/software/guile/libraries/#tools">Tools</a></li>
<li><a href="/software/guile/libraries/#apps">Applications</a></li>
</ul>
</section>
<section>
<h3>Contribute</h3>
<ul>
<li><a href="/software/guile/contribute/">Project summary</a></li>
<li><a href="/software/guile/contribute/#bugs">Report bugs</a></li>
<li><a href="https://savannah.gnu.org/git/?group=guile">Source code</a></li>
</ul>
</section>
</footer>
</div>
{% if piwik %}
<!-- Piwik -->
<script type="text/javascript">
var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
var u="{{ piwik_base_url }}/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', {{ piwik_site_id }}]);
var d=document, g=d.createElement('script'),
s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js';
s.parentNode.insertBefore(g,s);
})();
</script>
<noscript><p><img src="{{ piwik_base_url }}/piwik.php?idsite={{ piwik_site_id }}"
style="border:0;" alt="" /></p></noscript>
<!-- End Piwik Code -->
{% endif %}
</body>
{% if piwik %}
<!-- Piwik -->
<script type="text/javascript">
var _paq = _paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
var u="{{ piwik_base_url }}/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setSiteId', {{ piwik_site_id }}]);
var d=document, g=d.createElement('script'),
s=d.getElementsByTagName('script')[0];
g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js';
s.parentNode.insertBefore(g,s);
})();
</script>
<noscript>
<p><img src="{{ piwik_base_url }}/piwik.php?idsite={{ piwik_site_id }}" style="border:0;" alt="" /></p>
</noscript>
<!-- End Piwik Code -->
{% endif %}
</body>
</html>
{% extends "base.html" %}
{% set active_page = "homepage" %}
{% set page_title = "Welcome to the Mutalyzer website" %}
{% block content %}
<p>
The aim of this program suite is to support checks of sequence variant
nomenclature according to the
<a href="http://www.hgvs.org/mutnomen/">guidelines</a> of the
<a href="http://www.hgvs.org">Human Genome Variation Society</a>.
</p>
<div class="row">
<div class="col-md-12">
<div class="thumbnail clickbox thumb-home thumb-large">
<div class="caption">
<h3><a href="{{ url_for('.name_checker') }}">Name Checker</a></h3>
<p>The Name Checker takes the complete sequence variant description as input and checks whether it is correct.</p>
<p>Examples:
<code class="example-input" data-for="description">AB026906.1:c.274G&gt;T</code>,
<code class="example-input" data-for="description">NG_012337.1(SDHD_v001):c.274G&gt;T</code>
</p>
<!-- <a href="{{ url_for('.name_checker') }}" class="btn btn-default btn-small btn-primary">Try
this</a> -->
<form class="form" action="{{ url_for('.name_checker') }}" method="get">
<div class="input-group">
<input class="form-control form-control-small form-pre" type="text" name="description" id="description" value="{{ description }}" placeholder="Variant description using HGVS format">
<span class="input-group-btn">
<input type="submit" class="btn btn-primary pull-right" value="Check variant description">
</span>
</div>
</form>
</div>
</div>
</div>
</div>
<div class="row">
<div class="col-md-3">
<div class="thumbnail thumb-home clickbox color-1">
<div class="caption">
<h3><a href="{{ url_for('.syntax_checker') }}">Syntax Checker</a></h3>
<p>Takes the complete sequence variant description as input and checks whether the syntax is correct.</p>
</div>
</div>
</div>
<div class="col-md-3">
<div class="thumbnail thumb-home clickbox color-2">
<div class="caption">
<h3><a href="{{ url_for('.position_converter') }}">Position Converter</a></h3>
<p>Converts chromosomal positions to transcript orientated positions and vice versa.</p>
</div>
</div>
</div>
<div class="col-md-3">
<div class="thumbnail thumb-home clickbox color-3">
<div class="caption">
<h3><a href="{{ url_for('.snp_converter') }}">SNP Converter</a></h3>
<p>Allows you to convert a dbSNP rsId to HGVS notation.</p>
</div>
</div>
</div>
<div class="col-md-3">
<div class="thumbnail thumb-home clickbox color-4">
<div class="caption">
<h3><a href="{{ url_for('.name_generator') }}">Name Generator</a></h3>
<p>A user friendly interface that helps to make a valid HGVS variant description.</p>
</div>
</div>
</div>
</div>
<div class="row">
<div class="col-md-3">
<div class="thumbnail thumb-home clickbox color-5">
<div class="caption">
<h3><a href="{{ url_for('.description_extractor') }}">Description Extractor</a></h3>
<p>Allows you to generate the HGVS variant description from a reference sequence and an observed sequence.</p>
</div>
</div>
</div>
<div class="col-md-3">
<div class="thumbnail thumb-home clickbox color-6">
<div class="caption">
<h3><a href="{{ url_for('.reference_loader') }}">Reference File Loader</a></h3>
<p>Allows you to load and use your own reference sequence.</p>
</div>
</div>
</div>
<div class="col-md-3">
<div class="thumbnail thumb-home clickbox color-7">
<div class="caption">
<h3><a href="{{ url_for('.batch_jobs') }}">Batch Checkers</a></h3>
<p>Interfaces accepting a list of inputs that can be used for large quantities of checks.</p>
</div>
</div>
</div>
<div class="col-md-3">
<div class="thumbnail thumb-home clickbox color-8">
<div class="caption">
<h3><a href="{{ url_for('.webservices') }}">Web Services</a></h3>
<p>Provides instructions for the web services.</p>
</div>
</div>
</div>
</div>
<!--
<ul>
</ul> -->
<p>
GenBank sequences are retrieved from the <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a> (<a href="http://eutils.ncbi.nlm.nih.gov/About/disclaimer.html" >Copyright and Disclaimers</a>).
</p>
<p>
This project is sponsored by <a href = "http://www.sun.com">SUN Microsystems</a> with server hardware within the scope of the Academic Excellence Grant (AEG) program (award EDUD-7832-080223-CNE).
</p>
<script>
$(document).on('click', ".clickbox", function(e){
window.location=$(this).find("a").attr("href");
e.preventDefault();
e.stopPropagation();
});
$(document).on('click', ".clickbox input", function(e){
e.stopPropagation();
});
</script>
<section id="featured-box" class="info-box text-left">
<div>
<h2>Mutalyzer is an HGVS variant nomenclature checker</h2>
<img src="{{ url_for('static', filename='images/kid-programming-a-robot.png') }}" alt="" />
<p>The aim of this program suite is to support checks of sequence variant nomenclature according to the <a href="http://www.hgvs.org/mutnomen/">guidelines</a> of the <a href="http://www.hgvs.org">Human Genome Variation Society</a>.</p>
<form action="{{ url_for('.name_checker') }}" method="get">
<input type="text" class="text" name="description" id="description" value="{{ description }}" placeholder="Variant in HGVS format">
<p class="examples">Examples: <a class="example-input" data-for="description">AB026906.1:c.274G&gt;T</a>, <a class="example-input" data-for="description">NM_012337.1:c.274Gdel</a>, <a class="example-input" data-for="description">NG_012337.1(SDHD_v001):c.274G&gt;T</a></p>
<input type="submit" class="btn btn-primary" value="Check variant">
</form>
</div>
</section>
<section id="featured-tools" class="free-flow-box gears-bg">
<a id="tools"></a>
<h2>Mutalyzer tools</h2>
<p>The Mutalyzer suite consists of several tools designed to assist you bladiebla.</p>
<a class="tool" href="{{ url_for('website.position_converter') }}">
<pre class="code">some picture</pre>
<h3>Variant liftover</h3>
<p>Converts chromosomal positions to transcript orientated positions and vice versa.</p>
</a>
<a class="tool" href="{{ url_for('website.snp_converter') }}">
<pre class="code">another picture</pre>
<h3>dbSNP to HGVS</h3>
<p>Allows you to convert a dbSNP rsId to HGVS notation.</p>
</a>
<a class="tool" href="{{ url_for('website.description_extractor') }}">
<pre class="code">an image</pre>
<h3>Generate HGVS</h3>
<p>Allows you to generate the HGVS variant description from a reference sequence and an observed sequence.</p>
</a>
</section>
<section class="info-box text-right">
<div>
<h2>Webservices</h2>
<img src="{{ url_for('static', filename='images/kid-robot-and-extension-legs.png') }}" alt="" />
<p>Most Mutalyzer functionality is programmatically available through two interfaces: a SOAP webservice and an HTTP/RPC+JSON webservice.</p>
<p>And then a little bit more text. We should really have some more text in this box, or choose a smaller picture next to it. Otherwise the next box will move over the picture. I think we are ok with just one more sentence here. But this is a bit fragile, we should check this over different resolutions.</p>
</div>
</section>
<section class="info-box text-left">
<div>
<h2>Batch jobs</h2>
<img src="{{ url_for('static', filename='images/robots-and-extension-legs-1.png') }}" alt="" />
<p>If you want to run a tool on a large set of inputs, you can use the batch interfaces. Bladiebla some more text here and it should be at least two or three sentences. This makes it three.</p>
<p>And then a little bit more text. We should really have some more text in this box, or choose a smaller picture next to it. Otherwise the next box will move over the picture. I think we are ok with just one more sentence here. But this is a bit fragile, we should check this over different resolutions.</p>
</div>
</section>
{% endblock content %}
......@@ -38,6 +38,43 @@
{% block content %}
<section class="page-summary centered noise-bg">
<h1>HGVS check</h1>
<form class="wide" action="{{ url_for('.name_checker') }}" method="get">
<label for="description">Variant description</label>
<input class="text" type="text" name="description" id="description" value="{{ description }}" placeholder="Variant description in HGVS format">
<p class="examples">Examples: <a class="example-input" data-for="description">AB026906.1:c.274G&gt;T</a>, <a class="example-input" data-for="description">NM_012337.1:c.274Gdel</a>, <a class="example-input" data-for="description">NG_012337.1(SDHD_v001):c.274G&gt;T</a></p>
<input type="submit" class="btn btn-primary" value="Check variant description">
<a class="btn right" href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/NameChecker" target="new">Help</a>
</form>
</section>
<div class="relative">
<nav class="toc">
<h2>Contents</h2>
<ul>
<li><a href="">Genomic description</a></li>
<li><a href="">Transcript descriptions</a></li>
<li><a href="">Reference info</a></li>
<li><a href="">Legend</a></li>
<li><a href="">Download</a></li>
</ul>
</nav>
<section class="sheet">
<h2>Name Checker results</h2>
<section class="resource">
<h3>Genomic description</h3>
<p>NG_24232.1:g.34del</p>
<h3>Transcript descriptions</h3>
<p>NG_24232.1:g.34del</p>
<p>NG_24232.1:g.34del</p>
<p>NG_24232.1:g.34del</p>
<p>NG_24232.1:g.34del</p>
</section>
</section>
</div>
{% if not standalone %}
<p>
Please insert the variant description using
......
......@@ -5,41 +5,40 @@
{% block content %}
<p>
Please supply the genome assembly which you want to use to convert your
position.
</p>
<p>
<b>Note:</b> The Position Converter does NOT check the description or
normalize it to HGVS. Use the <a href="{{ url_for('.name_checker') }}">Name Checker</a> for this.
</p>
<form class="form" role="form" action="{{ url_for('.position_converter') }}" method="get" enctype="multipart/form-data">
<div class="form-group">
<label for="assembly_name_or_alias">Build</label>
<select name="assembly_name_or_alias" id="assembly_name_or_alias" class="form-control">
<section class="page-summary centered noise-bg">
<h1>Variant liftover</h1>
<form class="wide" action="{{ url_for('.position_converter') }}" method="get">
<label for="description">Variant description</label>
<input class="text" type="text" name="description" id="description" value="{{ description }}" placeholder="Variant description in HGVS format">
<p class="examples">Examples: <a class="example-input" data-for="description">NM_003002.3:c.274G&gt;T</a>, <a class="example-input" data-for="description">chr11:g.111959693G&gt;T</a> and <a class="example-input" data-for="description">NC_000011.9:g.111959693G&gt;T</a></p>
<label for="assembly_name_or_alias">Genome assembly</label>
<select name="assembly_name_or_alias" id="assembly_name_or_alias">
{% for assembly in assemblies %}
<option value="{{ assembly.name }}"{% if assembly_name_or_alias in (assembly.name, assembly.alias) %} selected="selected"{% endif %}>{{ assembly.taxonomy_common_name }} &mdash; {{ assembly.name }}{% if assembly.alias %} ({{ assembly.alias }}){% endif %}</option>
{% endfor %}
</select>
</div>
<div class="form-group">
<label