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‎CNAME

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www.rnalab.ca
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biosyntax.org

‎_config.yml

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title: RNAlab
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description: The Laboratory for RNA-Based Lifeforms
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title: bioSyntax
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description: Syntax Highlighting for Computational Biology
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disqus_shortname:
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reading_time: false
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words_per_minute: 120
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words_per_minute: 200
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# Your site's domain goes here (eg: https://mmistakes.github.io, http://yourdomain.com, etc)
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# When testing locally leave blank or use http://localhost:4000
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url: https://www.rnalab.ca
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enforce_ssl: rnalab.ca
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url: https://biosyntax.org
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enforce_ssl: biosyntax.org
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#url: localhost:4000
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# Owner/author information
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owner:
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name: A. Babaian
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name: bioSyntax
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avatar: atcg.png
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bio: "The Laboratory for RNA-Based Lifeforms"
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email: [email protected]
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address: The Donnelly rm.610
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address2: 160 College St. Toronto.
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address3: M5S 3E1
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bio: "Syntax Highlighting for Computational Biology"
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email: [email protected]
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# Social networking links used in footer. Update and remove as you like.
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twitter: https://twitter.com/RNA_Life
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scholar: https://scholar.google.ca/citations?user=FCjKSWcAAAAJ
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github: ababaian
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focus: Research focus | Computational Virology & Molecular Genetics
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twitter:
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facebook:
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github: bioSyntax/bioSyntax
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version: v1.0.0
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release:
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release: https://www.bioSyntax.org/release
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stackexchange:
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linkedin:
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instagram:
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# google plus id, include the '+', eg +mmistakes
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google_plus:
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# Links
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link:
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resume: https://rRNA.ca
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mogen: https://moleculargenetics.utoronto.ca/
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donnelly: https://thedonnellycentre.utoronto.ca/
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# Background image to be tiled on all pages
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background:
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bing_verify:
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# http://en.wikipedia.org/wiki/List_of_tz_database_time_zones
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timezone: America/Toronto
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timezone: America/Vancouver
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future: true # publish future dated posts -- true, false (default)
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highlighter: rouge
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markdown: kramdown

‎_includes/footer.html

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<!-- <span>&copy; {{ site.time | date: '%Y' }} {{ site.owner.name }}. Powered by <a href="http://jekyllrb.com" rel="nofollow">Jekyll</a> using the <a href="https://mademistakes.com/work/hpstr-jekyll-theme/" rel="nofollow">HPSTR Theme</a>.</span> -->
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<style>
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* {
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box-sizing: border-box;
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}
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/* Create three equal columns that floats next to each other */
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.column {
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float: left;
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width: 20%;
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padding: 10px;
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height: 100px; /* Should be removed. Only for demonstration */
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}
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/* Clear floats after the columns */
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.row:after {
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content: "";
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display: table;
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clear: both;
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}
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</style>
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{% include navigation_banner.html %}
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<span>
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<div class="row">
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<div class="column">
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<!-- empty -->
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</div>
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<div class="column" style="background-color:#ddd;">
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<p>
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<a href="mailto:{{ site.owner.email }}">Contact RNAlab</a> <br>
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<a href="mailto:{{ site.owner.email }}"><i class="fa fa-fw fa-envelope"></i></a>
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<a href="{{ site.owner.twitter }}"><i class="fa fa-fw fa-twitter"></i></a>
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</p>
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</div>
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<div class="column" style="background-color:#ccc;">
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<p>Member of <b><a href="{{ site.link.donnelly }}">The Donnelly</a></b><br>
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& <b><a href="{{ site.link.mogen }}">University of Toronto</a></b></p>
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</div>
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<div class="column" style="background-color:#ddd;">
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{{ site.owner.address }} <br>
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{{ site.owner.address2 }}<br>
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{{ site.owner.address3 }}
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</div>
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<div class="column">
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<!-- empty -->
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</div>
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</div>
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</span>
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<a href="mailto:{{ site.owner.email }}">Contact us: <i class="fa fa-fw fa-envelope"></i></a> &ensp;|&ensp;
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<a href="http://www.hackseq.com"><img src="{{ site.url }}/images/hackseq_project_tag.png"></a> &ensp;|&ensp;
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<a href="https://github.com/{{ site.owner.github }}">Source: <\></a>
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<!-- &ensp;|&ensp;
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github Star Button
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<iframe src="https://ghbtns.com/github-btn.html?user=bioSyntax&repo=bioSyntax&type=star&count=true&size=large&v=2" frameborder="0" scrolling="0" width="160px" height="30px" style="margin-bottom: -13px"></iframe>
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-->
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</span>

‎_includes/head.html

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<!-- HTTPS redirect for website -->
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<script type="text/javascript">
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var host = "";
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var host = "biosyntax.org";
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if ((host == window.location.host) && (window.location.protocol != "https:"))
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window.location.protocol = "https";
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</script>

‎_includes/navigation.html

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<nav id="dl-menu" class="dl-menuwrapper" role="navigation">
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<button class="dl-trigger">Open Menu</button>
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<ul class="dl-menu">
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<li><a href="{{ site.url }}/"><font face="Courier Bold" color="#CEDA27" >RNA</font><font face="Courier Bold" color="#FFFFFF">lab</font><font face="Courier" color="white">:</font></a></li>
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<li><a href="{{ site.url }}/research">Research</a></li>
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<li><a href="{{ site.url }}/team">Scientists</a></li>
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<li><a href="{{ site.url }}/join">Join RNAlab</a></li>
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<li><a href="{{ site.url }}/"><font face="Courier" color="#47FF19" >bio</font><font face="Courier" color="#FF0000">Syntax</font><font face="Courier" color="white">:</font></a></li>
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<li><a href="{{ site.url }}/install">Installing</a></li>
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<li>
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<a href="#">Contact</a>
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<a href="#">Documentation</a>
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<ul class="dl-submenu">
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<li>
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<p><img src="{{ site.url }}/images/tRNA.gif" alt="{{ site.owner.name }}" class="author-photo"></p>
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<h4>A. Babaian</h4>
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<p>The Donnelly rm.610
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160 College St. Toronto.
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M5S 3E1
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</p>
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<p><a href="{{ site.url }}/man">Manual</a></p>
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<p><a href="{{ site.url }}/man#getting-started">Getting Started</a></p>
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<p><a href="{{ site.url }}/man#reading-data">Reading Data</a></p>
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<p><a href="{{ site.url }}/man#supported-file-formats">File Formats</a></p>
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<p><a href="{{ site.url }}/man#support">Support</a></p>
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<p><a href="{{ site.url }}/dev">Collaborating</a></p>
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</li>
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</ul><!-- /.dl-submenu -->
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</li>
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<li><a href="{{ site.url }}/screenshots">Screenshots</a></li>
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<li>
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<a href="#">Developers</a>
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<ul class="dl-submenu">
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<a href="{{ site.link.resume }}"><i class="fa fa-university"></i> eCV Site</a>
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<p><img src="{{ site.url }}/images/{{ site.owner.avatar }}" alt="{{ site.owner.name }}" class="author-photo"></p> <h4>Developers:</h4>
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<p><a href="https://github.com/ababaian">A.Babaian</a></p>
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<p><a href="https://github.com/ebedthan">A.Ebou</a></p>
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<p><a href="https://github.com/alyeffy">A.Fegen</a></p>
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<p><a href="https://github.com/lazypanda10117">J.Kam</a></p>
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<p><a href="https://github.com/fransilvion">G.Novakovskiy</a></p>
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<p><a href="https://github.com/liyao001">L.Yao</a></p>
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<p><a href="https://github.com/Jwong684">J.Wong</a></p>
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</li>
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<li>
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<a href="{{ site.url }}/dev"><span class="btn btn-inverse">Collaborate!</span></a>
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</li>
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{% if site.owner.github %}<li>
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<a href="https://github.com/{{ site.owner.github }}"><i class="fa fa-fw fa-github"></i> Github</a>
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<a href="https://github.com/{{ site.owner.github }}"><i class="fa fa-fw fa-github"></i> Source</a>
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</li>{% endif %}
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{% if site.owner.email %}<li>
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<a href="mailto:{{ site.owner.email }}"><i class="fa fa-fw fa-envelope"></i> Contact</a>
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<a href="mailto:{{ site.owner.email }}"><i class="fa fa-fw fa-envelope"></i> Contact Us</a>
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</li>{% endif %}
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<li>
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<a href="{{ site.url }}/research"><span class="btn btn-inverse">Collaborate!</span></a>
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</li>
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</ul><!-- /.dl-submenu -->
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</li>
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</nav><!-- /.dl-menuwrapper -->

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‎_layouts/page.html

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</div><!-- /.entry-header -->
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{% endif %}
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</header>
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<div class="entry-content">
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{{ content }}
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<footer class="entry-meta">
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{% if page.modified %}<span>Updated on <span class="entry-date date published updated"><time datetime="{{ page.modified }}">{{ page.modified | date: "%B %d, %Y" }}</time></span></span>
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<span class="author vcard"><span class="fn">{{ site.owner.name }}</span></span>{% endif %}
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{% if page.share != false %}{% include social-share.html %}{% endif %}
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</footer>
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</div><!-- /.entry-content -->
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{% if page.comments != false and site.disqus_shortname %}<section id="disqus_thread"></section><!-- /#disqus_thread -->{% endif %}
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</article>

‎_layouts/site-index.html

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{% if page.image.feature %}
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<div class="entry-image">
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<img src="{{ site.url }}/images/bg/{{ page.image.feature }}" alt="{{ page.title }}">
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<img src="{{ site.url }}/images/{{ page.image.feature }}" alt="{{ page.title }}">
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</div><!-- /.entry-image -->
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<div class="header-title">
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<b>
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<a style="text-align:center;font-family:Courier; font-weight: bold; color:#FFFFFF; font-size: 40px;">The Laboratory for <br></a>
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<a style="font-family:Courier; font-weight: bold; color:#ceda27; font-size: 60px;">RNA-Based Lifeforms</a>
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<a style="font-family:Courier; font-weight: bold; color:#FFFFFF; font-size: 60px;">:</a>
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<img src="{{ site.url }}/images/cursor.gif" style="height: 50px; margin-left: -10px; margin-bottom: 35px">
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</b>
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<b><a style="font-family:Courier; font-weight: bold; color:#47FF19; font-size: 60px;">bio</a>
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<a style="font-family:Courier; font-weight: bold; color:#FF0000; font-size: 60px;">Syntax</a
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><a style="font-family:Courier; font-weight: bold; color:#7a937f; font-size: 60px;">:</a>
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<img src="{{ site.url }}/images/cursor.gif" style="height: 50px; margin-left: -10px; margin-bottom: 35px"></b>
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<!-- <h2>{{ site.description }}</h2> -->
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</div><!-- /.header-title -->
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<!-- MAIN CONTENT -->
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<a style="display:inline-block; font-style: italic; color:#333333; line-height:0px;
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font-size: 14px;">&nbsp;&nbsp; {{ site.owner.version }}</a>
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<!-- Lab Research -->
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<a href="{{ site.url }}/research"><span class="btn btn-danger">Research</span></a>
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<!-- Scientist Profiles -->
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<a href="{{ site.url }}/team"><span class="btn btn-warning">Scientists</span></a>
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<!-- Publications -->
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<a href="{{ site.url }}/lit"><span class="btn btn-info">Publications</span></a>
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<!-- Media -->
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<a href="{{ site.url }}/media"><span class="btn btn-info">Media</span></a>
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<!-- Join the RNAlab! -->
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<a href="{{ site.url }}/join"><span class="btn btn-success">Join the RNALab</span></a>
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<a href="{{ site.owner.release }}"><span class="btn btn-danger">Download</span></a>
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<a href="{{ site.url }}/install"><span class="btn btn-warning">Install</span></a>
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<a href="{{ site.url }}/man"><span class="btn btn-success">Documentation</span></a>
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<a href="{{ site.url }}/screenshots"><span class="btn btn-info">Screenshots</span></a>
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<a href="https://github.com/{{ site.owner.github }}"><span class="btn btn-info">View Source</span></a>
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‎_posts/2017-12-01-index_post.md

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layout: post
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---
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The Laboratory for RNA-Based Lifeforms (<b>RNAlab</b>) @ University of Toronto is a combined <i>Computational</i> and <i>Molecular</i> research team. Our passion is in understanding the interplay between RNA elements and Genetics. The primary domain where we interrogate this question is through the exploration of the vast evolution and biodiversity of <b>Earth's RNA viruses<b>. <br>
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## Syntax Highlighting for Computational Biology.
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Our goal is to make data intuitive for scientists and help you navigate and comprehend its significance. Currently supporting `.sam`, `.vcf`, `.fasta`, `.fastq`, `.gtf`, `.bed`, `.pdb`, `.cwl`, [& more formats](https://biosyntax.org/man#supported-file-formats).
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## Our Work
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<div style="text-align:center">
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<script src="https://asciinema.org/a/153567.js" id="asciicast-153567" async></script>
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</div>
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### Serratus: Foundations for a *Planetary-Scale Virus Surveillance Network*
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<!--[<img src="http://biosyntax.org/images/sam-less-2.gif">](images/screens/sam-less.png)
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-->
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<iframe width="560" height="315" src="https://www.youtube.com/embed/ckulYdtTEa0" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
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### [Tell us how bioSyntax can develop to help your workflow. (Survey ~5m)](https://goo.gl/forms/YO89fEPw71JpH3Ac2)
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DNA and RNA sequencing data is growing exponentially, outpacing Moore’s Law. Currently, public databases contain 60+ million gigabytes (60 petabytes) of sequencing data from 10+ million samples, and this doubles every 18 months. Samples range from cancer cells in a lab at UofT, to anal swabs of penguins in Antarctica and everything in-between. Along with what researchers intended to study, sequences from the viruses can also be captured, yet go unanalyzed.
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### [INSTALL bioSyntax](install)
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At most 0.1% of Earth’s viruses have been identified, so to characterize the full diversity of the viruses on Earth, we develop computing algorithms and techniques to analyze sequencing data at the <b>petabyte-scale</b>. In effect, we recycle billions of dollars of data to drive biological discovery. Recently, in one 11-day analysis we discovered 130,000+ new species of RNA viruses, nearly 10x more than were previously known (including nine new species of surprising Coronaviruses). Moving forward we are developing a system to monitor this global-stream of sequencing data to identify where and when pathogens of pandemic potential show up. It is better that we find them, before they find us.
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### Usage
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------------------------------------------------------------------------------
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bioSyntax integrates seamlessly with **vim**, **less**, **gedit**, & **sublime** to automatically recognize [your favorite biological file formats](man#supported-file-formats). To gain the most insight from your data, read our brief [bioSyntax Manual](man).
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Large data can also be directly piped into **less** with `sam-less`, `vcf-less`, ..., `xyz-less` commands.
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![Example less command](images/sam-less_command.gif)
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## News
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&nbsp;
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#### 2023-05-05 - RNA virus / Viroid Hybrid Publication
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### Collaborate
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[Hybrids of RNA viruses and viroid-like elements replicate in fungi](https://www.nature.com/articles/s41467-023-38301-2). We massively (+20,000 species) expand the universe of viroid-like agents, including the characterization of a Viroid-like RNA virus (or RNA virus-like Viroid) hybrid infectious agent. This work joins two kingdoms of infectious agents, and offers insights into how primordial viruses may have arisen.
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We're actively developing bioSyntax; we'd love to hear your comments, feedback and suggestions for further development. [Drop us a line on github](https://github.com/bioSyntax/bioSyntax/issues) or [email](mailto:[email protected]).
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If you'd like to help out, have intimate understanding of a scientific data-type, or are looking for a fun design / optimization problem check the [development page](dev).
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------------------------------------------------------------------------------
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#### 2023-05-01 - Summer intake & awards
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## Updates
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The RNAlab is booting up. Welcome Declan, Aiden*, and Jawad* (research assistants); as well as Luke and Alex (engineers) to the lab! * : Recieved UROP awards.
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#### 2018-08-22 - bioSyntax publication
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- Our manuscript has been accepted for [publication in BMC Bioinformatics](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2315-y)
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#### 2018-08-13 - bioSyntax v1.0 Release
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#### 2023-01-10 - Research Symbiont Award 2022
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- Syntax highlighting for FASTA, FASTQ, CWL, BED, GTF, PDB, PML, SAM, VCF file formats
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- Available for: `less`, `vim`, `gedit`, `sublime` and `VScode`
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- Updated installer script + packaged documentation
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- Welcome Dylan Aissi + Li Yao on as developers
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Artem/Serratus has been [awarded](https://twitter.com/jbrianbyrd/status/1614433561079062531) the coveted 2023 [Research Symbiont Award](https://researchsymbionts.org/) for outstanding data-sharing resulting in a substantial impact on human health.
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#### 2018-04-11 - bioSyntax v0.1-beta4 + Development Survey
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- We're working on a [user experience survey](https://goo.gl/forms/YO89fEPw71JpH3Ac2) to focus development.
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- New Syntax `vim-nexus`
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- New Syntax `vim-pml` & `sublime-pml`(Pymol Script Language)
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- New Syntax `cwl-sublime` and `cwl-vim` (Common Workflow Language)
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- Add `bam-less` alias for `sam-less` by default
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- Removed `sudo` requirements for linux-gedit & linux-less installations
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- Alternative Syntax: `vim_fasta-ORF`: Syntax for finding and highlighting Open Reading Frames
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#### 2022-10-22 - Founding of RNAlab
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#### Thanks to
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- [Luis Carvalho](https://vim.sourceforge.io/scripts/script.php?script_id=964) for `vim-nexus`
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- @manabuishii for `cwl-sublime` and `cwl-vim`
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- @speleo3 for `vim-pml` & @bbarad for `sublime-pml`
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The *Laboratory for RNA-Based Lifeforms* is officially opening it's doors in The Donnelly Centre for Cellular + Biomolecular Research at the University of Toronto.
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#### Past releases
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- [bioSyntax Publication](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2315-y)
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- [Release History](https://github.com/bioSyntax/bioSyntax/releases)

‎_sass/_page.scss

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padding: 50px 80px;
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@include font-size(20);

‎alt/vim_Fasta-ORF.png

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