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<!DOCTYPE html>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width">
<link rel="stylesheet" href="lib/css/font-awesome.min.css">
<link rel="stylesheet" href="custom.css">
<!-- 1. Title -->
<section style="text-align:center;padding-top:2.5em;">
<a href="http://amp.pharm.mssm.edu/clustergrammer/" target="_blank">
<img src="img/clustergrammer_logo_border.png" alt="snowball_bio_hairball" style="width:35%; "><br>
</a>
<p class='main_title'>
Web-Based Visualization and Analysis Tool for <br>
High-Dimensional Biological Data
</p>
<p class="grey">
<text style="color:orange;"> Nicolas Fernandez </text><br>
Ma'ayan Lab<br>
Icahn School of Medicine at Mount Sinai<br>
BD2K-LINCS Data Coordination and Integration Center<br>
Data Blitz 2016<br>
<a href="http://bit.ly/clustergram-blitz">
bit.ly/clustergram-blitz
</a>
</p>
</section>
<!-- 3. Hairballs -->
<section class='main_section'>
<p class='section_title'>
Biological Data is Difficult to Visualize
</p>
<div class="wrap">
<div class="fleft" style="width:30%">
<p>
Biological data can be very high dimensional<br>
  <br>
This can lead to hairballs
</p>
<br>
<br>
<div>
<a style='margin-top: 1em; font-size: 90%;' href="http://bit.ly/clustergram-blitz">bit.ly/clustergram-blitz</a>
</div>
</p>
</div>
<div class="fright" style="width:65%">
<img src="img/snowball_bio_hairball.png" alt="snowball_bio_hairball" style="width:100%; float:right">
<br>
<div class='image_ref'>
adapted from <a href="https://twitter.com/drob/status/768484539052228608" target='_blank'>@drob</a> and <a href="http://kittentoob.com/cat-news/the-daily-strut-the-411-on-hairballs-and-ear-mite-tips-cat-friendships-zazzle-to-dazzle-cat-artistry-and-helping-cats-in-need/" target='_blank'>kittentoob.com</a>
</div>
</div>
</div>
</section>
<!-- 4. Heatmap/Clustergram Visualizations (part 1) -->
<section class='main_section'>
<p class='section_title'>
Heatmap/Clustergram Visualizations
</p>
<div class="wrap">
<div class="fleft" style="width:40%">
<p>
Heatmaps enable direct visualization of high-dimensional data<br>
  <br>
It is currently difficult to share interactive heatmaps
</p>
<br>
<div>
</div>
</p>
</div>
<div class="fright" style="width:55%">
<img src="img/R_heatmap_narrow.png" alt="sky" style="width:100%; float:right">
<br>
<div class='image_ref'>
adapted from <a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/heatmap/">www2.warwick.ac.uk</a>
</div>
</div>
</div>
</section>
<!-- 6.1 Clustergrammer Intro -->
<section class='main_section'>
<p class='section_title'>
Clustergrammer Web App
</p>
<div class="wrap">
<div class="fleft" style="width:50%">
<p>
Web built Clustergrammer to address these problems<br>
<br>
Features <br>
<ul class='custom_list' >
<li>Easily generate interactive and shareable heatmaps</li>
<li>User friendly data exploration</li>
<li>Free and open source</li>
</ul>
<br>
</p>
</p>
</div>
<div class="fright" style="width:50%; ">
<img src="img/clustergrammer_homepage.png" alt="sky" style="width:90%; float:right; margin-top:-0.5em; margin-right: 0.5em;">
<br>
<div class='image_ref' style="margin-right:1.0em;">
<a href="http://amp.pharm.mssm.edu/clustergrammer/">http://amp.pharm.mssm.edu/clustergrammer/</a>
</div>
</div>
</div>
</section>
<!-- 6.2 Clustergrammer Web App -->
<!-- <section class='main_section'>
<p class='section_title'>
Clustergrammer Web App
</p>
<div class="wrap">
<div class="fleft" style='width:30%'>
<p>
Upload a matrix to generate an interactive and shareable clustergram
<br>
<br>
Zoom, reorder, filter, etc.
<br>
<br>
link: <a href="http://amp.pharm.mssm.edu/clustergrammer/" target="_blank">web app</a>
<div>
</div>
</p>
</div>
<div class="fright" style='width:70%'>
<iframe src="example_clust.html?file=default_example.json&wait_time=1000" class='iframe_clust'></iframe>
</div>
</div>
</section> -->
<!-- 7. CST Phosphoryaltion -->
<section class='main_section'>
<p class='section_title'>
Lung Cancer Post-Translational Modification Signaling
</p>
<div class="wrap">
<div class="fleft" style='width:30%; font-size: 90%;'>
<p>
Collaborators at Cell Signaling Technology measured phosphorylation levels in 42 lung cancer cell lines
<br>
<br>
We are using Clustergrammer to analyze their data
<br>
<br>
</p>
</div>
<div class="fright" style='width:70%'>
<iframe src="example_clust.html?file=cst_cell_lines_phos.json&wait_time=2000" class='iframe_clust'></iframe>
</div>
</div>
</section>
<!-- 8. CST Gene expression -->
<section class='main_section'>
<p class='section_title'>
Lung Cancer Gene Expression
</p>
<div class="wrap">
<div class="fleft" style='width:30%; font-size: 90%;'>
<p>
Gene expression data was also obtained from the Cancer Cell Line Encyclopedia
<br>
<br>
Cell lines cluster similarly based on phosphorylation and expression
<br>
<br>
<div>
</div>
</p>
</div>
<div class="fright" style='width:70%'>
<iframe src="example_clust.html?file=ccle.json&wait_time=3000" class='iframe_clust'></iframe>
</div>
</div>
</section>
<!-- 9. Conclusions -->
<section class='main_section'>
<p class='section_title'>
Conclusions
</p>
<div class="wrap">
<div class="fleft" style="width:45%">
<p>
Clustergrammer can visualize a wide variety of data <br>
<br>
Provides visualizations for several Ma'ayan lab apps <br>
<br>
Also available as an IPython/Jupyter Notebook Widget
<br>
</p>
</p>
</div>
<div class="fright" style="width:55%; ">
<img src="img/maayan_apps.png" alt="sky" style="width:90%; float:right; margin-top:-0.5em; margin-right: 0.5em;">
<br>
<div class='image_ref' style="margin-right:1.0em;">
<a href="http://amp.pharm.mssm.edu/clustergrammer/">http://amp.pharm.mssm.edu/clustergrammer/</a>
</div>
</div>
</div>
</section>
<!-- 10. Acknowledgments -->
<section class='main_section'>
<p class='section_title'>
Acknowledgments
</p>
<div class="wrap">
<div class="fleft acknowledge" style='width:40%'>
<a href="">Avi Ma'ayan</a><br>
Greg Gundersen<br>
Michael McDermott<br>
Matthew Jones<br>
Andrew Rouillard<br>
Qiaonan Duan<br>
Zichen Wang<br>
Alexander Lachmann<br>
Maxim Kuleshov<br>
Neil Clark<br>
Caroline Monteiro<br>
Simon Koplev <br>
Anders Dohlman<br>
Troy Goff<br>
Edward He<br>
<br>
</div>
<div class="fright acknowledge" style='width:60%'>
<img src="img/bd2k_idg_logos_vert.png" alt="sky" style="width:30%; float:right">
<a href="">Cell Signaling Technology Inc</a><br>
Klarissa Rikiova<br>
Peter V. Hornbeck<br>
<br>
<a href="">University of Montana</a><br>
Mark Grimes<br>
<div class='associations'>
<a href="">BD2K-LINCS Data Coordination and Integration Center</a>
<br>
<br>
<a href="">Illuminating the Druggable Genome</a>
</div>
<div class='acknowledge_links'>
links<br>
<a href="http://bit.ly/clustergram-blitz">bit.ly/clustergram-blitz,</a>
<a href="https://github.com/MaayanLab/clustergrammer-blitz" >github-slides</a><br>
<a href="http://amp.pharm.mssm.edu/clustergrammer/" style='word-wrap:break-word;' target="_blank">http://amp.pharm.mssm.edu/clustergrammer/</a><br>
<a href="https://github.com/MaayanLab/clustergrammer" >github-clustergrammer</a>
</div>
</div>
</div>
</section>
<script src="lib/js/d3.js"></script>
<script src="stack.v1.min.js"></script>
<script>
var mystack = stack();
</script>