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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<title>Ben Vandervalk CV</title>
<link href="style.css" media="all" rel="stylesheet" type="text/css">
<link href="gray-minimal.css" media="all" rel="stylesheet" type="text/css" class="resume-style">
</head>
<body>
<div id="resume">
<div class="header"></div>
<h1 class="name">
<span class="first-name">Ben</span>
<span class="last-name">Vandervalk</span>
<span class="headline">Bioinformatics Software Developer</span>
<span class="contact-line">
<a href="mailto:[email protected]">[email protected]</a>
<span class="phone">| +1-604-803-4988</span>
</span>
</h1>
<div class="clear">
<h1 class="name"></h1>
</div>
<!--
<div class="section contact">
<h2 class="section-header">
<span class="text">Contact</span>
</h2>
<div class="content">
<div class="main-address">
<span class="label">Address:</span>
</div>
</div>
<div class="clear"></div>
</div>
-->
<!--
<div class="section specialties">
<h2 class="section-header">
<span class="text">Specialties</span>
</h2>
<div class="content">
<p>Bioinformatics, Web Services, Databases, Semantic Web</p>
</div>
<div class="clear"></div>
</div>
-->
<div class="section goals">
<h2 class="section-header">
<span class="text">Career Interests</span>
</h2>
<div class="content">
<p>Algorithm/Software Development for Next Gen Sequence Analysis</p>
</div>
<div class="clear"></div>
</div>
<div class="section skills">
<h2 class="section-header">
<span class="text">Skills</span>
</h2>
<div class="content">
<ul>
<li>Software Development (C++, Java, Perl)</li>
<li>Algorithm Design and Analysis</li>
<li>Mathematics (Calculus, Linear Algebra, Combinatorics)</li>
<li>Unix/Linux</li>
<li>Revision Control Systems (Git)</li>
<li>Cluster Computing (SGE, SLURM)</li>
<li>Relational Databases (MySQL)</li>
<li>Semantic Web Standards/Technologies (RDF, OWL, SPARQL)</li>
</ul>
</div>
<div class="clear"></div>
</div>
<div class="section bioinformatics">
<h2 class="section-header">
<span class="text">Bioinformatics Knowledge</span>
</h2>
<div class="content">
<ul>
<li>Standard Algorithms (e.g. Smith-Waterman, Progressive MSA)</li>
<li>Principles of Molecular Biology (e.g. Molecular Dogma)</li>
<li>Principles of Molecular Methods (e.g. Next Gen Sequencing Technologies, PCR)</li>
<li>Usage of Next Gen Seq Tools (e.g. BWA, FastQC)</li>
</ul>
</div>
<div class="clear"></div>
</div>
<div class="section educations">
<h2 class="section-header"><span class=
"text">Education</span></h2>
<div class="content">
<div class="education first">
<div class="school-name">
University of British Columbia
</div>
<div class="dates">
<span class="start-year">2007</span> <span class=
"date-separator">-</span> <span class=
"end-year">2010</span>
</div>
<div class="program">
<span class="degree">M. Sc.,</span>
<span class="field-of-study">Bioinformatics</span>
</div>
<div class="thesis">
Thesis: <a href="https://circle.ubc.ca/handle/2429/34088">The SHARE System: a Semantic Web Based Approach for Evaluating Queries
Across Distributed Bioinformatics Databases and Software</a>
</div>
</div>
<div class="education">
<div class="school-name">
University of Waterloo
</div>
<div class="dates">
<span class="start-year">1998</span> <span class=
"date-separator">-</span> <span class=
"end-year">2003</span>
</div>
<div class="program">
<span class="degree">B. Math., Computer
Science</span>
</div>
</div>
</div>
<div class="clear"></div>
</div>
<div class="section positions">
<h2 class="section-header">
<span class="text">Experience</span>
</h2>
<div class="content">
<div class="position first">
<div class="company-name">
Michael Smith Genome Sciences Centre, BC Cancer Agency
</div>
<div class="dates">
<!-- <span class="start-month">01 /</span> -->
<span class="start-year">2013</span>
<span class="date-separator">-</span>
<span class="is-current">Present</span>
</div>
<div class="title">
Computational Biologist
</div>
<div class="projects">
<!--
Currently, there is a bug in wkhtmltopdf that makes it necessary to put these links on
separate lines. Otherwise, the targets of links will all be those of the last link
(SADI Personal Health Lens)
-->
<div>
Algorithm Development for <a href="https://github.com/bcgsc/abyss">ABySS Genome Assembler</a>
</div>
<div>
<a href="https://genome.cshlp.org/content/early/2017/02/23/gr.214346.116">ABySS 2.0</a>
</div>
<div>
<a href="http://www.bcgsc.ca/platform/bioinfo/software/konnector">Konnector</a>
</div>
</div>
</div>
<div class="position">
<div class="company-name">
University of British Columbia
</div>
<div class="dates">
<!-- <span class="start-month">01 /</span> -->
<span class="start-year">2011</span>
<span class="date-separator">-</span>
<span class="is-current">2012</span>
</div>
<div class="title">
Software Developer for <a href="http://sadiframework.org/">SADI Web Services Framework</a>
</div>
<div class="projects">
<!--
Currently, there is a bug in wkhtmltopdf that makes it necessary to put these links on
separate lines. Otherwise, the targets of links will all be those of the last link
(SADI Personal Health Lens)
-->
<div>
<a href="http://sadiframework.org/documentation/rfc/draft-bvandervalk-sadi-00.txt">SADI Spec</a>
</div>
<div>
<a href="http://code.google.com/p/sadi/wiki/SADIforGMOD">SADI for GMOD</a>
</div>
<div>
<a href="http://search.cpan.org/dist/SADI-Simple/lib/SADI/Simple.pm">SADI::Simple</a>
</div>
<div>
<a href="https://code.google.com/p/cardioshare/wiki/PersonalHealthLens">SADI Personal Health Lens</a>
</div>
</span>
</div>
</div>
<div class="position">
<div class="company-name">
Peninsula Graphite Inc. (Family Business)
</div>
<div class="dates">
<!-- <span class="start-month">01 /</span> -->
<span class="start-year">2005</span>
<span class="date-separator">-</span>
<span class="end-year">2007</span>
</div>
<div class="clear"></div>
<div class="mandate">
Electrode Supplier for Canadian Steel Mills
</div>
<div class="title">
Sales, Cash Flow, Shipping/Customs, Contract Negotiations
</div>
</div>
<div class="position">
<div class="company-name">
Electronic Arts Canada
</div>
<div class="dates">
<!-- <span class="start-month">01 /</span> -->
<div>
<span class="start-year">2002</span>
<span class="date-separator">-</span>
<span class="end-year">2003</span>
</div>
<div>
<span class="months">(8 months)</span>
</div>
</div>
<div class="title">
Intern Software Developer: <a href="http://www.gamespot.com/ssx-3/">SSX 3</a> Snowboarding Game
</div>
<div class="projects">
Lightmap Processing Algorithm (Texture Compression)
</div>
</div>
<div class="position">
<div class="company-name">
Xandros Linux
</div>
<div class="dates">
<!-- <span class="start-month">01 /</span> -->
<div>
<span class="end-year" style="float:right;">2002</span>
</div>
<div>
<span class="months">(4 months)</span>
</div>
</div>
<div class="title">
Intern Software Developer: "da Vinci" Remote Workstation Admin App
</div>
<div class="mandate">
Remote Task Scheduling Module (a la 'cron')
</div>
</div>
<div class="position">
<div class="company-name">
Inscriber Technology Co. (now Harris)
</div>
<div class="dates">
<div>
<span class="end-year" style="float:right;">2001</span>
</div>
<div>
<span class="months">(4 months)</span>
</div>
</div>
<div class="title">
Intern Software Developer: FX Keyframe Video Editor
</div>
<div class="mandate">
Multi-select, Refactoring, Code Documentation
</div>
</div>
<div class="position">
<div class="company-name">
Inscriber Technology Co. (now Harris)
</div>
<div class="dates">
<div>
<span class="end-year" style="float:right;">2000</span>
</div>
<div>
<span class="months">(4 months)</span>
</div>
</div>
<div class="title">
Intern Software Developer: 3D Effects
</div>
<div class="mandate">
Deformation Effects for Video Transitions (e.g. Wedding Videos)
</div>
</div>
</div>
<div class="clear"></div>
</div>
<div class="section publications">
<h2 class="section-header">
<span class="text">Publications</span>
</h2>
<div class="content">
<!-- Example HTML for publication
<div class="publication first">
<div class="publication-title">
SHARE & the Semantic Web - This Time it's Personal with a really long title!
</div>
<div class="dates">
<span class="start-year">2010</span>
</div>
<div class="publication-details">
<span class="dot-separator">·</span>
<span class="authors">
<span class="authors-label">Authors:</span>
<span class="author">B. Vandervalk,</span>
<span class="author">E. L. McCarthy,</span>
<span class="author">M. D. Wilkinson,</span>
</span>
<span class="publisher">Proceedings of OWLED 2010,</span>
<a href="http://www.oboedit.org/BOSC2011/BOSC2011-program.pdf">http://www.oboedit.org/BOSC2011/BOSC2011-program.pdf</a>
</div>
</div>
-->
<!-- BEGIN AUTOGENERATED PUBLICATIONS HTML -->
<div class="publication first">
<div class="publication-details">
<a href="https://genome.cshlp.org/content/27/5/768">ABySS 2.0: Resource-efficient Assembly of Large Genomes using a Bloom Filter</a>,
<span class="authors">
<span class="author">S. D Jackman,</span>
<span class="author">B. P Vandervalk,</span>
<span class="author">H. Mohamadi,</span>
<span class="author">J. Chu,</span>
<span class="author">S. Yeo,</span>
<span class="author">S A. Hammond,</span>
<span class="author">G. Jahesh,</span>
<span class="author">H. Khan,</span>
<span class="author">L. Coombe,</span>
<span class="author">R. L Warren,</span>
<span class="author"> others,</span>
</span>
<span class="publisher">Genome Research.</span>
</div>
<div class="dates">
<span class="start-year">2017</span>
</div>
</div>
<div class="publication">
<div class="publication-details">
<a href="https://doi.org/10.1186/1755-8794-8-S3-S1">Konnector v2. 0: Pseudo-long Reads from Paired-end Sequencing Data</a>,
<span class="authors">
<span class="author">B. P Vandervalk,</span>
<span class="author">C. Yang,</span>
<span class="author">Z. Xue,</span>
<span class="author">K. Raghavan,</span>
<span class="author">J. Chu,</span>
<span class="author">H. Mohamadi,</span>
<span class="author">S. D Jackman,</span>
<span class="author">R. Chiu,</span>
<span class="author">R. L Warren,</span>
<span class="author">I. Birol,</span>
</span>
<span class="publisher">BMC Medical Genomics.</span>
</div>
<div class="dates">
<span class="start-year">2015</span>
</div>
</div>
<div class="publication">
<div class="publication-details">
<a href="https://doi.org/10.1109/BIBM.2014.6999126">Konnector: Connecting Paired-end Reads using a Bloom Filter de Bruijn Graph</a>,
<span class="authors">
<span class="author">B. P Vandervalk,</span>
<span class="author">S. D Jackman,</span>
<span class="author">A. Raymond,</span>
<span class="author">H. Mohamadi,</span>
<span class="author">C. Yang,</span>
<span class="author">D. A Attali,</span>
<span class="author">J. Chu,</span>
<span class="author">R. L Warren,</span>
<span class="author">I. Birol,</span>
</span>
<span class="publisher">Bioinformatics and Biomedicine (BIBM) 2014.</span>
</div>
<div class="dates">
<span class="start-year">2014</span>
</div>
</div>
<div class="publication">
<div class="publication-details">
<a href="http://dx.doi.org/10.1093/bioinformatics/btt178">Assembling the 20 Gb White Spruce (Picea glauca) Genome From Whole-Genome Shotgun Sequencing Data</a>,
<span class="authors">
<span class="author">I. Birol,</span>
<span class="author">A. Raymond,</span>
<span class="author">S. D. Jackman,</span>
<span class="author">S. Pleasance,</span>
<span class="author">R. Coope,</span>
<span class="author">G. A. Taylor,</span>
<span class="author"> Macaire Man Saint Yuen,</span>
<span class="author">C. I. Keeling,</span>
<span class="author">D. Brand,</span>
<span class="author">B. P. Vandervalk,</span>
<span class="author">H. Kirk,</span>
<span class="author">P. Pandoh,</span>
<span class="author">R. A. Moore,</span>
<span class="author">Y. Zhao,</span>
<span class="author">A. J. Mungall,</span>
<span class="author">B. Jaquish,</span>
<span class="author">A. Yanchuk,</span>
<span class="author">C. Ritland,</span>
<span class="author">B. Boyle,</span>
<span class="author">J. Bousquet,</span>
<span class="author">K. Ritland,</span>
<span class="author">J. MacKay,</span>
<span class="author">J. Bohlmann,</span>
<span class="author">S. J. M. Jones,</span>
</span>
<span class="publisher">Bioinformatics.</span>
</div>
<div class="dates">
<span class="start-year">2013</span>
</div>
</div>
<div class="publication">
<div class="publication-details">
<a href="http://dx.doi.org/10.2196/resprot.2315">The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions</a>,
<span class="authors">
<span class="author">B. Vandervalk,</span>
<span class="author">E. L. McCarthy,</span>
<span class="author">J. Cruz-Toledo,</span>
<span class="author">A. Klein,</span>
<span class="author">C. J. Baker,</span>
<span class="author">M. Dumontier,</span>
<span class="author">M. D. Wilkinson,</span>
</span>
<span class="publisher">JMIR Research Protocols.</span>
</div>
<div class="dates">
<span class="start-year">2013</span>
</div>
</div>
<div class="publication">
<div class="publication-details">
<a href="http://dx.doi.org/10.1007/978-3-642-34032-1_6">OWL-DL Domain-Models as Abstract Workflows</a>,
<span class="authors">
<span class="author">I. Wood,</span>
<span class="author">B. Vandervalk,</span>
<span class="author">L. McCarthy,</span>
<span class="author">M. D. Wilkinson,</span>
</span>
<span class="publisher">Leveraging Applications of Formal Methods, Verification and Validation: Applications and Case Studies.</span>
</div>
<div class="dates">
<span class="start-year">2012</span>
</div>
</div>
<div class="publication">
<div class="publication-details">
<a href="http://ceur-ws.org/Vol-774/ben.pdf">SADI for GMOD: Semantic Web Services for Model Organism Databases</a>,
<span class="authors">
<span class="author">B. Vandervalk,</span>
<span class="author">M. Dumontier,</span>
<span class="author">E. L. McCarthy,</span>
<span class="author">M. D. Wilkinson,</span>
</span>
<span class="publisher">Proceedings of the Canadian Semantic Web Symposium (CSWS) 2011.</span>
</div>
<div class="dates">
<span class="start-year">2011</span>
</div>
</div>
<div class="publication">
<div class="publication-details">
<a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3212890/?tool=pmcentrez&rendertype=abstract">The Semantic Automated Discovery and Integration (SADI) Web Service Design-Pattern, API and Reference Implementation</a>,
<span class="authors">
<span class="author">M. D. Wilkinson,</span>
<span class="author">B. Vandervalk,</span>
<span class="author">E. L. McCarthy,</span>
</span>
<span class="publisher">Journal of Biomedical Semantics.</span>
</div>
<div class="dates">
<span class="start-year">2011</span>
</div>
</div>
<div class="publication">
<div class="publication-details">
<a href="http://www.webont.org/owled/2010/papers/owled2010_submission_22.pdf">SHARE & The Semantic Web - This Time it's Personal!</a>,
<span class="authors">
<span class="author">B. Vandervalk,</span>
<span class="author">E. L. McCarthy,</span>
<span class="author">M. D. Wilkinson,</span>
</span>
<span class="publisher">Proceedings of OWL Experiences and Directions (OWLED) 2010.</span>
</div>
<div class="dates">
<span class="start-year">2010</span>
</div>
</div>
<div class="publication">
<div class="publication-details">
<a href="http://dx.doi.org/10.1186/1471-2105-11-s12-s7">SADI, SHARE, and the In Silico Scientific Method</a>,
<span class="authors">
<span class="author">M. D. Wilkinson,</span>
<span class="author">E. L. McCarthy,</span>
<span class="author">B. Vandervalk,</span>
<span class="author">D. Withers,</span>
<span class="author">E. Kawas,</span>
<span class="author">S. Samadian,</span>
</span>
<span class="publisher">BMC Bioinformatics.</span>
</div>
<div class="dates">
<span class="start-year">2010</span>
</div>
</div>
<div class="publication">
<div class="publication-details">
<a href="http://dx.doi.org/10.1093/bib/bbn051">Moby and Moby 2: Creatures of the Deep (Web)</a>,
<span class="authors">
<span class="author">B. Vandervalk,</span>
<span class="author">E. L. McCarthy,</span>
<span class="author">M. D. Wilkinson,</span>
</span>
<span class="publisher">Briefings in Bioinformatics.</span>
</div>
<div class="dates">
<span class="start-year">2009</span>
</div>
</div>
<div class="publication">
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<a href="http://dx.doi.org/10.1109/cse.2009.144">Optimization of Distributed SPARQL Queries Using Edmonds' Algorithm and Prim's Algorithm</a>,
<span class="authors">
<span class="author">B. Vandervalk,</span>
<span class="author">E. L. McCarthy,</span>
<span class="author">M. D. Wilkinson,</span>
</span>
<span class="publisher">Proceedings of the IEEE International Conference on Computational Science and Engineering (CSE) 2009.</span>
</div>
<div class="dates">
<span class="start-year">2009</span>
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<div class="publication-details">
<a href="http://dx.doi.org/10.1007/978-3-642-10871-6_27">SHARE: A Semantic Web Query Engine for Bioinformatics</a>,
<span class="authors">
<span class="author">B. Vandervalk,</span>
<span class="author">E. L. McCarthy,</span>
<span class="author">M. D. Wilkinson,</span>
</span>
<span class="publisher">Proceedings of the Asian Semantic Web Conference (ASWC) 2009.</span>
</div>
<div class="dates">
<span class="start-year">2009</span>
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