Download JELAI WANG PROFESSIONAL EXPERIENCE Wang Scientific Software Solutions, LLC Founder

JELAI WANG
PROFESSIONAL EXPERIENCE
January 2014
To Present
Wang Scientific Software Solutions, LLC
Founder
Started a new company to explore business opportunities and market scientific software
products.
Selected highlights include:
Released StatGenLab, a virtual machine for genetics data analysis, read more at
http://www.statgenlab.com/. Put together with VirtualBox and CentOS minimal, package
repository includes PLINK, Bioconductor, MACH, minimac, CpGassoc, SKAT,
PennCNV, bowtie, MACS, IGV, bsseq, DSS, HapSeq, and many other commonly used
programs.
Designed and implemented a popular and representative-of-real-world-workflows handson computing lab experience for the NHGRI-funded Short Course on Next-Generation
Sequencing (2014 – present), http://www.soph.uab.edu/ssg/nhgri_r25/fourthshortcourse,
and NIGMS-funded Short Course on Statistical Genetics and Genomics (2014 – 2016),
http://www.soph.uab.edu/ssg/nigmsstatgen/fourth. Course evaluations from attendees,
usually 50+ per course, have been very positive, highlighting StatGenLab and my
stewardship of the hands-on lab as key strengths.
Started a new Youtube channel for providing technical support to short course attendees
at https://www.youtube.com/channel/UCjGuzmr2DHRAdefNIV-10RQ. Released “Linux
Primer with StatGenLab”, “StatGenLab Quick Test”, and “Shared Folders with
StatGenLab” videos for July 2016 short course, to positive initial reviews from both
attendees and instructors.
January 2003
To
December 2013
University of Alabama at Birmingham
Section on Statistical Genetics, Department of Biostatistics
System Programmer Lead
Led the in-house computing team, which was primarily responsible for implementing
newly-developed statistical methods, performing high-quality applied data analysis, and
writing new software for research application. This multidisciplinary team of statisticians,
programmers, and bioinformaticians, which I helped to assemble, leveraged software
practices like unit testing, refactoring, and version control and made thoughtful use of
available high-performance computing resources, like clusters and shared memory
supercomputers, to help the SSG achieve its mission of research and teaching excellence.
In addition to supervising and coordinating the activities of up to 7 FTE, helping on
grants, and balancing budgets, I wrote software, analyzed data, and published papers.
Selected highlights include:
Released GWA Test Driver http://gwatestdriver.ssg.uab.edu/, a web application to help
researchers with power and sample estimates for planning genome-wide association
studies. Written with Java Servlets/JSP, commons-mixomatic, Visual Numerics JMSL,
Jsci, Apache Commons Math, IO, and FileUpload, and JFreeChart, amongst others. See
UAB Reporter article at http://www.uab.edu/reporter/know-more/research/item/247-gwatest-driver-expands-researchers-calculating-power.
Was a part of many successful grants while at UAB, but especially proud of an NIH S10
Shared Instrumentation grant (1S10RR026723) we were awarded in 2010 titled “Dell
high performance computing cluster and associated Hitachi terabyte data storage”. I took
a lead role in writing this and the $500,000 award helped us expand the existing cluster
by a much-needed 576 cores and 120 TB of storage.
Released ssglabvm, http://www.ssg.uab.edu/ssglabvm/, which was a key component of
our “mobile lab” at an NSF-funded Short Course on Statistical Genetics in Hawaii,
http://www.soph.uab.edu/ssg/nsfstatgen/nsfsecondannual.
Wrote two Java API libraries, commons-datamgmt and commons-mixomatic, with
reusable objects for solving statistical genetics programming problems. See
https://github.com/jelaiw/commons-datamgmt and https://github.com/jelaiw/commonsmixomatic for source code and javadocs.
Published “The Power Atlas: a power and sample size atlas for microarray experimental
design and research” in BMC Bioinformatics, see http://dx.doi.org/10.1186/1471-2105-784.
Honored as UAB Employee of the Month, September 2006. See UAB Reporter article at
http://www.uab.edu/reporterarchive/42225-wang-s-behind-the-scenes-work-key-to-uabresearchers.
Worked with School of Engineering to create an “HPC bootcamp” for teaching best
practices to various groups across campus engaged in high-performance computing. See
http://www.soph.uab.edu/ssg/courses/hpcbootcamp for past agenda and videos from 2006
to 2013.
Published HDB Stat! paper in BMC Bioinformatics, see http://dx.doi.org/10.1186/14712105-6-86.
Released the Power Atlas http://poweratlas.ssg.uab.edu/, a web application that provides
power and sample size estimates for planning microarray experiments. Written with Java
Servlets/JSP, MySQL, and Apache Commons DBCP (database connection pool) and
FileUpload, amongst others.
Released HDB Stat! http://www.ssg.uab.edu/hdbstat/acknowledgments.html, a fast, userfriendly, and platform-independent desktop application for microarray data analysis.
Written with Java Swing, Visual Numerics JMSL, dom4j, Velocity, log4j, JfreeChart,
Apache POI, JSci and deployed with Java Web Start.
Wrote and contributed histogram source code to David Gilbert's open-source and free
software Java charting library, JFreeChart at http://www.jfree.org/jfreechart/. See
https://github.com/jfree/jfreechart/tree/master/src/main/java/org/jfree/data/statistics,
especially HistogramDataSet, HistogramBin, etc. That's my original histogram demo at
http://www.jfree.org/jfreechart/images/HistogramDemo.png, which was featured on the
screenshots page at http://www.jfree.org/jfreechart/samples.html and should still be in the
developer guide demo bundle.
February 2001
To
June 2002
Celera Diagnostics, Alameda, California
Statistical Genetics
Senior Software Engineer
Designed and implemented software components for solving genetics problems. Wrote a
data-handling framework that could read and write data from different file formats,
databases, and simulation sources through an easy-to-use API. Various in-house programs
were developed using these libraries, including the Celera Genetics Analysis Tool CGAT,
a Java Swing desktop application.
Moderated a design patterns study group that met weekly to study patterns and discuss
object-oriented design issues.
Put together a statistical genetics software library of in-house, licensed, and public
domain software, compiling each program from source if necessary, writing installation
guides for the more troublesome programs, but in general just making them work.
November 1999
To
January 2001
Pfizer Global Research, Alameda, California
Department of Human, Statistical, and Pharmacogenetics
Software Engineer
Developed custom software to streamline in-house data analysis workflows, including
PGXT, a pharmacogenetics study design application, and CT, a human genetics file
format conversion framework. Both written in Java.
PROFESSIONAL DEVELOPMENT
Workshops and Courses
 1st Short Course on Next-Generation Sequencing: Technology and Statistical
Methods, received certificate of completion.
 BST 675 Introduction to Statistical Genetics, Jose Fernandez, got an “A”.
 Two-day Tutorial in R Statistical Computing, UAB, Thomas Lumley
 Parallel Processing with JINI and JavaSpaces, Georgetown University
 JDBC and Client/Server Programming, UC Berkeley Extension
 Java: AWT and Swing, UC Berkeley Extension, Allen Holub
Certifications
 Sun Certified Programmer for the Java 2 Platform
 Brain Bench Certified Java 1 Programmer, Transcript #75324
SELECTED SKILLS
Java, Linux, object-oriented design patterns, unit testing, refactoring, high-performance
computing, informatics, big data, JDBC, SQL, relational databases like MySQL, dom4j,
XML, Hibernate, Castor, continuous integration, Hudson (now Jenkins), Java
Servlets/JSP, JUnit, mock objects, log4j, HTML, CSS, Java Swing, JFreeChart, VNI
JMSL, Apache Tomcat, vim, IntelliJ IDEA, Subversion, git, ant, javadoc, Atlassian
Confluence, JIRA, bash, R, VMware, VirtualBox.
PUBLICATIONS IN PEER-REVIEWED JOURNALS
1. Trivedi P, Edwards JW, Wang J, Gadbury GL, Srinivasasainagendra V, Zakharkin
2.
3.
4.
5.
SO, Kim K, Mehta T, Brand JP, Patki A, Page GP, Allison DB. HDBStat!: A
platform-independent software suite for statistical analysis of high dimensional
biology data. BMC Bioinformatics 2005, 6:86. http://dx.doi.org/10.1186/14712105-6-86.
Page GP, Edwards JW, Gadbury GL, Yelisetti P, Wang J, Trivedi P, Allison DB.
The PowerAtlas: a power and sample size atlas for microarray experimental
design and research. BMC Bioinformatics 2006, 7:84.
http://dx.doi.org/10.1186/1471-2105-7-84.
Wu X, Wang J, Cui X, Maianu L, Rhees B, Rosinski J, So WV, Willi SM, Osier
MV, Hill HS, Page GP, Allison DB, Martin M, Garvey TW. The effect of insulin
on expression of genes and biochemical pathways in human skeletal muscle.
Endocrine, February 2007, Volume 31, Issue 1, pp 5-17.
http://dx.doi.org/10.1007/s12020-007-0007-x.
Barger JL, Kayo T, Vann JM, Arias EB, Wang J, Hacker TA, Wang Y, Raederstorff
D, Morrow JD, Leeuwenburgh C, Allison DB, Saupe KW, Cartee GD, Weindruch
R, Prolla TA. A Low Dose of Dietary Resveratrol Partially Mimics Caloric
Restriction and Retards Aging Parameters in Mice. PLOS ONE, June 2008.
http://dx.doi.org/10.1371/journal.pone.0002264.
Bangalore SS, Wang J, Allison DB. How accurate are the extremely small Pvalues used in genomic research: An evaluation of numerical libraries.
Computational Statistics & Data Analysis, May 2009, Volume 53, Issue 7, Pages
2446-2452. http://dx.doi.org/10.1016/j.csda.2008.11.028.
6. Klimentidis YC, Abrams M, Wang J, Fernandez JR, Allison DB. Natural selection
at genomic regions associated with obesity and type-2 diabetes: East Asians and
sub-Saharan Africans exhibit high levels of differentiation at type-2 diabetes
regions. Human Genetics, April 2011, Volume 129, Issue 4, pp 407-418.
http://dx.doi.org/10.1007/s00439-010-0935-z.
7. Perera MA, Cavallari LH, Limdi NA, Gamazon ER, Konkashbaev A, Daneshjou
R, Pluzhnikov A, Crawford DC, Wang J, Liu N, Tatonetti N, Bourgeois S,
Takahashi H, Bradford Y, Burkley BM, Desnick RJ, Halperin JL, Khalifa SI,
Langaee TY, Lubitz SA, Nutescu EA, Oetjens M, Shahin MH, Patel SR, Sgreiya
H, Tector M, Weck KE, Rieder MJ, Scott SA, Wu AH, Burmester JK, Wadelius
M, Deloukas P, Wagner MJ, Mushiroda T, Kubo M, Roden DM, Cox NJ, Altman
RB, Klein TE, Nakamura Y, Johnson JA. Genetic variants associated with
warfarin dose in African-American individuals: a genome-wide association study.
The Lancet, Volume 382, No. 9894, p790-796, 31 August 2013.
http://dx.doi.org/10.1016/S0140-6736%2813%2960681-9.
SELECTED PRESENTATIONS
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“StatGenLab, a virtual machine for genetics data analysis”, NHGRI-funded Short
Course on Next-Generation Sequencing, Dec 2014-2015, UAB.
“StatGenLab, a virtual machine for genetics data analysis”,NIGMS-funded Short
Course on Statistical Genetics and Genomics, Jul 2014-2016, UAB.
“PLINK, ssglabvm”, 2nd Short Course on Statistical Genetics and Genomics, July
2012, 3rd Short Course on Statistical Genetics and Genomics, July 2013, UAB.
“PLINK, GWA Test Driver, IMPUTE2”, 1st Short Course on Statistical Genetics and
Genomics, July 2011, UAB.
“Microarray Software Demo & Hands-on”, Second Annual NSF-funded Short
Course on Statistical Genetics & Statistical Genomics, July 2009, Hawaii.
“HDBSTAT, Power Atlas - Genomics Microarray”, First Annual NSF-funded Short
Course on Statistical Genetics & Statistical Genomics, July 2008, UAB.
“Demonstration and Supervised Practice(Microarray)”, Fifth Annual Short Course on
Statistical Genetics for Obesity and Nutrition Researchers, May 2005, UAB.
Plant Microarray Workshop, Dec 2004, University of Arizona
Microarray Research Coordination Network Retreat, Sept 2004, Mohonk Mountain
“Why software engineering? Taking a closer look at the software development
process”, Nov 2000, Pfizer Global Research Alameda
EDUCATION
University of Alabama at Birmingham, August 1999, GPA 3.97
Bachelor of Science Degree with University Honors in Computer Science
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Accepted to UAB Honors Program.
Accepted to Computer and Information Sciences Honors Research Program.
Represented UAB at 1998 ACM Regional Collegiate Programming Contest.
Honored with Outstanding Student Award from the School of Natural Sciences and
Mathematics.