Bioinformatics, Java, Ruby on Rails

William D. Nelson

*** ******* **.

Half Moon Bay, CA 94019

Phone: 650-***-****

********@*****.***

Summary of Qualifications

Over ten years of experience designing, implementing, and supporting enterprise data

management platforms for systems biology applications.

Primary languages: Java, SQL, RUBY, PERL, DHTML, XML, R, Python.

Primary platforms and tools: Linux, Windows, MacOS, MySQL, Oracle,Tomcat, Rails, GWT,

SWING, JFreeCharts, JasperReports, ANT, Subversion, Git, IntelliJ, NetBeans, Eclipse,

RStudio.

Professional Experience

Carnegie Institute of Washington April 2011 - Present

Bioinformatics Developer - Stanford, CA

● Development and maintenance for The Arabidopsis Information Resource (TAIR).

Arabidopsis a model organism for plants. Its data resource is web based with an

enterprise infrastructure based on Java, Perl, et.al. It provides a very comprehensive

set of data mining tools.

● Provide bioinformaitcs support for the Department of Plant Biology.

Most of the data is Illumina, paired end reads. I assemble (Velvet, Oases), annotate

(Blast, InterproScan, MapMan, Blast2go, etc.), perform differential expression (BWA,

SAM tools, DESeq, EdgeR), and provide custom analyses. Results are presented in

custom Ruby on Rails web applications.

● Support a TORQUE cluster. The cluster is mainly used for InterProScan and Blast.

I maintain the software and databases and provide tech support.

● Develop in Java, Perl, Ruby, Python, R, ETL and SQL on Apache, Jboss, Tomcat and

Rails.

iRhythm Technologies July 2010-April 2011

Software Engineer – San Francisco, CA

Developed desktop applications used for the analysis of large volumes of

●

electrocardiogram data in a production, FDA regulated environment.

Developed reports that deliver a summarized analysis of up to fourteen days of

●

electrocardiogram data to prescribing physicians.

Developed with MySQL, JFreeCharts, NetBeans Platform, SWING, Jasper Reports.

●

University of Kentucky 2005-2010

Bioinformatics Developer – Lexington, KY

Designed and implemented an integration of Amazon Web Services with LabKey Server

●

to provide on-demand high performance computing resources. The application searches

for post translational modifications, in parallel, on separate EC2 nodes. Implemented

with IntelliJ, Subversion, ANT, Mule ESB, Java, R, Ruby, SAX, Typica and JetS3 for

EC2, S3, and SQS control.

Contributed the universal proteomics search engine user interface (supports

●

Mascot, X! Tandem, SEQUEST, and SEQUEST Cluster to the Labkey server (http://

www.labkey.org) Proteomics module; an open source J2EE bioinformatics infrastructure.

Implemented with Google Web Toolkit, IntelliJ, Subversion, ANT, and Spring.

Implemented and maintained a 10 node ROCKS cluster for generic proteomics pipeline

●

processing and a 12 node SEQUEST Cluster. Administration with: Sun Grid Engine,

GlobusWS, PVM, ActiveMQ

Added a validation algorithm to the Xpress software package; an open source

●

program for MS/MS isotope labeled protein quantitation experiments; Nelson W. D.;

Viele K.; Lynn B. An integrated approach for automating validation of extracted ion

chromatographic peaks. Bioinformatics 2008 24, 2103-2104. Implement in C++ with

Visual Studio.

Contributed the SEQUEST analysis pipeline to the LabKey server project. Implemented

●

with IntelliJ, Subversion, ANT, JUnit, Java, JSP, SAX, Struts, PERL, web services, and

servlets.

Implemented and customized the Institute for Systems Biology’s trans-proteomic

●

pipeline to be used as a shared resource between five MS proteomics labs at the

University of Kentucky and the University of Louisville. Customized with PERL-CGI.

Provide general bioinformatics support to researches in Kentucky through the University

●

of Kentucky’s bioinformatics core lab. This is mostly BLAST automation and simple web

interfaces. Implement with PERL, PostgreSQL, Tomcat, and Java.

Provide support and training for proteomics infrastructure. Environment: CentOS 5.0,

●

Windows 2000, Apache-Tomcat, IIS, PostgreSQL, Samba, Sun Grid Engine, ActiveMQ,

GlobusWS, and Amanda.

Solexa, Inc. 2000- 2005

Software Engineer – Hayward, CA

Introduced Agile software development practices. SCRUM master for a commercial

●

software package that controlled their nextGen sequencing instrument.

Developed user interface for nextGen sequencing instrument. Developed with Java/

●

SWING, Eclipse, CVS, ANT, JUnit, MySQL, and Hibernate.

Project leader and primary developer for Solexa’s Signature Genome Browser a web

●

application for analyzing Massively Parallel Signature Sequencing (MPSS) expression

data. The application was based on UCSC’s Genome Browser. The application was

accessible at the NCBI website until the MPSS technology was no longer supported.

Developed with Eclipse, CVS, ANT, Java, DHTML, JSP, Java2D, JBDC, MySQL, and

Tomcat.

Developed, managed, and implemented a Cimarron Laboratory Information

●

Management System (LIMS), through in-house resources or contractors. The system

included bar coding and integration with instruments. Also created custom LIMS-like

applications for specific in-house needs. Successfully implemented two workflow based

LIMS. Developed with Borland Code Warior, CVS, Java, JSP,SAX, DHTML, ODBC,

JDBC, SQL, Tomcat, Cold Fusion, Weblogic, Sybase, and MySQL.

Database administrator for Solexa’s Sybase, MySQL production and development

●

databases. Tools used: Embarcadero, SQL.

Applied Biosystems, Inc. 1991-2000

Senior Application Specialist- Paris, France

Provided sales application support for the enterprise bioinformatics product line.

●

Created applications for sales demonstrations. Developed with PERL-GGI, NCSA

●

server, ODBC, pl/sql, Oracle, and Sybase.

Provided administration for bioinformatics products for the in-house sales demonstration

●

lab. Environments: Solaris, Oracle, Sybase.

Installation and training on bioinformatics products at customer sites. Environments:

●

Solaris, Oracle, Sybase.

Managed three application specialists.

●

Service Specialist - Foster City, CA

Created and implemented the support infrastructure (training, documentation, and

●

escalation support) for enterprise bioinformatics product line. Environment: Solaris,

Bourne shell, Sybase.

Sales Specialist- Raleigh, NC

Direct sales of protein biochemistry products.

●

Hewlett Packard 1990-1991

Sales Engineer- Washington, DC

Provided all field functions for protein sequencer instruments.

●

Applied Biosystems 1985-1990

Field Application Specialist - Washington, DC

Provided pre-sales support for protein biochemistry products.

●

Service Specialist - Foster City, CA

● Created and implemented the support infrastructure (training, documentation, and

escalation support) for the protein sequencing instruments product line.

Field Service Engineer - Washington, DC

Provided service support for the protein biochemistry instrument product line.

●

California Institute of Technology 1984-1985

Research Assistant – Pasadena, CA

Performed manual and automated peptide synthesis in Leroy Hood’s group.

●

Education

Western Connecticut State University 1984

B.A., Chemistry, Biochemistry Option

University of Kentucky 2009

Graduate Certificate, Bioinformatics

Certifications

Sun Certified Programmer for the Java 2 Platform 1.4

●

Sun Certified Business Component Developer Java 2 Platform, Enterprise Edition 1.3

●

Sun Certified SA-270 Solaris System Administration 4.X

●

Contact this candidate