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Senior Scientific Programmer in the Department of Genetics

Redwood City, CA

your.email@example.com
111-222-3333
www.your-website.com

Summary

  • Experienced graphical user interface developer and full stack developer for scientific projects, specifically
flow cytometry, genomics, and bioinformatics.
  • Javascript, Java Servlets, Java Swing, JDBC, C, XML, HTML, Motif, Perl, python.
  • Mac OS10, Windows 7, Windows 2000, XP, various flavors of Unix (Solaris, HPUX, SunOS, Linux).
  • Eclipse, Netbeans, cvs, SVN, Oracle, mysql, postgresql, BerkeleyDB, ant, tomcat, glassfish.
  • Experience working with large, legacy code base, data design, and architecture.
  • Particularly skilled in gathering user requirements, writing requirements, functional specification
documents and user manuals, code development, and testing/validation.
  • Proven collaborator with scientists to design useable software tools and solutions.
  • Experience as lead for small teams and especially enjoys working in multi-disciplinary teams.
  • Experienced presenter and trainer of complex information.

Work Experience

Senior Scientific Programmer in the Department of Genetics

Stanford University, Stanford, CA

2006Jan 2013

Department of Genetics
  • Develop front-end and middle layer for research project to automatically calculate compensation matrices for flow cytometry data in collaboration with expects in the field. Develop and code an algorithm that
will apply the Delaunay triangulation to flow data to detect clusters. Java, Java Swing.
  • Research Bioconductor (in R) to mine gene expression data from public databases for Post-doc studying
hematopoietic stem cells. Present results to the laboratory for further research. R
  • Member of five-person team to develop experimental design and annotation software for Flow
Cytometry, known as CytoGenie. Java, postgreSQL, javascript, html.
  • Train laboratory scientists to use CytoGenie from desktop experimental design through to flow
cytometry data collection to the Stanford Shared Facs Facility (SSFF) data archiving.
  • Present CytoGenie to potential investors and visitors to the Lab in person and using Adobe Connect
desktop sharing software.
  • Created functional specifications, directed the work and developed code with our team in India to develop a javascript/Ajax/Java servlets/postgres account management tool.
  • Designed and developed a web-based ontology widget using javascript, html, AJAX (Asyncronous
Javascript) and Java that enables browsing of complex biomedical ontology trees and selection of terms with type-ahead suggestions. The ontology terms are used to annotate bio-medical experiments to enrich the archived data.
  • Collaborated with a colleague to build the initial web services to support the ontology widget;
maintained and expanded widget after the build.

Beauheim 1
  • Maintained 45 ontologies in an Oracle relational database that the ontology widget and web services used to find terms and ontology relationships. The web services are written in Java and Java Servlets. The
ontology widget is cross-platform and cross-browser compatible.

Bioinformatics Programmer in the Laboratory of Computational Genomics

Washington University in Saint Louis, St. Louis, MO

2005 2006

St. Louis, MO 2005 - 2006
Bioinformatics Programmer in the Laboratory of Computational Genomics (LCG), Department of Computer
Science and Engineering, headed by Dr. Michael Brent.
  • Member of seven-person team contracted to verify mammalian genes for the Mammalian Gene Collection
(MGC), NIH. Designed and developed an interactive sequence curation tool, jExonAlign, for the team's
sequence gazer, based on an algorithm developed within the team. The curation tool interacts with the
UC Santa Cruz Genome Browser and database as well as LCG's local mysql and Berkeley DB databases.
jExonAlign is written in Java.
  • Developed a non-interactive, batch version of jExonAlign that can filter 1000 sequence mismatches per
hour of MGC clones. Batch jExonAlign can effectively and quickly filter for and verify novel SNP's,
becoming a tool that contributes to our quarterly clone verification goal.
  • Retrieve, format and verify data to be published at NBCI in the Trace and EST databases using perl.
Retrieve, format and verify LCG's gene prediction tracks to be published in the UCSC Genome Browser.

Software Engineer

Gene Logic Genomics Company, Berkeley, CA

2001 2003

3 with the User Interface team.
  • Member of user interface team responsible for the updated release of Genesis 2.0 project, Gene Logic's
flagship expression data management platform used for delivering Gene Logic's expression data to over 25 pharmaceutical and biotech companies. Joined user interface development team for Genesis 2.0 in
mid-development and quickly became familiar with the 1000 + class library to contribute to team effort.
  • Contributor to functional specifications and partner in code development for complex, form-based,
interactive data entry tool for tissue sample database (Oracle). Researched, analyzed, and reported on the useability of the data entry tool with respect to industry guidelines.

Senior Software Engineer

BioRad Laboratory, Hercules, CA

2000 2001

Implemented database for proteomics data in Java.

Senior Software Engineer

Berlex Laboratory, Richmond, CA

1998 2000

Assigned to Molecular Informatics in the IT Group to develop software in Java for micro-array analysis and other projects for this multi-national pharmaceutical company.

Scientist

geneNetworks, Alameda, CA

1997 1998

Developed software in collaboration with scientists focusing on human and mouse genomics. Java, C.

Software Engineer

Lawrence Berkeley National Laboratory, Berkeley, CA

1996 1997

Worked on the Human Genome Project team to develop software for DNA sequencing pipeline in Java and C.

Member of Technical Staff

Los Alamos National Laboratory, Los Alamos, NM

1993 1996

Assigned to the Computing, Information, and Communication Division / Software Application Group 
(CIC 12) to work primarily to the Human Genome Project, primarily in C and Motif. 
 
Beauheim 2

Education

M.S. in Computer Science

University of New Mexico, Albuquerque, NM

B.S. in Anthropology

University of Wisconsin, Madison, WI

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