Joseph Lemaire
10 Star Lane, Amesbury, MA 01913
[Send email to request phone number] 34-6564 (Home)
617-901-8678 (Cell) [Send email using form at
bottom]
Primary Skills
Data analysis, Web UI, Datacenter management, Cluster computing, Linux,
Java/php/Perl/Scripting
Work Experience
Partners Healthcare, Charlestown, MA
Jan 09 - Present
Senior Software Developer
* Implemented a web-based query tool that displays dynamically-generated graphs
of patient head trauma data. This project uses PHP, CSS and JPgraph open-source
graphing software, communicating with a MySQL backend database.
* Designed and implemented a Content Management System (CMS) using the
open-source drupal framework, based on php and mySql; this allows researchers to
independently maintain and update their own websites for project collaboration.
* Using Java and SWT UI tools, designed an application for hospital researchers
to easily use a centralized cluster computing resource for CPU-intensive disease
studies. This application used core Java and open-source Java widgets (SWT
components such as stylized buttons and scrollable text areas) to communicate
with an Oracle backend via Java Web Services.
* Created a browser-based Java software pipeline to provide immediate access to
large volumes of genetic research data and automate the scientific analysis of
that data. This project used Java JSPs to render the data and Servlets to
communicate with the MySQL database via JDBC.
* Created a data processing pipeline using Java to interact with the Partners
Computing Grid via LSF cluster access to maximize parallel computing resources.
This task involved Java JSPs, Servlets, jquery, CSS, YUI, JDBC, and Apache Axis2
Web Services to communicate with the cluster farm of 128 computers. The IDE used
was eclipse.
Sanofi-aventis, Cambridge, MA
Sep 07 - Dec 08
Bionformatics Software Developer
* Redesigned and added functionality to proprietary drug analysis software using
Java, Swing and RMI technology.
This project used Java Webstart to deploy the stand-alone application as a
web-based tool.
* Developed software parsers in core Java to convert and validate external
biological databases into XML for in-house data integration.
Genomics Collaborative, Cambridge, MA
Jan 01 - Sep 07
Senior level software developer
* Built a database and query interface to allow flexible analysis of clinical
patient demographic data linked to their associated tissue and DNA samples. This
interface was built using Java J2EE with Spring, in a Weblogic IDE.
* Developed a graphical editing tool using Java J2EE and Swing GUI components
to facilitate the selection of human genetic sequence mutations (SNPs) for
clinical study.
* Using Java, perl and Oracle, implemented an in-silico quality control pipeline
to verify the quality of genetic mutations for subsequent laboratory assay
design.
* Designed and implemented SNP scoring algorithms to assist in the automated
analysis of the human genome. This code was written in perl.
* Created a web interface to easily view and score genotyping results for
in-house sequencing experiments. This project was written in perl and perl DBI
communicating with an Oracle database.
* Designed and created software that calculates and displays cross-species
synteny for coding SNPs in the human genome. This tool was written in perl and
Tcl.
* Developed a case/control matching algorithm with a nearly 100% success rate;
able to match on age/gender/ethnicity/BMI/birth_country. This tool was written
in SAS.
Programming Languages and Technologies
Java, PHP, Perl, SQL, JavaScript, CSS, jQuery, SAS, C, HTML, XML, Linux
DBI, J2EE, JDBC, Eclipse, Tomcat, Ant, Hibernate, BLAST, Platform LSF, Oracle,
MySQL, SVN
Education
BS in Computer Science, Hofstra University, New York. Minors in Art and
Mathematics.
Hobbies
Woodworking and cycling; tuning and repairing pianos.
Hand-crafted wooden ship model of the Santa Maria is on permanent
display at the Maritime Museum in San Pedro, CA.
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