Programmer Analyst
Columbia University - New York, NY

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Job Description:
An experienced Java programmer is sought to participate in the continued design and development of geWorkbench, a flexible, open-ended platform for bioinformatics data integration and analysis. The platform being developed allows programs or algorithms, which may be written with no knowledge of each other, to exchange data and to call on or provide visualization and data management services. This open-source platform distributes computations across client, server and grid components, scaling
from small local calculations to major cluster-based calculations. Development of geWorkbench is conducted under MAGNet, the National Center for the Mulitscale Analysis of Genomic and Cellular Networks (, one of the 8 National Centers for Biomedical Computing ( The candidate will be a member of the in-house development team and will participate in the development of the geWorkbench platform. The candidate is expected to contribute in architecture design, implementing new algorithms, integrating existing programs, developing graphical user interfaces for visualizing analysis results, troubleshooting problems, and producing technical documentation. The types of data and algorithms encountered include sequence and microarray gene expression analysis, metabolic and regulatory network inference, and pattern detection and evaluation. This is a period of major growth for this project and the candidate will be able to make a significant contribution. It is noted that the geWorkbench development team is also supporting other software efforts related to the activities of faculty at Columbia's Center for Computational Biology and Bioinformatics (C2B2, Accordingly, the candidate is also expected to work on other development projects as they arise and perform programming related duties as assigned.

Minimum Qualifications for Grade
Applicant MUST meet these minimum qualifications to be considered an applicant

Requires a Bachelor's Degree or equivalent in education and experience, plus three (3) years of related experience.

Additional Position-Specific Minimum Qualifications
Applicant MUST meet these minimum qualifications to be considered an applicant

Bachelor's Degree (Master's preferred) in Computer Science, Engineering, Mathematics, Physics, Bioinformatics or a similar field. At least 3 years experience programming with Java is required, including (1) experience with object-oriented design, program architecture and structured programming, (2) GUI implementation and understanding of the issue of multi-thread applications, and (3) the full software development cycle from writing for Use Cases to implementation and testing.

Preferred Qualifications

Knowledge of general bioinformatics principles and experience in programming bioinformatics related software would be very helpful. Also desirable is familiarity with database driven projects using MySQL or a similar database system, SQL, JDBC, Linux, and use of appropriate IDEs (e.g., eclipse), project management tools (e.g., ant, subversion), web technologies (JavaScript, tomcat, web service, HTML, CSS, php, drupal), and experience with other programming languages (e.g., C/C++).

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Founded in 1922, Columbia University's Mailman School of Public Health pursues an agenda of research, education, and service to address the...