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Opportunity: BIOINFORMATICS Software Developer -- Sequencing Analysis (#74817) @ DOE Joint Genome Institute -- Walnut Creek, CA (US)
Submitted by Bill Cannan; posted on Wednesday, January 09, 2013
The DOE Joint Genome Institute (JGI) in Walnut Creek, CA (a division of the Lawrence Berkeley National Lab) has an exciting Software Developer position available to support the sequence Quality Control (QC) and Analysis Team. Work will affect projects on climate change, biofuel production and genomic research. Software projects will utilize the latest bioinformatics technologies to perform sequence analysis on a wide variety of genome sequencing data. Assignments will span the full software development lifecycle, including participation in requirements gathering, implementation, testing, maintenance, deployment and support of existing systems. Position reports to the QC group lead.

Specific Job Duties:
* Develop and incorporate bioinformatics analysis software into the QC pipelines and analysis systems.
* Design, implement, and update high-throughput automated sequence analysis systems.
* Provide support for existing analysis systems, including resolution of custom user and data retrieval requests.
* Stay current with new bioinformatics analysis tools and software technologies.
* Present technical and analytical status in weekly meetings and contribute to publications.
* Follow best practises for software version control, testing and release engineering.
* Train biologists and other lab staff on how to use QC and Analysis systems.
* Provide status updates in regular team meetings, and coordinate development work with other members of the QC and Analysis Group and Sequencing Informatics group.
* Analyze the impact of process, hardware or software changes on production line performance.
* Attend technical workshops and conferences related to software development and bioinformatics.

Essential Duties for the Software Developer 3 - In addition to the required duties for a level 2, the Software Developer 3 will:
* Work at a higher level of independence and responsibilities in carrying out assignments.
* Develop and implement substantial, known or novel, computational methods to improve the capabilities and output of the team.
* Troubleshoot more complex systems and data analysis problems.

Key Success Factors:
Essential Skills:
* B.S. in Computer Science or a related scientific or technical field (or equivalent experience) and a minimum of two years related experience
* Demonstrated experience with one or more of the following programming languages: Python, Perl, Java, C#, C++, Ruby
* Demonstrated experience with database programming and interfaces, preferably in MySQL or Oracle
* Demonstrated Linux shell scripting experience
* Used cvs, svn or similar version control systems

Desired Skills:
* Demonstrated experience with the following: git, Perl/CGI & javascript (jQuery)
* Demonstrated experience in providing support for production software systems
* Experience working with bioinformatics tools and/or analysis techniques, ideally with next-generation sequencing platforms
* Experience with high performance and/or parallel computing
* Experience developing web-based GUI
* Experience working with scientific users

Essential Qualifications for the Software Developer 3 - In addition to the required qualifications for the Software Developer 2, the Software Developer 3 will have:
* Bachelor's degree in Computer Engineering, Bioinformatics or a related field with a minimum of five years of work experience, or an equivalent combination of education and experience. MS degree is preferred.
* Demonstrated expertise creating systems and software for processing large volumes of data
* Ability to troubleshoot complex systems and data management problems

The selected candidate will be hired at the Software Developer 2 or 3 classification depending on the candidate's level of experience and qualifications.

DOE Joint Genome Institute
Walnut Creek, CA
Organization: GN-Genomics

Apply directly online at and follow the instructions to complete the application process.

Berkeley Lab is an Affirmative Action/Equal Employment Opportunity employer committed to the development of a diverse workforce.

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