Software Developer 2/3 - Plant Genomics

Lawrence Berkeley National Laboratory
Job Location: 
Walnut Creek, CA
Job Description: 

Software Developer 2/3- Plant Genomics - 74959
Organization: GN-Genomics

The DOE Joint Genome Institute in Walnut Creek, CA has an exciting Software Developer position available to support the Plant Genomics Program. Under general supervision, will be responsible for contributing to the development of short-read genome assembly software, including but not limited to our home-grown assembler Meraculous. Will serve as the primary contact for a potentially fast-growing user base as well as troubleshoot and debug Meraculous code base issues and problems.

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

Specific Job Duties
Essential -
• Work as part of a small team to modify, develop and enhance software and algorithms that perform whole genome shotgun assembly on short-read sequence data.
• Collaborate with users inside and outside of the Joint Genome Institute and serve as the primary contact for support.
• Troubleshoot and debug existing meraculous code base issues and problems.
• Set up and manage a system for tracking feature support requests and bugs for Meraculous.
• Perform data analysis on sequence data to assess suitability for genome assembly.
• Read and discuss journals to stay current with evolving technology related to whole-genome assembly.

Marginal -
• Develop and present updates and reports at group meetings.
• Support internal and external collaborators with systems enhancements, data exchange and custom data analysis when needed.

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 analysis capabilities and output of the group.
• Troubleshoot more complex systems and data analysis problems.


Key Success Factors
Essential -
• Bachelor's degree in Computer Science, Engineering, Bioinformatics, or related field with a minimum of two years of work experience, or an equivalent combination of education and experience.
• Demonstrated experience utilizing Perl, C, UNIX, and subversion/cvs.
• Ability to discuss and manipulate algorithms and effectively work with advanced data structures.
• Ability to optimize at the code level and at the algorithmic / run-time complexity level.
• Demonstrated experience utilizing disciplined and modern coding habits such as self-documenting code, unit testing, and pair-programming.
• Strong problem-solving, decision-making, and analytical skills to make sound judgments and recommend creative solutions to moderately complex problems.
• Strong interpersonal skills with the ability to work with scientific and administrative customers to define needs and priorities.
• Detail-oriented with strong organizational interpersonal skills to address user needs in an effective and timely manner.

Marginal -
• Demonstrated experience with C++/boost established best practices.
• Ability to think quantitatively and employ statistical methods to evaluate sequence data.
• Interest and facility in algorithmic research involving graph theory, string comparison, or other bioinformatically-relevant areas of computer science.
• Experience developing for parallel environments such as Sun Grid Engine and pbx.

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 or Master's degree in Biology, Bioinformatics, Computer Science or related field with a minimum of five years of work experience, or an equivalent combination of education and experience.
• Demonstrated expertise processing large volumes of data, whole-genome data analysis, phylogenetics, and comparative genomics.
• Ability to troubleshoot complex systems and data analysis problems.

Berkeley Lab is an affirmative action/equal opportunity employer committed to the development of a diverse workforce.

Contact Information: 

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