Software Developer/Engineer 2/3- Annotation and Analysis of Eukaryotic Genomes

Organization
Lawrence Berkeley National Laboratory
Job Location
Walnut Creek, CA 94598
Job Description

Software Developer/Engineer 2/3- Annotation and Analysis of Eukaryotic Genomes - 80671
Organization:  GN-Genomics

The Department of Energy(DOE) Joint Genome Institute (JGI), a division of the Lawrence Berkeley National Laboratory (Berkeley Lab) has an exciting opportunity available for an experienced software developer/engineer. Will be responsible for development of software for annotation and analysis of eukaryotic genomes such as JGI annotation pipeline and web-based analysis tools.  As a team member participate in developing and testing the JGI genome annotation pipeline, its modules and interfaces, and for support of the pipeline users who run the pipeline for production genome annotations. Must demonstrate detailed knowledge and strong technical ability in full lifecycle software development, database design and access, software design,development and deployment. Will interact will team members as well as technical, administrative, and scientific staff.  Position reports to the Fungal Genomics Program Lead.
 
The selected candidate will be hired as at the 2 or 3 level depending on the candidate's level of skills and experience.
 
Specific Job Duties
Essential
• Work as part of the team that develops and supports JGI annotation pipeline and web-based tools for genome analysis.
• Design and develop software for the Fungal Program.
• Design effective solutions compatible with existing systems.
• Interface with end-users to gather feedback and requirements.
• Provide daily client support, including occasional evening and weekends.
• Observe and promote configuration management and deployment policies.
• Participate in formal and informal design and code reviews.
• Work with other pipeline developers, systems administrators, to optimize hardware and configuration for maximal pipeline performance and stability.

Marginal
• Work on special projects as requested to help troubleshoot production problems, data management issues, working with collaborators or JGI staff, etc.
• Train new group members on use of annotation tools.
• Participate in group meetings, present work to group members.

Essential Duties for the Software Developer/Engineer 3 - In addition to the required duties for a level 2, the Software Developer/Engineer 3 will:
• Work at a higher level of independence and responsibilities in carrying out assignments.
• Work closely with Systems Administration group to optimize hardware and configuration for maximal portal performance and stability.
• Troubleshoot more complex systems and data analysis problems.

Requirements

Qualifications
• B.S. Degree in Computer Science, Bioinformatics, Life Sciences, or related field with minimum two years of programming experience. Or an equivalent combination of education and experience.
• Demonstrated experience with Perl, Python, C/C++, java or another language in UNIX environment.
• Strong SQL skills, with good knowledge of database performance optimization related to schema design.
• Good working knowledge of basic genomic concepts, data types, and data analysis methods, and their representation in software systems.
• Genomic analysis software experience, and substantial knowledge of various bioinformatics algorithms related to sequence analysis.
• Demonstrated knowledge and technical ability in full life-cycle software development,database design and access, web user interface design, development and deployment.
• Demonstrated success designing, implementing, and supporting large complex systems and software in a scientific or technical environment.
• Excellent analytical, problem-solving and decision-making skills to independently make sound judgments and creative solutions to moderately complex problems.
• Effective time management, organization and planning skills; ability to work effectively in team environment.
• Ability to apply analytical skills and creativity to solve diverse and challenging problems.
• Demonstrated expertise with software development practices – self-documenting code, source control, bug tracking.

Preferred
• Experience with SGE or other HPC environments
• Experience with large MySQL-based datasets.  

Essential Qualifications for the Software Developer/Engineer 3 - In addition to the required qualifications for the Software Developer/Engineer 2, the Software Developer/Engineer 3 will have:
• Bachelor's degree in Computer Science, Engineering, Bioinformatics, or related field with a minimum of five years of work experience, or an equivalent combination of education and experience.  Advanced degree (MS / Ph.D.) preferred.
• Extensive genomic analysis software experience, and knowledge of various bioinformatics algorithms related to sequence analysis.
• Must demonstrate detailed knowledge and strong technical ability in full life-cycle software development, database design and access, web user interface design, development and deployment
• Ability to troubleshoot complex web component and database systems issues.

Notes:  This is a one year term appointment with the possibility of renewal and with the possibility of conversion to career based upon satisfactory job performance, continuing availability of funds, and ongoing operational needs.  Work will be performed at the DOE Joint Genome Institute (JGI) in Walnut Creek, CA.  Job may require occasional travel, weekend, and after-hours work.  Detailed information about the Joint Genome Institute program can be found on the World Wide Web at the following location: http://www.jgi.doe.gov.

About Us   
Rapid technological advances in genomics have transformed modern biology. From its inception, the Department of Energy Joint Genome Institute has been at the forefront of large-scale sequence-based science. Learn more at www.jgi.doe.gov

Lawrence Berkeley National Laboratory addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Berkeley Lab’s science is a global enterprise. Our scientists work at the frontiers of knowledge to better understand our universe and to address the challenges facing our nation and our planet. Read about our excellent benefits (http://ucnet.universityofcalifornia.edu/compensation-and-benefits/health...).  

Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age or protected veteran status. www.lbl.gov

How to Apply

Apply directly online at http://50.73.55.13/counter.php?id=31412 and follow the instructions to complete the application process.

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