Software Developer/Engineer 3 - Annotation and Analysis of Eukaryotic Genomes - 80671

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

Software Developer/Engineer 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 BerkeleyNational 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 testingthe JGI genome annotation pipeline, its modules and interfaces, and for supportof 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 theFungal Genomics Program Lead.
 
The selected candidate willbe hired as at the 2 or 3 level depending on the candidate's level of skills andexperience.
 
Specific Responsibilites:
• 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.

Addiitonal desired responsibilities:
• 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.

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

Required 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.

Additional desired qualifications:
• Experience with SGE or other HPC environments
• Experience with large MySQL-based datasets.  

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 1 year term appointment with the possibility of renewal and with the possibility of conversion to career.  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 programcan be found on the World Wide Web at the following location: http://www.jgi.doe.gov.
 
Rapid technologicaladvances 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 about JGIhappenings at jgi.doe.gov and jgi.doe.gov/careers.
 
Berkeley Lab 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. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science.

Equal Employment Opportunity: Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. Click here (http://www.dol.gov/ofccp/regs/compliance/posters/pdf/eeopost.pdf) to view the poster: "Equal Employment Opportunity is the Law".

How to Apply

Apply directly online at http://50.73.55.13/counter.php?id=40271 and follow the on-line instructions to complete the application process.

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