The DOE Joint Genome Institute (JGI) is searching for an experienced Software Developer / Engineer to support the genomics research facility in Walnut Creek, CA. The mission of the JGI is applying genomic science to the critical fields of bioenergy, bioremediation and carbon cycle management. The JGI applies both the latest high-volume sequencing technology and classic Sanger processes to sequence and analyze thousands of large and small genomes. As a Software Developer within the QA / QC Group, you will be responsible for developing computational tools for DNA sequence analysis and analyzing data for production and R&D projects. Software development tasks will include identifying client needs, gathering requirements, developing, testing, integrating and deploying new and/or existing software applications and working with other developers and analysts. Analysis tasks typically involve complex problems in the domain of DNA requiring in-depth evaluation of various factors and application of knowledge and expertise in DNA sequence technology, computer science and statistics. Assignments include problem definition, evaluation of requirements, and implementation of systems to meet goals. The candidate is expected to work with minimal supervision, and demonstrate creativity and initiative in developing methods for problem solving.
Responsibilities may also include performing thorough quality and assembly analysis of DNA sequence data and participating in a team effort to develop sequence analysis tools and pipelines. The candidate will recommend improvements to data analysis systems, will assess and improve existing tools, implement new tools for general use, and provide technical and analytical interpretation of data. The candidate will have a significant role in defining post-sequencing quality metrics and in developing algorithms and tools for calculating these metrics. Position reports to the Production QA/QC Group Lead.
Specific Job Duties
Essential -
- Gather feedback and requirements to develop software to support analysis of DNA sequence data.
- Create, manage, and query MySQL databases.
- Develop and utilize Perl classes, modules, and scripts for managing data and performing analyses; and Perl/CGI web pages for providing user access.
- Provide responsive customer support, assisting users with the prompt resolution of data entry errors, software malfunctions and other system needs.
- Communicate regularly with customers and supervisory staff about plans, designs and progress.
- Follow prescribed practices for software version control, testing and release engineering.
- Define quality metrics for assessing library and sequencer performance.
- Independently and proficiently utilize genome assemblers (such as Arachne, Newbler, PCAP etc), visualization tools, and other genome assembly and analysis software.
- Provide high quality professional reports on data analysis and results.
- Present technical and analytical status in weekly meetings and contribute to publications.
Marginal -
- Perform Qualify Control research and development work to investigate improved methods for performing data analysis.
- Mentor and cross-train other team members in software development and design.
- Stay current with new sequencing technologies.
- Train biologists to use the available data analysis tools.
- Analyze the impact of process, hardware or software changes on production line performance.
Key Success Factors
Essential -
- B.S. in Computer Science or a related scientific or technical field (or equivalent experience) and a minimum of five years related experience.
- Demonstrated experience with Perl and experience with database design and performance tuning.
- Full life-cycle software development experience with the ability to work with scientific and administrative customers to define needs and priorities.
- Demonstrated success designing and implementing systems and software in a scientific or technical environment, e.g., University, National Laboratory, corporate R&D center or automated manufacturing facility.
- Ability to effectively learn and apply new technology concepts to troubleshoot and solve problems and challenges of a diverse scope.
- Effective interpersonal communication, public speaking, and presentation skills.
- Effective time management, organization, and planning skills.
- Talent for working well under short deadlines and handling multiple tasks simultaneously.
- Ability to work effectively in a diverse team environment.
Marginal -
- Experience developing large, complex Perl based software systems and large-scale MySQL database experience preferred.
- Experience developing web-based GUIs.
- Experience utilizing bioinformatics tools and/or analysis techniques.
- Experience analyzing scientific data
Notes
This is a 2 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. Two positions are available. Work will be performed at the DOE Joint Genome Institute (JGI) Production Genomics Facility (PGF) 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.
How To Apply
To apply from this page, click the "Apply Now" link (above), and follow the on-line instructions to complete the application process. As part of the online application process, please submit a single attachment that includes both your resume and a cover letter. Please be sure to reference where you found out about the position.
Berkeley Lab is an affirmative action/equal opportunity employer committed to the development of a diverse workforce
23598
|
