Berkeley Lab's Environmental Genomics & Systems Biology Division has an opening for a Software Developer. This position will play an important role as part of a multifunctional team working to use advanced metabolomic technologies to examine the metabolic activities of soil microbial communities. This particular position will be focused on developing and applying algorithms, user interfaces, and new programmatic capabilities to accelerate metabolite identification and metabolomics data analysis. This applicant will develop Python workflows that combine data management and analysis algorithms on high-performance computing hardware at NERSC. As part of the team, this individual will identify weaknesses in the current code-base and workflows, propose solutions, and implement them using best practices. Thus, necessary skills include python programming; linux shell; version control; unit-testing and test-driven design. Familiarity with cutting edge data analysis approaches in machine learning is a preferred qualification.
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.
What You Will Do:
Work as part of the team that develops and supports Metabolite Atlas, MAGI, MZebra, Pactolus, and OpenMSI resources.
Develop and apply innovative computational approaches to accelerate the analysis of mass spectrometry data.
Continuously debug, improve and extend the above mentioned resources to accommodate more diverse and everlarger data.
Ensure that the users of these resources can produce the best science possible with our tools.
Employ solid software engineering practices: design and code reviews, source control and versioning, issue tracking, unit testing, iterative development, effort estimation
Release data onto public data repositories.
Present on new developments and improvements alone or collaboratively at workshops, conferences, and scientific journals.
What is Required:
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.
Experience in Python for identification of metabolites using experimental data and reference databases of fragmentation spectra.
Familiarity using custom Python code for processing of raw metabolomics data.
Experience in statistical analysis or machine learning for metabolite classification.
Specific experience using graph theory for analysis of metabolomic fragmentation data.
Demonstrated success designing, implementing, and supporting moderately complex systems and software related to metabolomic data.
Specific experience submitting batch jobs using super computing resources.
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.
Moderate level of command line comfort in a Unix-like environment.
Comfort with relational database concepts and SQL.
Good working knowledge of basic genomic, biochemical, and cellular concepts, data types, and data analysis methods, and their representation in software systems.
Experience with one or more of the following databases: mySQL, postgreSQL, MongoDB.
The posting shall remain open until the position is filled.
This is a full time, 1 year, term appointment with the possibility of extension or conversion to Career appointment based upon satisfactory job performance, continuing availability of funds and ongoing operational needs.
Full-time, M-F, exempt (monthly paid) from overtime pay.
Salary is commensurate with experience.
This position may be subject to a background check. Any convictions will be evaluated to determine if they directly relate to the responsibilities and requirements of the position. Having a conviction history will not automatically disqualify an applicant from being considered for employment.
Work will be primarily performed at DOE Joint Genome Institute (JGI) — 2800 Mitchell Dr., Walnut Creek, CA.
Berkeley Lab (LBNL) 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. Berkeley Lab is in compliance with the Pay Transparency Nondiscrimination Provision under 41 CFR 60-1.4. Click here to view the poster and supplement: "Equal Employment Opportunity is the Law."
Internal Number: 85570
About Lawrence Berkeley National Laboratory
In the world of science, Lawrence Berkeley National Laboratory (Berkeley Lab) is synonymous with excellence. Thirteen scientists associated with Berkeley Lab have won the Nobel Prize. Fifty-seven Lab scientists are members of the National Academy of Sciences (NAS), one of the highest honors for a scientist in the United States. Thirteen of our scientists have won the National Medal of Science, our nation's highest award for lifetime achievement in fields of scientific research. Eighteen of our engineers have been elected to the National Academy of Engineering, and three of our scientists have been elected into the Institute of Medicine. In addition, Berkeley Lab has trained thousands of university science and engineering students who are advancing technological innovations across the nation and around the world. Berkeley Lab is a member of the national laboratory system supported by the U.S. Department of Energy through its Office of Science. It is managed by the University of California (UC) and is charged with conducting unclassified research across a wide range of scientific disciplines. Located on a 200-acre site in the hills above the UC Berkeley campus that offers spectacular... views of the San Francisco Bay, Berkeley Lab employs approximately 4,200 scientists, engineers, support staff and students. Its budget for 2011 is $735 million, with an additional $101 million in funding from the American Recovery and Reinvestment Act, for a total of $836 million. A recent study estimates the Laboratory's overall economic impact through direct, indirect and induced spending on the nine counties that make up the San Francisco Bay Area to be nearly $700 million annually. The Lab was also responsible for creating 5,600 jobs locally and 12,000 nationally. The overall economic impact on the national economy is estimated at $1.6 billion a year. Technologies developed at Berkeley Lab have generated billions of dollars in revenues, and thousands of jobs. Savings as a result of Berkeley Lab developments in lighting and windows, and other energy-efficient technologies, have also been in the billions of dollars. Berkeley Lab was founded in 1931 by Ernest Orlando Lawrence, a UC Berkeley physicist who won the 1939 Nobel Prize in physics for his invention of the cyclotron, a circular particle accelerator that opened the door to high-energy physics. It was Lawrence's belief that scientific research is best done through teams of individuals with different fields of expertise, working together. His teamwork concept is a Berkeley Lab legacy that continues today.