The Biological Data Management and Technology Center (BDMTC) serves as a source of expertise in and provides support for data management and bioinformatics tool development projects at the Joint Genome Institute (JGI), the Life Sciences and Physical Biosciences Divisions at LBNL, Biomedical Centers at UCSF, the California Institute for Quantitative Biomedical Research (QB3), and other similar organizations in the Bay Area. The Center enables collaborating organizations to share experience, expertise, technology, and results across projects, employing industry practices in developing data management systems and bioinformatics tools, while maintaining academic high standards for the underlying data generation, interpretation, and analysis methods and algorithms. BDMTC currently has an opening for a Computer Systems Engineer 2 .
Under the guidance of senior BDMTC scientists and software engineers, this position will work in a production environment on:
- User requirements and system analysis for the Integrated Microbial Genomes (IMG) and Integrated Microbial Genomes with Microbiome Samples (IMG/M).
- Database design and tuning for IMG and IMG/M.
- Data loading and integration from diverse sources into IMG and IMG/M.
- Computational methods for analysis and functional annotation of microbial genomes.
- Perl scripts C programs for IMG and IMG/M data processing pipeline.
- Data quality control for IMG and IMG/M.
Qualifications
- Bachelor of Science degree in Computer Science, Life Sciences, Bioinformatics, or related field or equivalent experience.
- At least five years experience as a software engineer or database administrator working in a team environment.
- Experience with source control, revision management, object-oriented design.
- Experience with biological data, computational biology tools and resources, such as BLAST, HMMER, CLUSTALW, EMBOSS, Genbank, protein and domain databases.
- Familiarity with basic concepts in molecular biology, nucleotide and protein sequence alignment, clustering, expression analysis, and biostatistics.
- Ability to deal with scalability issues in RDMS, file storage, and computation over large volumes of data.
- Experience with Linux clusters, parallel computing, bioinformatics processing pipelines.
- Ability to work with complex data structures and algorithms.
- Able to think independently and assess requirements for short and long term goals.
- Competent in organizing, prioritizing and scheduling, and creating realistic plans.
- Proficiency with at least one of the following: Perl, Java, or C/C++, in UNIX environment.
- Experience with SQL, and at least one of the following RDBMS: Oracle, Postgres or MySQL.
- Excellent interpersonal skills for working in a diverse team environment.
Notes
This is one-year (term) full time 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.
Equal Employment Opportunity
Berkeley Lab is an affirmative action/equal opportunity employer committed to the development of a diverse workforce.
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