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    Opportunity: Programmer/Analyst 3, Biological Data Engineer, UCSC Genome Browser (#1002812) @ UCSC--Santa Cruz, CA (US)
    Submitted by Branwyn Wagman; posted on Wednesday, December 22, 2010


    The Center for Biomolecular Science & Engineering (CBSE, at the University of California, Santa Cruz---a research group with a diverse set of projects at the cutting edge of biomedical research, focusing on high-throughput genomic analysis---seeks a talented bioinformatician, biologist, or software engineer with a strong biology background to work with an international consortium of scientists to collect and import their experimental results into the UCSC Genome Browser or UCSC Cancer Genomics Browser database and web site.

    The center develops and manages the widely used UCSC Genome Browser and associated tools and manages data coordination for the ENcyclopedia Of DNA Elements (ENCODE) consortium, funded by the National Human Genome Research Institute.

    The cancer genomics group develops and manages the UCSC Cancer Genomics Browser and is a data analysis center for multiple cancer research collaborations, including The Cancer Genome Atlas (TCGA) project, Stand Up To Cancer (SU2C), and the UCSF Helen Diller Family Comprehensive Cancer Center's breast oncology and pancreas programs.


    Under general supervision, the biological data engineer imports biomedical data into the UCSC Genome Browser or UCSC Cancer Genomics Browser databases and web site and guides others in this function. This position works closely with external research laboratories to capture their experimental results and methods and with internal software developers and database testing staff to make the data accessible to the worldwide scientific community.

    Job Duties:
    Managing data: Determine appropriate database and file formats for biological data that will be imported; download data files from external databases or web sites, reformatting as needed using existing tools and developing new scripts if needed; collect experimental methods and parameters, incorporating into documentation and controlled vocabularies as required; manage data from automated submission pipelines; load databases and configure display settings for viewing in the UCSC Genome Browser and the UCSC Cancer Genomics Browser; review data for quality and consistency, with an eye to biological significance; specify and implement validation tools; package data for release and work with quality assurance team to facilitate final review

    Communication and collaboration: Serve as primary liaison with external laboratories to facilitate data import and appropriate representation of the data at UCSC; provide instruction and feedback regarding data formatting and quality issues to informatics staff at external laboratories; participate in relevant research group teleconferences and meetings; serve as knowledge resource within the UCSC Genome Bioinformatics group for experimental results in the data manager's purview; contribute to project discussions and informational documentation via collaborative tools such as Wiki and Google documents

    Writing: Provide technical review and edit experiment documentation provided by research labs or from publications; expand and revise for clarity, consistency, and completeness; add background and overview for a broad audience of biomedical users; describe conventions and user guidance relevant to use within the UCSC web site; contribute to research papers and grant reporting; document processes used during data import; contribute to FAQs, tutorials, and user guides related to areas of expertise

    Software design, documentation, and testing: Work with software developers to improve existing programs and create new programs, focusing on providing usability feedback and testing to ensure that the software works correctly


    • Bachelor's degree in bioinformatics or a biological science or equivalent experience
    • Demonstrated proficiency in UNIX/Linux command-line use
    • Demonstrated competency in UNIX shell scripting and Perl programming (or a comparable programming language)
    • Proficiency with relational database concepts and SQL
    • Knowledge, background, or experience in molecular biology concepts and current methods
    • Ability to work effectively and diplomatically with a wide range of people in a fast-paced team environment
    • Demonstrated ability to communicate effectively, both orally and in writing
    • Ability to quickly learn and interpret biological and technical information
    • Ability to organize work and manage time to effectively balance priorities and conflicting demands
    • Ability to work independently and follow through on assignments with minimal direction
    • Ability to ensure quality and timeliness in performance of work tasks
    • Ability to complete assignments with a high level of attention to detail, following specified guidelines
    • Ability to be resourceful when faced with obstacles and to show initiative in identifying resources and methods for resolving issues


    • Master's degree in bioinformatics or a biological science or equivalent experience
    • Kowledge, background, or experience in high-throughput sequencing technologies
    • Familiarity with common bioinformatics tools and databases
    • Experience in a large-scale scientific data management environment
    • Experience with software engineering tools for version control, software build, automated testing
    • Familiarity with current web technologies


    Santa Cruz, CA


    Apply for this job online at; search for job number 1002812

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