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    Opportunity: Software Developer, UCSC Cancer Genomics Browser (#1103001) @ University of California--Santa Cruz, CA (US)
    Submitted by Branwyn Wagman; posted on Monday, February 14, 2011


    The UCSC Cancer Genomics Group in the Center for Biomolecular Science & Engineering (CBSE, at UC Santa Cruz seeks an experienced and motivated software engineer to work with us on a new, computationally intensive and personalized approach to cancer through DNA and RNA sequencing. The cancer genomics group works with leading cancer research groups worldwide to apply new methods of DNA and RNA analysis. The successful candidate must be an experienced programmer, able to learn and integrate information quickly, able to rise to challenges, articulate, and have a strong commitment to quality and best engineering practices. The position requires independence, creativity, and self-motivation in a team environment.

    The cancer genomics group is a talented cross-disciplinary team that builds bioinformatics databases and software tools that host, visualize, and analyze cancer genomics data on the UCSC Cancer Genomics Browser ( The group is closely associated with the UCSC Center for Genomic Sciences, which develops and supports the UCSC Genome Browser ( The cancer browser facilitates an integrative, interactive, and versatile display and comprehensive analysis of cancer genomic and clinical data that helps cancer biologists and clinical oncologists translate molecular data from DNA, RNA, and other measurements into personalized cancer treatment. The browser makes it possible to identify genes, pathways, profiles, and other genomic characteristics that have been changed in tumors or are predictive for treatment response, disease prognosis, and other clinical phenotypes. Investigators interact with the browser to order, filter, aggregate, and display data according to data values, chromosomal coordinates, clinical features, and biological pathways.

    The cancer genomics group at UCSC is one of the genome data analysis centers for The Cancer Genome Atlas (TCGA) project and is a member of the Stand Up To Cancer (SU2C) dream team. The group also collaborates with the International Cancer Genomics Consortium (ICGC), the UCSF Helen Diller Family Comprehensive Cancer Center's breast oncology and pancreas programs, Lawrence Berkeley National Laboratory, the Knight Cancer Institute at Oregon Health & Science University, and the Buck Institute for Age Research and participates in the I-SPY and I-SPY2 breast cancer clinical trials.


    Under general supervision, the software developer works with other engineers to develop new analysis and data visualization capabilities and maintain the UCSC Cancer Genomics Browser. The incumbent builds data wrangling tools, contributes to the development of the data analysis pipeline, and transforms research prototype code to polished engineering components for the cancer genomics project. The position interacts with scientific collaborators and creates presentations and publications about technical aspects of the project.


    • Bachelor's degree in computer science or equivalent education
    • One year of college-level biology or equivalent education
    • Extensive experience working with C, JavaScript, web programming, and a scripting language
    • Extensive experience working in a UNIX or Linux environment
    • Extensive experience facilitating visualization of large data sets via an interactive web interface
    • Extensive bioinformatics experience in developing software tools for data analysis
    • Experience in application-level and server-level access control and data security
    • Familiarity with relational and document-oriented databases
    • Knowledge of bioinformatics methods and applications
    • Articulate, with strong verbal and written communications skills
    • Able to analyze and assimilate technical structure, data, and requirements of genome analysis software
    • Able to grasp new concepts quickly and integrate them into projects as appropriate and to rapidly determine the required action in a new situation
    • Effectively identifies and solves challenging problems
    • Demonstrates a commitment to software quality and engineering best practices
    • Able to work effectively and diplomatically with a wide range of people and to work harmoniously in a fast-paced team environment
    • Able to work in a self-motivated manner with a minimal amount of supervision


    • Knowledge or background in molecular biology or cancer biology
    • Experience with clinical trials or statistical analysis
    • Training or experience in data visualization and analysis of high throughput genomics data
    • Experience with programming languages in addition to C, such as R and Python


    University of California, Santa Cruz


    Starting salary: $54,500-80,000/ year, commensurate with qualifications and experience


    Visit and search for job #1103001


    Initial review date is 2/28/11; position is open until filled

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