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    Opportunity: Computational Systems Biology Software Developer (#76427) @ Lawrence Berkeley National Laboratory -- Berkeley, CA
    Submitted by Jeff Todd; posted on Wednesday, October 02, 2013



    In this position, you will be responsible for working with a team on the creation, elaboration and maintenance of innovative software systems to aid in bio-manufacturing through iterative design, build and test cycles. The project seeks to apply statistical modeling, mechanistic modeling and machine learning to large data sets for the improvement of metabolic engineering of hosts and pathways. The Incumbent will have to work as part of a team comprised of wet lab experimentalists and computational biologist, and will also have to show independence in research and development. The team will be composed of scientists at the Joint BioEnergy Institute (JBEI), the Joint Genome Institute (JGI), the DOE Systems Biology Knowledgebase (KBase) and LBNL Computational Research Division (CRD). The incumbent shall also be expected to present work, keep a record of activities and aid in publication of papers and writing grants.


    • Play the lead role and make sound judgments while coordinating with the PI and other members of group in designing, developing and distributing software for pathway engineering and sophisticated data analysis integrated with KBase and project databases.
    • Under broad supervision, define software requirements and take a lead role in determining the week to week direction of the work.
    • Identify problems and recommend viable solutions to software and data management issues.
    • Providing guidance and training to other members of the group.
    • Work closely with experimentalists and users of the analysis software to ensure that their needs are being met.
    • Publish documentation, including tutorials, on using analysis tools developed.
    • Work with users to test and debug applications.
    • Prepare presentations for internal use and peer-reviewed publication.
    • Maintenance of accurate documentation and source-code control for all work-product
    • As part the data management and analysis team, assist in the implementation of a database to store experimental data and related metadata from a diverse set of microbiology experiments from JBEI & JGI.
    • Codevelop the designs for interrelating this data with other information including pathway data, engineering tools, biomolecular structures, and literature.
    • Aid in development of software to reliably track experiments and data, load data into the database, and analyze the data.
    • Aid in devising quality control methods to check the consistency of data and information in the database.
    • Integrate public data into KBase.


    • Five years of experience developing software in a research or technical filed or for scientific applications.
    • Demonstrated skills, knowledge and work experience in engineering, computer science, and biology especially in regard to functional and/or comparative genomics, genetic networks, metabolic engineering, systems biology, and or synthetic biology.
    • Demonstrated experience with problem solving in computational biology.
    • Experience in bioinformatics software design and engineering, mathematical analysis and comparative and functional genomics.
    • Must posses both high analytical skills and programming skills (language unspecified but prefer C, C++, or Java and Perl or Python), when working with projects of moderate scope where data requires a review of identifiable factors.
    • Experience with tools such as matlab and Mathematica.
    • Ability to creatively work with problems in comparative and functional microbial genomics and network biology, exercising judgment within defined procedures and practices to determine appropriate action.
    • Ability to collaborate with a team of scientists.
    • Effective interpersonal, verbal and written communication skills with ability to accomplish goals as a team member.
    • Demonstrated ability to work collaboratively with programmers, engineers, post-docs, graduate students, and undergraduates from diverse backgrounds.
    • Must have ability to handle multiple projects and tasks.


    This is a 1-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.




    For full consideration, follow the link to the job posting and apply directly to Berkeley Lab. As part of the online application process, please complete a profile, including uploading attachments relevant to the opportunity. Be sure to reference where you found the position (Bioinformatics.Org).[...]76427


    Berkeley Lab is an affirmative action/equal opportunity employer committed to the development of a diverse workforce.

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