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    Opportunity: Senior Software Developer -- Pathogen Genomics (#81579) @ Wellcome Trust Sanger Institute -- Hinxton/Cambridge, UK
    Submitted by Sam Bowker; posted on Wednesday, October 02, 2013


    A highly motivated Software Developer is required, to design and implement a web based application to store and display details for over 40,000 bacterial and viral genomes.

    The Wellcome Trust Sanger Institute (WTSI) is Europe's leading genome research institute. Funded primarily by the Wellcome Trust, we use high-throughput genomics-based techniques to investigate host and pathogen genetics. The pathogen group is applying large-scale next-generation sequencing technologies to pathogen populations to track transmission pathways and identify determinants of drug resistance and virulence.

    Recently the Pathogen Genomics group at the WTSI has been funded as part of an international consortium to develop an effective programme of surveillance to control infectious diseases. An important component of this is to be able to identify the causative pathogens. Accurate identification would allow strains to be compared to confirm whether or not an outbreak involving spread of a particular strain is occurring, and could be used as an early warning system to detect the spread of certain strains of clinical importance through the population.

    Therefore, we aim to work together with our partners to develop a technological solution based on the comparison of bacterial and viral genome sequences. A database will be required to store and query the meta-data (e.g. sample identifiers, geographical origin, infection severity etc.) for 20,000 bacterial genomes (~60Gb) and 20,000 viral genomes (0.3 Gb). The assembled genome sequences will be provided from an already existing pipeline for each sample.


    We are seeking a strong scientific programmer to design and develop this tracking and data analysis system. An important component of this work will be to develop web based interfaces to the system to link and present the data for both internal and external partners in the project.


    • Significant programming experience in one or more modern programming languages (e.g. Perl, Python, C etc.)
    • Experience of object oriented development
    • Knowledge of relational database systems and manipulation via SQL
    • Demonstrable experience of using UNIX / LINUX
    • Proven experience of designing and developing web based applications for support of scientific projects
    • A high level of communication skills to be able to elicit complex requirements from, and convey complex information to, groups with different levels of technical knowledge
    • Ability to quickly adapt to new problems and ideas
    • Excellent problem-solving skills


    • Some knowledge or experience in bioinformatics
    • Experience with managing large volumes of data
    • Experience with running software on a compute farm or cluster


    Salary range: GBP 29,750 to GBP 37,525pa dependent on experience.

    We offer a competitive reward package, including excellent benefits. In addition, the Institute benefits from world class computational and data centre facilities. There is a first names culture, informal dress code, company social calendar and modern offices set in the 55 acre grounds of Hinxton Hall and associated wet land reserve.


    This position is a fixed term 3-year contract in the first instance.


    Please apply online through our website:[...]71555

    For further details about this post please contact hrservices[at]


    Closing Date: 20th October 2013

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