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Bioinformatics Programmer
Ref No.: 17-02767
Location: Emeryville, California
Start Date / End Date: 10/02/2017 to 10/02/2018
Infectious Diseases Bioinformatics Programmer

The Infectious Diseases (ID) Area at the Client Institutes for BioMedical Research in Emeryville, CA, is seeking a Bioinformatics Programmer to support software development efforts in the ID Bioinformatics group to bolster the team's support of the discovery and development of new antibacterials, antiparasitics, and antivirals. The successful candidate will have recent training in, or experience with, modern software development practices, with an interest in applying these skills to biological datasets and problems.

The ID Bioinformatics team is currently developing an extensive code-base, primarily written in Python, to support ID's broader data analysis needs, particularly in the realm of Genomics and other "-omics.” The Bioinformatics Programmer's primary responsibility will be to support the software development needs of the ID Bioinformatics group, including development and optimization of these data analysis pipelines. These analysis pipelines are ultimately served via an existing web front-end to experimentalists, enabling them to analyze their own datasets in a reliable, robust, and user-friendly way. These analysis pipelines fit into a larger vision of tracking metadata, data, and results end-to-end – from experimental design through results storage and visualization – leveraging other internal resources that will require adaptation to function correctly in Infectious Diseases workflows. The Bioinformatics Programmer will aid in the adaptation and integration of these existing databases, tools, and resources to the group's workflows, which ultimately enable the application of machine learning techniques to these large datasets.

We are looking for an eager and self-motivated programmer who wants to work in a small, embedded team of expert bionformaticists to help develop and optimize software that will have broad research and clinical implications across ID, while learning about drug discovery and applying modern bioinformatics approaches to scientific problems affecting human health globally.

Required Education / Experience:
  • Bachelor's Degree (or equivalent experience) in Computer Science, Bioinformatics, or related field
  • Demonstrated scientific / technological curiosity and initiative
  • Ability to work with a small team of developers, often autonomously
  • Fluency with the Linux command line interface (e.g. bash)
  • Expertise in Python and its scientific, numerical, and data visualization modules (e.g. pandas, NumPy, matplotlib)
  • Experience with code version control, preferably git
  • Track record of good software development practices (e.g. unit testing, regression testing, detailed documentation)
  • Experience developing in object-oriented or other programming paradigms
  • Track record of building software that validates user input and provides useful error messages
  • Strong interest in learning the biological concepts and rationale underlying the analysis pipelines she or he will be developing

Desired (but not required) Skills:
  • Experience working in HPC / Cloud Computing environments
  • Basic knowledge of biology; in particular, infectious diseases caused by bacteria and viruses
  • Background in statistics
  • Familiarity with machine (esp. "Deep”) learning approaches