Job: Computational Biologist/Scientific Software Developer
gravatar for peter.rose
5.2 years ago by
United States
peter.rose110 wrote:

The Structural Bioinformatics Group at the San Diego Supercomputer Center (SDSC) is seeking an exceptional scientific software developer to work on our new project “Compressive Structural Bioinformatics” funded by the US National Institutes of Health (NIH) Big Data to Knowledge (BD2K) initiative. The Challenge is to enable efficient research on the rapidly growing number of 3D molecular structures of ever increasing size and complexity, and develop highly scalable 3D structural search, analysis, workflow, data-exchange, and visualization tools.

Our team values open discussion and contribution. Starting from your first day, you will shape software and services used by thousands of people around the world. Have a great idea? Let's hear it. Want to try a new technology? Let's learn it. Want to write code at scale? Let's do it. Everyone at our organization is passionate about what we do, and that is why we are leaders in our field. We want to hear from skilled scientists and software developers, people passionate about their craft and what they can bring to the field.

The Structural Bioinformatics Group is involved in research and development activities centered around 3D structures of proteins and nucleic acids, the integration of structural data with other domains such as Medicine, Genomics, Biology, Drug Discovery, and the development of scalable solution to Big Data problems in Structural Bioinformatics. Our group leads the RCSB Protein Data Bank (PDB) ( west-coast operations, which represents the preeminent source of experimentally determined macromolecular structure information for research and teaching in biology, biological chemistry, and medicine. With over 300,000 unique users from over 160 countries around the world, the RCSB PDB is one of the leading worldwide Biological Databases.

This position researches, designs, develops, and deploys innovative, highly scalable solutions for 3D structure visualization, structural queries, and large-scale analyses of 3D macromolecular complexes. Develops protocols for the efficient network data transfer using custom compression and streaming techniques to facilitate 3D visualization of large complexes on any device from phone, tablet, to laptop and desktop. Designs distributed parallel workflows for structural queries and analysis of the PDB archive.


  • Bachelor's degree in Structural Bioinformatics, Bioinformatics, Computational Biology, Computer Science or comparable combination of education and experience with considerable focus in scientific software development demonstrated by publications, participation in open source or other types of software projects. Strong skills in applied Mathematics and algorithm design. M.S. or Ph.D. degree preferred.
  • Experience in the representation and data structures of ligands, proteins, nucleic acids, and associated sequence information. Experience with 3D structure and sequence analysis algorithms.
  • Advanced experience in one or more of the following object oriented programming languages:Java, JavaScript, C++, or Python. Experience with software development tools including IDEs, Maven, Git, and continuous integration tools.
  • Experience in one or more of the following: development of 3D visualization applications and knowledge of OpenGL/WebGL, development of distributed parallel programming models using "Big Data" frameworks such as Apache Hadoop or Spark, setup of these frameworks on compute clusters, or development of workflow applications.
  • Demonstrated effective communication and interpersonal skills. Demonstrated ability to communicate technical information to technical and non-technical personnel at various levels in the organization and to external research and education audiences.

For more requirements or to apply, please view the UCSD job page.


Peter Rose, Ph.D.
Site Head, RCSB Protein Data Bank West (
San Diego Supercomputer Center (
University of California, San Diego

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