[Biojava-l] [Job] Postdoctoral position: Big Data/Computational Biology at UC San Diego

Rose, Peter pwrose at ucsd.edu
Tue Mar 1 06:41:55 UTC 2016

Summary: We are looking for a highly motivated postdoc as part of our new project “Compressive Structural Bioinformatics” funded by the US National Institutes of Health (NIH) Big Data to Knowledge (BD2K) initiative.

The Challenge: To enable efficient research on the rapidly growing number of 3D molecular structures of ever increasing size and complexity. Current algorithms used in Structural Bioinformatics do not scale well with the rapid growth in structural data. In this project, we will employ the latest advances in computer science to develop highly scalable, distributed parallel algorithms to overcome these limitations.

Qualifications: Ph.D. in one or more of the following research areas

·       Computer Science with a focus on large scale scientific computing

·       Structural Bioinformatics with a focus on new methods development

·       Computational Structural Biology with a focus on improved structure solution methods

Experience with the development and performance optimization of scientific software. Demonstrated proficiency in a high-level programming language, such as Java or Python and experience with state of the art software development tools. Strong skills in applied mathematics and algorithm design are required. High productivity demonstrated by publications and contributions to open source software projects. Experience in the development and application of modern distributed parallel computing environments, such as Apache Big Data projects including Apache Spark is a plus. Excellent interpersonal, written, and oral presentation skills are essential.

Note, this position is reviewed annually on the basis of performance and can be renewed for a maximum of two years.

Our Environment:

The Structural Bioinformatics Group (http://bioinformatics.sdsc.edu<http://bioinformatics.sdsc.edu/>) at the San Diego Supercomputer Center (SDSC) (http://www.sdsc.edu<http://www.sdsc.edu/>) 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. The RCSB PDB (http://www.rcsb.org<http://www.rcsb.org/>) 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. Our group is involved in the National Institutes of Health (NIH) Big Data to Knowledge (BD2K) initiative.

As an Organized Research Unit of UC San Diego, SDSC is a world leader in data-intensive computing and cyber infrastructure, providing resources, services, and expertise to the national research community, including industry and academia.

To apply, please send cover letter and resume to Dr. Peter Rose (pwrose at ucsd.edu).

Peter Rose, Ph.D.
Site Head, RCSB Protein Data Bank West (http://www.rcsb.org<http://www.rcsb.org/>)
Principal Investigator, Structural Bioinformatics Laboratory (http://bioinformatics.sdsc.edu<http://bioinformatics.sdsc.edu/>)
San Diego Supercomputer Center (http://www.sdsc.edu<http://www.sdsc.edu/>)
University of California, San Diego
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