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Algorithm Developer Project Scientist

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POST DATE 9/2/2016
END DATE 10/29/2016

Lawrence Berkeley National Laboratory Berkeley, CA

Company
Lawrence Berkeley National Laboratory
Job Classification
Full Time
Company Ref #
82603
AJE Ref #
576077020
Location
Berkeley, CA
Experience
Entry Level (0 - 2 years)
Job Type
Regular
Education
Doctoral Degree

JOB DESCRIPTION

APPLY
Berkeley Lab is Bringing Science Solutions to the World, and YOU can be a part of it!

In the world of science, Lawrence Berkeley National Laboratory (LBNL) is synonymous with "excellence." That's why we hire the best - whether in research, science or operations. This is a great opportunity to bring your top-notch skills to bear in support of world-class scientific research that addresses national and global challenges!

Position Summary:

Berkeley Labs Molecular Biophysics and Integrated Bioimaging has an exciting opportunity for a Bioimaging Project Scientist to support the Sauter group and be responsible for developing algorithms for the increasingly complex analysis of large diffraction datasets in structural biology. We developed key software (DIALS and cctbx.xfel) for processing crystallography data at synchrotron and X-ray free-electron laser (XFEL) sources, and are currently using XFEL crystallography and spectroscopy to investigate the photosynthetic mechanism of water splitting, to probe other metalloenzyme reactions, and to test whether diffuse scattering can reveal correlated atomic motions in crystals. Many problems remain to be solved, including the details of how to optimally merge datasets from thousands of crystals.

Specific Responsibilities:

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Implement algorithms within the DIALS framework for primary data reduction of synchrotron and XFEL diffraction
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Fundamentally analyze the experimental geometry and physics to develop new insights and algorithms, especially to improve the accuracy of anomalous dispersion data, enable the analysis of overlapping Bragg lattices, develop physical models of protein crystal disorder, and interpret diffuse scattering
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Support new experimental configurations including new detectors and light sources
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Work with beamline scientists worldwide to customize and validate software at different locations
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Collaborate with users to gain an understanding of how the software is deployed in practice
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Elicit and anticipate user needs and respond to user feedback
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Take a team approach for integrating the new code into existing software systems, including various graphical displays and beamline systems
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Publish frequently as well as travel and participate in conferences
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Travel to light source facilities for data collection trips

Required Qualifications:

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PhD in Biophysics, Bioinformatics, Mathematics, Computer Science, Engineering or Physical Sciences or equivalent demonstrated research experience or expertise
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Expertise in one or more computational techniques including, but not limited to, ray tracing to test underlying physical models of the diffraction

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Bayesian approaches for refining model parameters, macromolecular modeling and refinement, neural networks for interpreting image features, as well as signal processing and denoising methods

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Comprehensive understanding of diffraction physics and numerical approaches to X-ray crystallography, with a demonstrated ability to analyze specific scenarios and develop an algorithmic strategy
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Demonstrated ability to organize a many-faceted project with only broad supervision, while running appropriate controls to validate the correct results
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Clear verbal presentation & written expression
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Ability to write clear computer documentation including Web-based documentation
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Experience with forefront approaches such as GPU computing or specialized hardware like neuromorphic chips

Additional Desired Qualifications:

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Strong interest in Structural Biology

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Software languages: C , Python, MATLAB
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Operating systems: Linux, Macintosh
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Ability to incorporate existing software libraries into new processes
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Development of graphical user interfaces
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Basic understanding of database systems & image formats

The posting shall remain open until the position is filled.

Notes:

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This is a one year term appointment with the possibility of renewal.
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Salary is commensurate with experience.
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This position requires completion of a background check.

Berkeley Lab addresses the worlds most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Labs scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energys Office of Science.

Equal Employment Opportunity: Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. Berkeley Lab is in compliance with the Pay Transparency Nondiscrimination Provision under 41 CFR 60-1.4. Click here to view the poster and supplement: "Equal Employment Opportunity is the Law.