[phenixbb] Project Scientist positions for computational methods

Nicholas Sauter nksauter at lbl.gov
Mon Jun 13 16:06:44 PDT 2016

Two Project Scientist positions are available in my group in the *Molecular
Biophysics and Integrated Bioimaging*
<http://biosciences.lbl.gov/divisions/mbib/> (MBIB) Division at Lawrence
Berkeley National Lab.

*Bioimaging Project Scientist*

Position Summary:

We have an exciting opportunity for a Bioimaging Project Scientist who will
apply neuromorphic computing techniques to structural biology problems in
X-ray diffraction, CryoEM, and CryoET.  This will be a cross-disciplinary
effort between MBIB and the Computational Research (CRD) Division at
Lawrence Berkeley National Laboratory.  The research group will include
investigators Nick Sauter (X-ray Crystallography), Karen Davies
(CryoEM/ET), and Chao Yang (Scalable Solvers).

Specific Responsibilities:


   Investigate how to apply deep learning algorithms to specific data
   processing and data interpretation problems in structural biology.

   Implement convolutional neural network (CNN) code on neuromorphic
   computing hardware such as the IBM TrueNorth chip.  Example problems
   include the identification of positive diffraction events in X-ray
   free-electron laser diffraction, conformational classification in CryoEM
   single particle reconstruction, and the identification of 3D sections for
   CryoET subtomogram averaging.

   Use tools such as MatConvNet, CAFFE, THEANO or TensorFlow to construct
   and train CNNs that can be used to optimally classify experimental data.

Required Qualifications:


   Research experience in Structural Biology, with expertise in allied
   fields such as Bioinformatics, Mathematics, Computer Science, or
   Engineering (Ph.D. + 3 years or equivalent)

   Strong background in image analysis and machine learning, including
   neural networks.

   Working knowledge of image classification and/or other image processing

   Proficient programming skills in MATLAB and/or Python.
   - Working knowledge of performance optimization for scientific codes.

*Algorithm Developer Project Scientist*

Position Summary:

We are seeking an algorithm developer for the increasingly complex analysis
of large diffraction datasets in structural biology.  Current projects
utilize XFEL crystallography and spectroscopy to investigate the
photosynthetic mechanism of water splitting and to probe other
metalloenzyme reactions.  We also wish 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.  Our software development projects (including
packages such as DIALS <http://dials.lbl.gov/> and cctbx.xfel
<http://cci.lbl.gov/xfel>) have been highlighted in several high-impact
publications listed HERE

Specific Responsibilities:

   - Continue work on the DIALS data integration suite.
   - Test new algorithms for optimally characterizing and merging data from
   serial crystallography experiments.
   - Analyze anomalous scattering from metalloenzymes using XFEL
   - Investigate whether diffuse scattering can reveal correlated atomic
   motions in crystals.

Required Qualifications:

   - Expertise in one or more computational techniques including, but not
   limited to, ray tracing to test underlying physical models of the
   diffraction, Bayesian approaches for refining model parameters,
   macromolecular modeling and refinement, neural networks for interpreting
   image features, as well as signal processing and denoising methods.
   - Extensive data analysis experience in crystallography or from more
   general bioimaging backgrounds are welcome.
   - We particularly encourage strong mathematical intuition and a track
   record of bringing new ideas and tools to fruition, as evidenced through
   written publication and clear presentation.

Candidates should send an expression of interest, CV, and list of three
references to Nick Sauter, nksauter at lbl.gov*. *Further details are posted
at https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=82554.

Nicholas K. Sauter, Ph. D.
Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Rd., Bldg. 33R0345
Berkeley, CA 94720
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