Dr. David E. Konerding, Ph.D.
dek@konerding.com
EMPLOYMENT AND EDUCATION
Aug 2008 - Present: Senior Engineer, Infrastructure, Google Inc
Aug 2007 - Aug 2008: Senior System Architect for Research Computing,
Genentech Inc
Aug 2003 - Aug 2007: Computer Scientist, Lawrence Berkeley National
Laboratory, Computational Research Division, Distributed Systems
Department
Oct 2002 - Aug 2003: Postdoctoral Scholar, University of California at
Berkeley, Department of Plant and Microbial Biology, Steven Brenner
Laboratory
Feb 2002 - Oct 2002: Postdoctoral Scholar, University of California at
Berkeley, Department of Bioengineering, Kimmen Sjolander Laboratory
2000 - 2002: Programmer/Analyst III, University of California at San
Francisco, Computer Graphics Laboratory
1995 - 2001: PhD candidate, University of California at San Francisco,
Graduate Group in Biophysics. PhD (Biophysics) awarded January 2001
1991 - 1995: Undergraduate, University of California at Santa
Cruz. B.A. (Biochemistry and Molecular Biology) awarded June 1995
CURRENT JOB FOCUS AND INTERESTS
Design and develop a highly scalable software infrastructure product.
Advise numerous internal projects on high performance scientific
computing. Contribute to academic scientific research projects.
SKILLS
o Accomplished scientist, software engineer and system administrator.
Highly skilled in developing highly scalable services for scientific
computing.
o Undergraduate, PhD and postdoc experience in computational biology,
structural biology, and bioinformatics.
o Highly experienced programmer with deep knowledge of open source
software development toolchains and operating systems. Extensive
experience managing Linux servers including customizing
distributions for high-performance scientific computing.
o Deep knowledge and experience designing, customizing, implementing
and tuning Linux clusters including high-performance networked file
systems, network interconnect, and batch queuing.
o Extensive experience in data modeling and query design to maximize
RDBMS performance using open source relational databases MySQL and
postgreSQL.
o Primary programming languages: C++ and Python with skill in Java and
Perl, and familiarity with all other major programming languages.
EXPERIENCE
Aug 2008 - present: Google Inc, Senior Engineer, Infrastructure.
Proposed, designed and actively developing a product as Technical Lead.
Aug 2007 - Aug 2008: Genentech Inc, Senior System Architect for
Research Computing
Provide Architectural oversight for Genentech Research Computing and
deploy solutions for scientists. Frequently did performance firefighting
and feature enhancements to ensure Genentech scientists were highly
productive.
Aug 2003 - Aug 2007: Computer Scientist, Distributed Systems Department,
Computational Research Division, Lawrence Berkeley National Lab.
Lead developer of ViCE (a visual programming/scientific workflow
execution system, based on Grid and Service Oriented Architecture
standards) and C-BEI (a scientific computational workflow management
infrastructure). Perform research into Computationals Grid including
grid system administration and scientific workflow management. Tune
applications and utilize high-performance computational grids composed of
multiple clusters with 500-1000 nodes each) to enable scale-out of large
computational biology workflows. Solve large-scale scientific problems
using high performance computing in collaboration with domain scientists.
Oct 2002 - Aug 2003: Postdoctoral Scholar, Steven Brenner Lab,
Department of Plant and Microbial Biology, University of California,
Berkeley. Evaluated and applied comparative protein structure
modeling methods for the Berkeley Structural Genomics Center. Managed
group 64-processor Linux cluster including application deployment and
performance tuning.
Feb 2002 - Oct 2002: Postdoctoral Scholar, Kimmen Sjolander Lab,
Department of Bioengineering, University of California, Berkeley.
Validated and improved subfamily hidden Markov Models (sHMMs)
specificity for functional classification and remote homolog
detection. Implemented a 16-processor Linux cluster for
high-throughput protein structure prediction and functional
annotation.
2000 - 2002: Programmer/Analyst III, Computer Graphics Lab, University
of California, San Francisco. Developed the Chimera Collaboratory
(http://www.cgl.ucsf.edu/Research/collaboratory). Maintained Linux
port of Chimera (http://www.cgl.ucsf.edu/chimera). Administered and
maintained various software packages including Apache, PHP, and MySQL
in support of bioinformatics projects.
1995 - 2001: Graduate Student in James lab, Graduate Group in
Biophysics University of California, San Francisco. PhD awarded
December 2001: "Structure of a Cytarabine-substituted Okazaki Fragment
Model". Determined the structure of gemcitabine- and
cytarabine-substituted Okazaki fragment model using restrained
molecular dynamics based on NMR-derived distance and torsional
restraints. Designed and implemented a Linux cluster for large-scale
molecular simulations of nucleic acids and proteins.
1991 - 1995: Department of Biochemistry and Molecular Biology,
University of California, Santa Cruz. B.A. awarded June 1995.
Undergraduate thesis submitted for completion of graduation at UCSC:
"Prediction of Gene-encoding regions in E.Coli DNA using an Optimal
Parse Method with Multiple Types of Evidence".
AWARDS AND ACHIEVEMENTS
o 2009, 2010 IEEE IPDPS Program Committee.
o 2006 LBNL LDRD: $90,000 grant to enhance C-BEI for parameter
optimization workflows.
o 2005 LBNL LDRD: $90,000 grant to develop C-BEI, a computational
workflow engine.
o 1998 ITD (Instructional Technologies Division) Personal Grant for
$5000 to develop the MidasMovie 3.0 application. Grant used to
purchase Dual PII 400MHz PC as a development workstation.
o 1997 ITD (Instructional Technologies Division) Personal Grant for
$5000 to develop the MidasMovie 2.0 application. Grant used to
purchase Dual Pentium Pro 200MHz PC as a development workstation.
o September 1997-May 1998 U.C. Regents Fellow
SCIENTIFIC PUBLICATIONS
Chandonia J-M, Konerding DE, Allen DG, Choi I, Yokota, H, Brenner SE.
Computational Structural Genomics of a Complete Minimal Organism.
Genome Informatics 2002, 13: 390-391
Konerding DE, James TL, Trump E, Soto AM, Marky LA and Gmeiner
WH. NMR Structure of a Gemcitabine-Substituted Model Okazaki
Fragment. Biochemistry, 2002, 41: 839-46.
Gmeiner WH; Cui W; Konerding DE; Keifer PA; Sharma SK; Soto AM; Marky
LA; Lown JW. Shape-Selective Recognition of a Model Okazaki Fragment
by Geometrically-Constrained bis-distamycins. Journal of Biomolecular
Structure and Dynamics, 1999 Dec, 17(3):507-18.
Gmeiner WH; Konerding D; James TL. Effect of cytarabine on the NMR
structure of a model okazaki fragment from the SV40 genome. Biochemistry,
1999 Jan 26, 38(4):1166-75.
Konerding DE; Cheatham TE 3rd; Kollman PA; James TL. Restrained
Molecular Dynamics of Solvated Duplex DNA Using the Particle Mesh
Ewald Method. Journal of Biomolecular NMR, 1999 Feb, 13(2):119-31.
Gmeiner WH; Konerding D; James TL. Effect of Cytarabine on the NMR
Structure of a Model Okazaki Fragment from the SV40 Genome.
Biochemistry, 1999 38: 1166-75.
TECHNICAL PUBLICATIONS
Konerding DE. Virtual Network Computing: Cross-Platform Remote
Display and Collaboration Software. Journal of Molecular Graphics and
Modeling, 2000 Apr, 17(2):151-4.
Konerding DE. The Ensemble/Legacy Chimera Extension: Standardized
User and Programmer Interface to Molecular Ensemble Data and Legacy
Modeling Programs. Pacific Symposium on Biocomputing 2000, 5:251-62
Gunter DK, Jackson KR, Konerding DE, Lee JR. Essential Grid Workflow Monitoring Elements
Conference on Grid Computing and Applications 2005
PAST SOFTWARE PROJECTS
o Technical lead and primary developer of ViCE, a visual programming
environment for composing workflows from web and grid services
http://dsd.lbl.gov/gtg/projects/vice/
o Technical lead and primary developer of C-BEI, an execution framework
for high-performance computational workflows composed of web and grid
services.
http://dsd.lbl.gov/gtg/projects/CBEI/
o Co-developer of pyGlobus, and pyGridware, software toolkits for grid
computing using python:
http://dsd.lbl.gov/gtg/projects/pyGlobus/
http://dsd.lbl.gov/gtg/projects/pyGridWare/
o (Previously) Sole developer of PyML, a Python interface to Mathematica:
http://www.konerding.com/~dek/pyml.html
o (Previously) Technical lead and primary developer of the Chimera
Collaboratory, a collaborative extension to the molecular modeling
application Chimera:
http://www.cgl.ucsf.edu/Research/collaboratory/
REFERENCES
Dr. Horst D. Simon, Associate Laboratory Director and Department Chair,
Computational Research Division MS 4230-50B, Lawrence Berkeley National
Laboratory, Berkeley, CA 94720
Dr. Reece Hart, Chief Scientist of the Genome Commons, QB3, Stanley Hall,
UC Berkeley, CA 94720