Software Computer Science

Brian J. Drawert

********@**.****.***

Department of Computer Science

University of California, Santa Barbara

Santa Barbara, CA 93106-5070

Research Group Website: http://www.cs.ucsb.edu/~cse/

Research Interest

I am interested in the development of Spatial Stochastic Algorithms as a solution to the

Reaction-

Diffusion Master Equation with a specific focus on their application to Systems Biology.

I am also

interested in the modeling and simulation of spatially inhomogeneous stochastic

biological systems.

Education

PhD. Computer Science University of California - Santa Barbara

(in progress) Computational Science & Engineering Emphasis.

Advisors: Linda R. Petzold, Dept. of Computer Science

Mustafa Khammash, Dept. of Mechanical Engineering

M.S. Physics, 2007 Depaul University

Advisor: Jesus Pando, Dept. of Physics

B.S. Computer Science, 2001 Illinois Institute of Technology

GraduatedCum Laude

Research Experience

Ph.D. Thesis Abstract: We are developing a spatial stochastic model of cell polarization

(in progress) in yeast, along with a computational framework for the accurate and

e cient simulation of this model. The new computational method is based on

a hybrid of the SSA and the Finite State Projection algorithm for

reaction-diffusion systems.

Master's Thesis Title:

Teaching Experience

Instructor Intro to Programming for Engineers, College of Engineering, UCSB

Aug-Sep 2010 & 2011 Instructor of record for summer session of ENG-3.

Educational Coordinator Intro to Programming for Engineers, College of Engineering, UCSB

Jun-Dec 2009 First worked to restructure the curriculum and create course content:

Moving from syntax oriented C to "Problem Solving" oriented Matlab.

Then worked to coordinate the team of teaching assistants, graders, and

tutors while maintaining the course instructional software site.

Teaching Assistant Intro to Physics 1, 2 & 3Physics Department, Depaul University

2004-2007 Led Discussion Sections, Held O ce Hours, Graded Exams & Homework

Mentored Students

Izaak Rozen In January 2012, Izaak began working with me on research project related to

my

Jan 2012 - systems biology research. I had previously written a software package for

image

analysis of timeseries GFP-tagged yeast cell microscopy images. The goal of our

project is to extend and refine the package, transforming this research code into

publicly usable software. We will release it as an open source project named

Stochastic Cell, providing installation scripts and documentation for maximum

usability and impact to the scientific community.

The software is freely available athttp://stochasticcell.sf.net.

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Brian J. Drawert - Curriculum Vitae - ********@**.****.***

Professional Experience

Skills: C/C++, Fortran 77/90/95, MATLAB, Perl, Java, Python, PHP, DHTML, XML,

MPI, POSIX Threads, TCP/IP, IPC, SQL, OOA/D, Distributed/Parallel Computing,

Clustering, HA/Fault-Tolerance, Unix Administration

Software ContractorMD Records, IncJun 2002 - Aug 2007 Chicago, IL

Software EngineerLeapfrog Online, IncJan 2003 - Jun 2004 Evanston, IL

Software EngineerPeriod 7, IncSept 2001 - Nov 2001 Chicago, IL

Software EngineerVicode, Inc. Aug 2001 - Sept 2001 Chicago, IL

Software EngineerL90, Inc. Jun 1999 - Aug 2001 Chicago, IL

Web EngineerMyPoints.com, Inc. Jun 1998 - Jun 1999 Schaumburg, IL

Honors and Awards

2007-2012 National Science Foundation IGERT Fellowship, UCSB

2001 Outstanding Community Contribution Award, IIT

1996-2001 Heald merit-based scholarship, IIT

Software Packages

URDME URDME is a general software framework for modeling and simulation of stochastic

reaction-diffusion processes on unstructured, tetrahedral meshes. The simulation

algorithms are based on the mesoscopic reaction-diffusion master equation model.

Stochastic Cell Stochastic Cell Image Analyzer - Analyze time series images of florescent

tagged

proteins in living cells.

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