Brian J. Drawert

briandrawert@gmail.combdrawert@cs.ucsb.eduDepartment of Computer ScienceUniversity of California, Santa BarbaraSanta Barbara, CA 93106-5070

Postdoctoral Researcher University of California - Santa BarbaraDepartment of Computer Science PI: Linda R. PetzoldOct 2013 - present Research Group Website: http://www.cs.ucsb.edu/ cse/Project: StochSS StochSS: Stochastic Simulation-as-a-Service.

Using the power of cloud computing to create an integratedplatform for stochastic simulation.Collaborating with Prof. Chandra Krintz.

Project: Yeast Polarization Modeling and simulation of the spatial stochastic biochemicaldynamics intrinsic to the process of polarization during matingin S. cerevisiae.Collaborating with yeast biologist Prof. Tau-Mu Yi.

Project: Yeast Cell Wall Modeling how the mechanical properties of the cell wall couplewith the biochemical processes that drive the deformation duringcellular polarization.Collaborating with Prof. Otger Campas and Prof. Tau-Mu Yi.

Project: Frog Conservation Modeling and simulation to find conservation methods for theendangered Sierra Mountain yellow-legged tree frogs Rana sierrae.Collaborating with ecologist Prof. Cherie Briggs.

AppScale Systems, Inc http://www.appscale.comSr. Engineer, AppScale is an open source Platform-as-a-Service (PaaS)Jan 2013 - Sep 2013 which is API compatible with Google’s App Engine cloud platform.

PaaS cloud computing extends virtualized infrastructure byautomatically configuring, deploying, and scaling users’ softwareapplications on demand.

Project: Continuous Testing Designed and implemented an automated testing system that buildsAppScale virtual images and runs a suite of API and Selenium drivenweb usability tests on them. This facilitates rapid developmentand increases the robustness and stability of our products.

Project: Open Pension Calculator A collaboration with the non-profit foundation, Novim, to developpublic domain tools based on the AppScale platform to aid thepublic’s understanding of these extraordinarily complex plans withthe expectation that education will lead to rational policy decisions.

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Brian J. Drawert - Curriculum Vitae - briandrawert@gmail.com

EducationPhD. Computer Science, 2013 University of California - Santa Barbara

Computational Science & Engineering Emphasis.Advisors: Linda R. Petzold, Dept. of Computer Science

Mustafa Khammash, Dept. of Mechanical EngineeringPh.D. Dissertation: Spatial Stochastic Simulation of Biochemical Systems

M.S. Physics, 2007 Depaul UniversityAdvisor: Jesus Pando, Dept. of Physics

Master’s Thesis: Spatial Anisotropy in the Cosmic Microwave Background Radiationvia Wavelet Analysis of the Wilkinson Microwave Anisotropy Probe.

B.S. Computer Science, 2001 Illinois Institute of TechnologyGraduated Cum Laude

Peer-Reviewed Journal Articles

B. Drawert, M. Trogdon, S. Toor, L. Petzold, A. Hellander “MOLNs: A cloud platform forinteractive, reproducible and scalable spatial stochastic computational experiments usingPyURDME”(under review)

A. Hellander, M. Lawson, B. Drawert, L. Petzold “Local Error Estimates for AdaptiveSimulation of the Reaction-Diffusion Master Equation via Operator Splitting” Journal ofComputational Physics (June 2014)

M. Lawson∗, B. Drawert∗, M. Khammash, L. Petzold, T-M. Yi “Stochastic Spatial DynamicsEnable Robust Cell Polarization” PLOS Computational Biology (July 2013)

B. Drawert, S. Engblom, A. Hellander “URDME: a modular framework for stochastic simulationof reaction-transport processes in complex geometries” BMC Systems Biology (Jun 2012)

C. Bunch, B. Drawert, N. Chohan, C. Krintz, L. Petzold, K. Shams “Language and RuntimeSupport for Automatic Configuration and Deployment of Scientific Computing Softwareover Cloud Fabrics” Journal of Grid Computing (Mar 2012)

B. Drawert∗, M. Lawson∗, L. Petzold, M. Khammash “The Diffusive Finite State ProjectionAlgorithm for Efficient Simulation of the Stochastic Reaction-Diffusion Master Equation”Journal of Chemical Physics (Feb 2010)

Peer-Reviewed Conference Proceedings

G. Douglas, B. Drawert, C. Krintz, R. Wolski “CloudTracker: Using Execution Provenanceto Optimize the Cost of Cloud Use” In Proceedings of: GECON14, 11th International

Conference on Economics of Grids, Cloud, Systems and Services (Sept 2014)

C. Horuk, G. Douglas, A. Gupta, C. Krintz, B. Bales, G. Bellesia, B. Drawert, R. Wolski,L. Petzold and A. Hellander “Automatic and Portable Cloud Deployment for ScientificSimulations” In Proceedings of: HPCS14, The 2014 International Conference on HighPerformance Computing & Simulation (July 2014)

P-O Ostberg, A. Hellander, B. Drawert, E. Elmroth, S. Holmgren, L. Petzold “ReducingComplexity in Management of Scientific Computations” In Proceedings of: CCGrid 2012,The 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing(May 2012)

∗Indicates co-first author

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Brian J. Drawert - Curriculum Vitae - briandrawert@gmail.com

P-O Ostberg, A. Hellander, B. Drawert, E. Elmroth, S. Holmgren, L. Petzold “Abstractionsfor Scaling eScience Applications to Distributed Computing Environments; A StratUmIntegration Case Study in Molecular Systems Biology” In Proceedings of:Bioinformatics 2012, International Conference on Bioinformatics Models, Methods,and Algorithms (Feb 2012)

Invited Talks

“Interactive, Distributed Spatial Stochastic Simulation with PyURDME and MOLNs”SIAM Conference on Computational Science & Engineering Salt Lake City, UT (Mar 2015)

“Conservation through Computation: Using Modeling and Simulation to Find Methods to SaveEndangered Amphibians” Scientific Computing Seminar - Uppsala UniversityUppsala, Sweden (Oct 2014)

“CloudTracker: Using Execution Provenance to Optimize the Cost of Cloud Use”GECON14, 11th International Conference on Economics of Grids, Cloud, Systemsand Services Cardiff, UK (Sep 2014)

“Adaptive Accelerate Spatial Stochastic Simulation of Biochemical System”SIAM Annual Meeting 2014 Chicago, IL (July 2014)

“StochSS: an Integrated Development Environment for Modeling and Simulation of StochasticBiochemical Systems“ Southern California Systems Biology Conference Irvine, CA (Jan 2014)

“Modeling Public Pensions with Mathematica and Python”Wolfram Technology Conference Champaign, IL (Oct 2013)

“Polarized Spatial Stochastic Amplification During Mating in Saccharomyces cerevisiae”2012 Annual Meeting for Society for Mathematical Biology Knoxville, TN (July 2012)

“Polarization in Yeast Mating: Modeling and Simulation of Spatial Stochastic Phenomena”Scientific Computing Seminar - Uppsala University Uppsala, Sweden (Mar 2011)

“Polarized Spatial Stochastic Amplification During Mating in Saccharomyces cerevisiae”International Conference on Systems Biology Edinburgh, Scotland (Oct 2010)

“Spatial Stochastic Simulation of Biochemical Systems”Theoretical Ecology Seminar UCSB (Mar 2010)

Workshop/Tutorial Presentations

“StochSS: an Integrated Development Environment for Modeling and Simulation of StochasticBiochemical Systems“ Cellular Dynamics & Models Meeting, Cold Springs Harbor Laboratory(Mar 2015)

“StochSS: an Integrated Development Environment for Modeling and Simulation of StochasticBiochemical Systems“ UCSB Graduate Bio-enginering Seminar (Feb 2015)

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Brian J. Drawert - Curriculum Vitae - briandrawert@gmail.com

Poster Presentations

“StochSS: Stochastic Simulation Service. An Integrated Development Environment for Simulationand Analysis of Discrete Stochastic Biochemical Models” B. Drawert, B. Bales, M. Gu,D. Banerjee, D. Nath, B. Daigle, P. Lotstedt, A. Hellander, C. Krintz, L. Petzold

Cellular Dynamics & Models Meeting, Cold Springs Harbor Laboratory (Mar 2015)“Simulating Yeast Polarization in the Cloud”

B. Drawert, M. Trogdon, M. Lawson, S. Toor, B. Bales, D. Banerjee, A. Hellander, T-M. Yi,L. Petzold Gordon Research Conference on Stochastic Physics in Biology (Jan 2015)

“StochSS: Stochastic Simulation Service. An Integrated Development Environment for Simulationand Analysis of Discrete Stochastic Biochemical Models” B. Drawert, G Bellesia, B. Bales, C. Horuk,B. Daigle, S. Wu, P. Lotstedt, A. Hellander, C. Krintz, L. Petzold NIH IMAG Multiscale Modeling

Consortium Meeting (Sep 2014)“StochSS: an Integrated Development Environment for Modeling and Simulation of Stochastic

Biochemical Systems“ B. Drawert, G Bellesia, B. Bales, C. Horuk, S. Wu, P. Lotstedt, A. Hellander,C. Krintz, L. Petzold Southern California Systems Biology Conference (Jan 2014)

“Efficient Stochastic Simulation of Spatially Inhomogeneous Biochemical Systems”B. Drawert, M. J. Lawson, A. Hellander, M. Khammash, L. PetzoldSouthern California Systems Biology Conference (Jan 2012)

“Efficient Stochastic Simulation of Spatially Inhomogeneous Biochemical Systems”B. Drawert, M. J. Lawson, A. Hellander, M. Khammash, L. PetzoldSouthern California Systems Biology Conference (Jan 2011)

“Efficient Stochastic Simulation of Spatially Inhomogeneous Biochemical Systems”B. Drawert, M. J. Lawson, A. Hellander, M. Khammash, L. PetzoldGordon Research Conference on Stochastic Physics in Biology (Jan 2011)

“Polarized Spatial Stochastic Amplification During Mating in Saccharomyces cerevisiae”B. Drawert, M. J. Lawson, L. Petzold, M. Khammash, T-M. Yi ICSB (Oct 2010)

“Stochastic Modeling and Simulation of Cell Polarization During Mating in Budding Yeast”B. Drawert, M. J. Lawson, T-M. Yi, L. Petzold, M. Khammash IGERT Project Meeting (May 2010)

“Stochastic Modeling and Simulation of Cell Polarization During Mating in Budding Yeast”B. Drawert, M. J. Lawson, T-M. Yi, L. Petzold, M. Khammash Q-Bio (Aug 2009)

Technical Reports

P. Bauer, B. Drawert, S. Engblom A. Hellander “URDME v. 1.2: Users manual”. TechnicalReport 2012-036, Department of Information Technology, Uppsala University (Dec 2012)

C. Bunch, B. Drawert, N. Chohan, A. Riofrio, C. Krintz, L. Petzold “MEDEA: A PluggableMiddleware System for Interoperable Program Execution Across Cloud Fabrics”Report 2012-11, University of California, Computer Science Department (Nov 2012)

B. Drawert, S. Engblom A. Hellander “URDME v. 1.1: Users manual”. Technical Report2011-003, Department of Information Technology, Uppsala University (Mar 2011)

C. Bunch, B. Drawert, M. Norman “MapScale: A Cloud Environment for Scientific Computing”Technical Report, University of California, Computer Science Department (Jun 2009)

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Brian J. Drawert - Curriculum Vitae - briandrawert@gmail.com

Teaching ExperienceInstructor 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, andtutors while maintaining the course instructional software site.

Teaching Assistant Intro to Physics 1, 2 & 3 Physics Department, Depaul University2004-2007 Led Discussion Sections, Held Office Hours, Graded Exams & Homework

Mentored Undergraduate StudentsIzaak Rozen Izaak worked with me on research project related to my systems biology research.

Jan - Jun 2012 We made contributions to a software package I had previously created for thepurpose of image analysis of timeseries GFP-tagged yeast cell microscopy images.The goal of our project was to extend and refine this package, transforming thisresearch code into publicly usable software. We have released it as an open sourceproject named Stochastic Cell, providing installation scripts and documentationfor maximum usability and impact to the scientific community. The software isfreely available at http://briandrawert.github.io/Stochastic-Cell/.

Professional ExperienceSkills: 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 Contractor MD Records, Inc Jun 2002 - Aug 2007 Chicago, ILSoftware Engineer Leapfrog Online, Inc Jan 2003 - Jun 2004 Evanston, ILSoftware Engineer Period 7, Inc Sept 2001 - Nov 2001 Chicago, ILSoftware Engineer Vicode, Inc. Aug 2001 - Sept 2001 Chicago, ILSoftware Engineer L90, Inc. Jun 1999 - Aug 2001 Chicago, ILWeb Engineer MyPoints.com, Inc. Jun 1998 - Jun 1999 Schaumburg, IL

Honors and Awards2007-2012 National Science Foundation IGERT Fellowship, UCSB2001 Outstanding Community Contribution Award, IIT1996-2001 Heald merit-based scholarship, IIT

Peer ReviewPerformed peer review for the following journals (Feb 2014 - present):

BioinformaticsComputer Physics CommunicationsIEEE IPDPS ( IEEE International Parallel & Distributed Processing Symposium)PLOS Computational BiologyACM TAAS (Transactions on Autonomous and Adaptive Systems)IEEE Transactions on Computational Biology and Bioinformatics

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Brian J. Drawert - Curriculum Vitae - briandrawert@gmail.com

Software PackagesStochSS StochSS is an open source IDE for discrete stochastic simulations of biochemical.

StochSS enabled systems biology researchers to simply define their model systemand type of simulations desired and then transparently executes the workflows oncomputational resources ranging from local workstations and clusters createdautomatically in public cloud infrastructures.

MOLNs MOLNs is a cloud computing appliance that configures, builds and manages avirtual appliance for spatial stochastic modeling and simulation on public, privateand hybrid clouds.

URDME URDME is an open source software for modeling and simulation of stochastic& PyURDME reaction-diffusion master equation (RDME) systems on unstructured, tetrahedral

meshes, allowing for handling of complex geometries often found in biologicalsystems. PyURDME is an python extension of the original URDME software thatremoves all binding to commercial software, increasing the impact and usable ofthis software on the systems biology community.

GillesPy An offshoot of the StochSS project, this python library is designed to supportdevelopment of discrete stochastic well-mixed models. Advanced simulationcapabilities are provided by integration with the best-of-breed software, StochKit.

Stochastic Cell Stochastic Cell Image Analyzer - Analyze time series images of florescent taggedproteins in living cells.

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