ER I C TOR S T EN SON SOFTWARE DEVELOPER

QualificationsSoftware developer with experience designing and developing complex software under many different environments. Expertise includes object oriented design using modern design patterns, meta-programming, multi-threaded and parallel applications, client-server interactions using TCP/IP, database design and use and producing effective solutions that can handle huge amounts of data such as audio processing and genome-wide data processing and analysis with or without access to a computation cluster.

Accomplishments‣ Codeveloped and implemented several programs to analyze genetic data in various

formats in languages such as C++, python and ruby.

‣ Developed several web applications for both internal and external use ranging from experiment design and execution to simple data presentation.

‣ Codeveloped and implemented new algorithmic designs which allowed a simulation software package to produce output at speeds orders of magnitudes faster than the previous approach.

‣ Redesigned biofilter and paris applications with generalizable database schemas tied together using traditional application software. Resource requirements of the redesigned software were fractions of the original, more flexible and required minimal instruction for new users.

‣ Improvements in a forward time simulation design allowed the application to produce simulated GWAS data on a single machine in under 24 hours-something which few, if any, other simulation tools are currently unable to do.

‣ Led a small team of developers to develop predictive application for Navy.

‣ Developed a data mining technique to identify patterns of behavior for simulated combatants. This data was used by another application which developed predictive models which would be used to provide estimates for simulation run times.

Developer Skills‣ Backend Web Development - Several years of web development using various

languages include Ruby, Python and PHP for projects of varying sizes and complexity.

1405 HEMLOCK AVE NASHVILLE, TNERIC.TORSTENSON@GMAIL.COM (615) 715-0650

‣ C++ Application Design and Development - Over 10 years professional experience designing, developing and maintaining complex applications in C++ in both Windows and Linux/Unix environments using object oriented technique.

‣ High Throughput Computing - Reworked several applications to improve memory requirements or performance using new approaches to memory layout or stepping down into a structured approach for crucial stages of the runtime.

‣ System Administration - Responsible for basic administration for several linux boxes running various versions of Ubuntu and Red Hat. Administrative responsibilities included basic admin tasks as well as installing and configuring web server and related software.

‣ Parallel and Multi-Threaded Computing - Extended several applications to incorporate multiple threads and/or parallel processing (MPI) to maximize real time performance.

‣ SQL - Over ten years of experience writing and incorporating complex SQL queries into applications using many of the most common databases today.

‣ Relational Database Schema Design - Responsible for schema design for several applications using various modern RDBMS.

‣ Various Scripting Languages - Written dozens of scripts of varying complexity in several different scripting languages. The biofilter database is populated using python scripts which extracts data from various international data repositories in an automated fashion. ASAP is an application that slices sequence data up for processing and automates the processing over a computation cluster.

‣ Strong Focus on User Interaction - When developing applications to which people must interface, it is a very high priority for me that the interface be clear and efficient whether it be a list of command line arguments, a configuration file or a Graphical User Interface.

‣ Project Management - Led a small team of developers to develop predictive application for Navy.

ExperienceHealth Systems Software Engineer IIICenter for Human Genetics Research; Vanderbilt University 2006-present

Design and Develop Applications for Ritchie Lab, Li Lab, Edwards Lab and Collaborators

‣ Developed web front end for TREAT prediction algorithm which aiding surgeons in diagnosing lung cancer. The web application is built using Python using the Pyramid web framework. It is currently under active development.

‣ Codesigned and developed MVTest and TBST, python programs used to analyze GWAS data. Both are written in Python, but leverage the power of various scientific

computing libraries, allowing them to perform comparably to a program written in a language like C++.

‣ Designed and developed Advanced Sequence Automated Pipeline (ASAP), an extensible framework used to manage the parallelization of sequence processing on modern computation cluster. ASAP allows the user to manage massive sequencing jobs on a cluster with minimal effort. Using task templates, users can dramatically extend the functionality of ASAP without having to alter any application code.

‣ Designed and developed online experiment management tool for EAGLE website allowing researchers and analysts to design experiments which were delivered to a remote site, executed, results collected and parsed using Ruby/Rails.

‣ Completely redesigned and developed biofilter, a stand alone C++ application which mines publicly available knowledge to produce candidates for epistasis. This application uses an SQL database to maintain the external knowledge and usually requires only an hour or two to complete.

‣ GenomeSIMLA - Made dramatic enhancements to genomeSIMLA , a forward time simulation tool, including huge efficiency bumps, improvements to the crossover simulation which allow more realistic results and added capacity for hot/cold spots.

‣ Offered scripting, instruction and general support to students and collaborators.

‣ Developed a front-end GUI for simulation package allowing users to perform simulations on their desktop, or define a configuration to be used on a local server machine.

Software EngineerLandmark Digital; Nashville ,TN 2005-2006

‣ Participated on a small team of C++ developers developing proprietary software for use by BMI subsidiary to audit terrestrial radio playlists.

‣ Wave Manager - Designed and developed the nodes that collected and identified remote audio data and stored audio and recognition results in an Oracle database. This application was the brain of a number of independent applications and was responsible for activation and configuration as well as data reception.

‣ Wave Listener - Codeveloped listener applications which collected audio data from airwaves and relayed data back to the local management server.

Software DeveloperOptimization Technology, Inc.; Huntsville, AL 2000-2005

‣ Lead developer, codesigner/investigator for Runtime Evaluation and Prediction System (REPS) Small Business Innovation and Research (SBIR).

‣ Developed software to manipulate an instrumented version of the simulation and collect runtime data into a relational database.

‣ Designed and developed the software that performed user data interpretation, predictor and calibration techniques.

‣ Codeveloped Rocket Motor Designer (RMD), a tool used by engineers at U.S. Army Space and Missile Defense Command. Responsible for Graphical User Interface (using windows MFC) which included various graphical and textual reports.

EducationMiddle Tennessee State University Murfreesboro, TN B.S. Computer Science

Programming Languages (5 years or more and current)C++ (boost, stl etc), Python (numpy, scipy, pandas, pyramid etc), SQL, bash, and HTML, ruby (rails)

Programming Languages (fewer than 5 years)php, CSS, pg-sql, perl, java, javascript, jquery, Objective C and Visual Basic, R, SAS

Software ExperienceLinux, OS X, Windows, Solaris, IRIX, HP-UX, STL, Boost, MPI, MySQL, PostgreSQL, Oracle, Cuda, gcc, rails, X Code, svn, gdb, valgrind, occi, soci, make, SQLite, googletest, meta programming, git, nginx, redcap, SLURM, TDD

PublicationsSamuels DC1, Li C, Li B, Song Z, Torstenson E, Boyd Clay H, Rokas A, Thornton-Wells TA, Moore JH, Hughes TM, Hoffman RD, Haines JL, Murdock DG, Mortlock DP, Williams SM: Recurrent tissue-specific mtDNA mutations are common in humans. PLoS Genetics. e1003929 (2013)

Cummings AC1, Torstenson E, Davis MF, D'Aoust LN, Scott WK, Pericak-Vance MA, Bush WS, Haines JL: Evaluating power and type 1 error in large pedigree analyses of binary traits. PLoS One. e62615 (2013)

Eric S Torstenson, Bingshan Li, Chun Li: ASAP: an environment for automated preprocessing of sequencing data. BMC Research Notes: 2013

Bush WS1, Boston J, Pendergrass SA, Dumitrescu L, Goodloe R, Brown-Gentry K, Wilson S, McClellan B, Torstenson E, Basford MA, Spencer KL, Ritchie MD, Crawford DC: Enabling high-throughput genotype-phenotype associations in the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) project as part of the Population Architecture using Genomics and Epidemiology (PAGE) study. Pacific Symposium on Biocomputing 2013: 373-84

Pendergrass SA1, Brown-Gentry K, Dudek S, Frase A, Torstenson ES, Goodloe R, Ambite JL, Avery CL, Buyske S, Bůžková P, Deelman E, Fesinmeyer MD, Haiman CA, Heiss G, HindorffLA, Hsu CN, Jackson RD, Kooperberg C, Le Marchand L, Lin Y, Matise TC, Monroe KR, Moreland L, Park SL, Reiner A, Wallace R, Wilkens LR, Crawford DC, Ritchie MD: Phenome-wide association study (PheWAS) for detection of pleiotropy within the Population Architecture using Genomics and Epidemiology (PAGE) Network. PLoS Genetics. e1003087 (2013)

Buchanan CC, Torstenson ES, Bush WS, Marylyn D. Ritchie: A comparison of cataloged variation between International HapMap Consortium and 1000 Genomes Project data. Journal of American Medical Informatics Association: 2012 Mar-Apr:289-294

Pendergrass SA, Brown-Gentry K, Dudek SM, Torstenson ES, Ambite JL, Avery CL, Buyske S, Cai C, Fesinmeyer MD,Haiman C, Heiss G, Hindorff LA, Hsu CN, Jackson RD, Kooperberg C, Le Marchand L, Lin Y, Matise TC, Moreland L,Monroe K, Reiner AP, Wallace R, Wilkens LR, Crawford DC, Ritchie MD: The use of phenome-wide association studies (PheWAS) for exploration of novel genotype-phenotype relationships and pleiotropy discovery. Genetic Epidemiology: 2011:May 18

Grady BJ, Torstenson ES, Ritchie MD: The effects of linkage disequilibrium in large scale SNP datasets for MDR. BioData Mining 2011:May 5

Benjamin J. Grady, Eric Torstenson, Paul J. Mclaren, Paul I. W. de Bakker, David W. Haas, Gregory K. Robbins, Roy M. Gulick, Richard Haubrich, Heather Ribaudo, Marylyn

D. Ritchie: Use of Biological Knowledge to Inform The Analysis of Gene-Gene Interactions Involved in Modulating Virologic Failure with Efavirenz-Containing Treatment Regimens in Art-Naive Actg Clinical Trials Participants. Pacific Symposium on Biocomputing 2011: 253-264

Brian L Yaspan, William S Bush, Eric S Torstenson, Deqiong Ma, Margaret A Pericak-Vance, Marylyn D Ritchie, James S Sutcliffe and Jonathan L Haines: Genetic analysis of biological pathway data through genomic randomization. Human Genetics (2011)

Tricia Thornton-Wells, Eric Torstenson, Scott Dudek, Marylyn Ritchie, Eden Martin, Margaret Pericak-Vance, Jonathan Haines: Discovery and Replication of Gene-Gene Interactions in Multiple Independent Datasets from the Alzheimer Disease Genetics Consortium. Alzheimers & Dementia 2011 (S197)

Emily Rose Holzinger, Carrie C. Buchanan, Scott M. Dudek, Eric Torstenson, Stephen D. Turner, Marylyn D. Ritchie: Initialization parameter sweep in ATHENA: optimizing neural networks for detecting gene-gene interactions in the presence of small main effects. GECCO 2010: 203-210

Grady BJ, Torstenson E, Dudek SM, Giles J, Sexton D, Ritchie MD.: Finding unique filter sets in plato: a precursor to efficient interaction analysis in gwas data. Pac Symp Biocomput. 315-26 (210)

Edwards TL, Turner SD, Torstenson ES, Dudek SM, Martin ER, Ritchie MD.: A general framework for formal tests of interaction after exhaustive search methods with applications to MDR and MDR-PDT. PLoS One. e9363 (2010)

Bush WS, Chen G, Torstenson ES, Ritchie MD.: LD-spline: mapping SNPs on genotyping platforms to genomic regions using patterns of linkage disequilibrium. BioData Mining 2009, 2:7(2009)

Edwards TL, Bush WS, Turner SD, Dudek SM, Torstenson ES, Schmidt M, Martin E, Ritchie MD.: Generating Linkage Disequilibrium Patterns in Data Simulations using genomeSIMLA. Lecture Notes Computer Sci. 4973(2008)

Todd L. Edwards, William S. Bush, Stephen D. Turner, Scott M. Dudek, Eric Torstenson, Mike Schmidt, Eden Martin, Marylyn D. Ritchie: Generating Linkage Disequilibrium Patterns in Data Simulations Using genomeSIMLA. EvoBIO 2008: 24-35

Ritchie MD, Bartlett J, Bush WS, Edwards TL, Motsinger AA, Torstenson ES: Exploring epistasis in candidate genes for rheumatoid arthritis. BMC Proc. (2007)