Testimonial - Kathy Chen, 2009
I have known Jason Zwolak for 10 years, and I am very impressed with his programming skills, his strong desire to develop computational tools for biologists to use, and his desire to make sure that the tools are user friendly. The tools Jason creates are intuitively easy to use, give understandable diagnostic error messages, and he fixes program bugs quickly.
I got to know Jason in the fall of 1999 when he joined Dr. John Tyson's lab of computational biology as an MS Degree student to develop an automatic parameter estimation program. He used, as a test case, a simplified model of MPF oscillation in Xenopus egg extract system (11 equations, 25 parameters). While he was working on parameter estimation, I was a research scientist, modeling the cell cycle control in budding yeast (33 equations, 140 parameters). At the time, I was laboring to fit the model by hand to more than 100 experimental data sets. It was a very painful, frustrating, and tedious process. As each parameter set I changed, required me to run 100+ simulations to find out if this parameter set will be able to explain all the experimental data. That would take me two days, and the process had to be repeated countless times as I searched the parameter space. Once Jason understood my problem, he volunteered to write a script program (called param-batch, the prototype for PET - Parameter Estimation Toolkit) that would automatically run all 100+ simulations with one command, and the results are conveniently displayed as a PDF file. This program really helped my progress, it reduced two days work to 30 min. It was a life-saver for me. He has made my career as a modeler successful and enjoyable.
Later on, Jason improved his param-batch program and developed it into PET, with a very good user interface. It integrates with a model builder program (that allows the user to edit the model) and does batch simulations (including nested pre-simulations) with multiple parameter sets (that allows the user to compare simulation results as the user is twiddling the parameters). PET makes parameter fitting much more efficient. It has now become an indispensable tool in model building.
During the many years we worked together, I learned that since childhood, Jason has been interested in computers, so we consider him a computer guru in the lab. Whenever we had problems, be it hardware failure or software bugs, we all went to Jason for help, even though there are many other CS students around. He is not only knowledgeable about hardware configurations, and about computer programming, on top of that, he has a very amiable personality. He is kind, willing to help others, very responsible, and easy to work with.
Besides his talent in computer programming, he is very creative and good at web design. He has the technical expertise in html and PHP. He helped design our webpages on budding yeast cell cycle modeling and our lab webpage and Dr. Tyson's home page.
Kathy Chen, Research Scientist,
Department of Biology,
Blacksburg, VA 24061