Lab Members

PI: Herbert M Sauro

email: hsauro at uw.edu

University of Washington Department of Bioengineering

Interests: Understanding the Design Principles of Cellular Networks; High-Performance Simulation Hardware and Software; Novel Model Approaches; Standards and Reproducibility of Simulation Studies; Education and Dissemination of Research

Postdoctoral Scholars

Michael Kochen

Specializes in signaling network modeling.

Jin Xu

Python and Julia programming

Research Scientists

Steve Andrews

Steve's background is in biophysics. His work focuses on the design principles of cellular networks, spatial simulation methods, and information transmission by signaling networks. He is the primary author of the Smoldyn software, which simulates cells at single-molecule resolution. He also wrote the undergraduate physics textbook Light and Waves: A Conceptual Exploration of Physics.

Programmer Scientists

Lucian Smith

Lucian Smith has been working for Herbert on and off for the last decade. He created the Antimony language and has worked extensively with SBML and SED-ML, having served on the editorial boards of both specifications and serving as the principal or contributing author to several SBML extensions. He currently continues to work on Antimony as well as a variety of other programs in the Tellurium suite of software.

Bart Jardine

Bart's research involves developing software tools for physiological modeling and data analysis, with an emphasis on systems biology and the cardiovascular system.

Developing a real-time simulator

Graduate Students

Janis Shin

"Due to climate change, humans are attempting to phase out their reliance on petroleum for products for environmentally friendlier solutions. One method to do this is by engineering the metabolism of organisms to produce chemicals of human interest. However, it is difficult to predict which strain designs will yield the most product. Historically, scientists have built large strain libraries and eliminated the worst produces to arrive at the best producer, but this is expensive and time consuming. Therefore, we are working on using Bayesian inference to infer elasticity coefficients of each reaction in a metabolic pathway. Using these elasticity coefficients, we will be able to identify gene targets that will be used to craft and test a few high-performing strains, saving time and labor." - Janis Shin

Janis is working on building gene-scale kinetic models or P. putida metabolism.