Teaching

2025

• Winter. Bioengineering 489/599. Control Engineering for Biomedical Systems.

• April, 2025. Control Engineering for Biomodeical Systems is a list course: BIOEN 438/538 with the Data Science Option.

2024

• Winter. Bioengineering 489/599. Advanced Controls for Biological Systems.

• Summer. Network Modeling Summer School.

• Fall. Bioengineering 437/537. Computational Systems Biology.

2023

• Winter. Bioengineering 489/599. Advanced Controls for Biological Systems.

• Summer. Network Modeling Summer School.

• Fall. Bioengineering 437/537. Computational Systems Biology.

2022

• Spring.  Bioengineering 498/599. Advanced Controls for Biological Systems.

• Summer. Network Modeling Summer School.

• Fall. Bioengineering 437/537. Computational Systems Biology.

2021

• "Computational Systems Biology for Medical Applications" becomes a numbered course: 437/537.

• Winter. Bioengineering  437/537. Computational Systems Biology for Medical Applications.

• Summer. Network Modeling Summer School.

• Fall. Bioengineering  498/598. Computational Systems Biology for Medical Applications.

2020

• Fall. Bioengineering  498/598. Computational Systems Biology for Medical Applications.

• Summer. Network Modeling Summer School.

2019

• Spring. DATA 515A. Software Development for Data Scientists.

• Fall. Computer Science & Engineering. 583. Software Development for Data Scientsts.

• Fall. Computer Science & Engineering. 599V. Computational Systems Biology for Medical Applications.

2018

• "Software Development for Data Scientists" becomes a numbered course. CSE 583.

• Spring. DATA 515A. Software Development for Data Scientists.

• Fall. Computer Science & Engineering. 583. Software Development for Data Scientsts.

• Fall. Computer Science & Engineering. 599V. Advancing Biomedical Modeling.

2017

• Winter. Computer Science & Engineering. 599B1. Software Development for Data Scientists.

• Spring. DATA 515A. Software Development for Data Scientists.

2016

• Winter. Computer Science & Engineering. 599B1. Software Development for Data Scientists.

• Fall. Computer Science & Engineering. 599B1. Software Development for Data Scientists.

2015

• Spring. Computer Science & Engineering. 490 B1. Software Engineering for Biologists.

2014

• Fall. Computer Science & Engineering. 599A. CSE Molecular Biology.

• Fall. Short Course. Modeling Biochemical Pathways.

2013

• Fall. Computer Science & Engineering. 599. Biochemistry for Computer Scientists.

University of WA Students Supervised

• Shengyi Yang, BA Computer Science, 2025. Supervised research project: BioModels Cache.

• Agastya Mongia, BA Computer Science, 2025. Supervised research Project: Browser only implementation of SBMLNetwork.

• Edison Shunming Eshao, BA Computer Science, 2023-2025. Antimony Web Editor.

• Kevin Nguyen, BA Computer Science, 2023-2025. Antimony Web Editor.

• Eva Liu, BA/MS Computer Science. 2022-2024. VSCode-Antimony and Antimony Web Editor.

• Sai Anish Konanki. BA Computer Science. 2022-2024.VSCode-Antimony and Antimony Web Editor.

• Juliette Park. MA Computer Science. 2023-2024. Reproducibility Portal.

• Tanya Naveem.  BA Computer Science. 2023-2024. Reproducibility Portal.

• Tony Yuan. BA Computer Science. Reproducibility Portal. 2023.

• Sam Chou. BA Computer Science. 2023-2024.

• Lillian Tatka,  PhD, BioEngineering, "Automated Credibility Assessment of Computational Models in Systems Biology", 2023.

• Veronica Porubsky, PhD, BioEngineering, "Python packages to support graph theory analysis and recurrent neural network models of neuronal population dynamics collected with calcium imaging", 2023.

• Janis Shin, PhD, BioEngineering, Building and validating kinetic models with in vivo data for more predictive metabolic engineering", 2023.

• Longxuan Fan, BA, Computer Science & Engineering

• Steve Ma. MS, Computer Science.

• Steve Ma, BA, Computer Science. Project: Testing Dynamical Systems - An Application to Systems Biology

• Khyati Parekh, Data Science Masters Program. Project: Phenotype prediction with Stahl Lab.

• Kyle Medley, BioEngineering. Project: Reproducible kinetics models.

• Kiri Choi, BioEngineering. Project: Engineering transcription factor binding sites.

• Woosub Shin. BioStatistics. Project: Linter for improving biomedical models.