Date of Award
2025
Document Type
Honors Thesis (Open Access)
Department
Colby College. Computer Science Dept.
Advisor(s)
Stephanie Taylor
Abstract
Modeling the light response system of Nannochloropsis oceanica brings
a set of challenges that make modeling difficult. Notably, potential models
may contain a large number of chemical species. A large number of
species creates a quadratic explosion in the number of potential pathways.
In addition, mathematically defining these pathways is error prone, yet
follows a surprising simple set of rules. We seek to create a domain specific
language which can precisely define these chemical reaction networks.
Once the networks have been defined, they can be exported as procedures
defined in popular programming languages for further analysis.
Keywords
domain specific language, differential equations, python, julia, systems biology
Recommended Citation
Day, Andy M., "Introducing Catalizer: A Framework for Prototyping Models of Biological Systems" (2025). Honors Theses. Paper 1505.https://digitalcommons.colby.edu/honorstheses/1505