BE 240, Spring 2020
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Open Source Tools for Biological Circuit Design | |
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Instructors
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Class meetings
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This is the course homepage for BE 240, Spring 2020.
This course covers the use of open source tools developed at Caltech for use in modeling and simulation of engineered biological circuits. Participants in the course will develop working knowledge of modeling, simulation, and design tools that are available for biological circuits and apply that knowledge to a circuit relevant to your research. Students will also gain insights into modeling and design choices, including what level of detail to include in a model based on the questions you are trying to ask. Finally, the course aims to expand the available applications of model-based design of biological circuits and/or the available tools for biological circuit design through open source implementations.
Lecture Schedule
| Date | Topic | Lecturer | Tools |
| W1 - 30 Mar | Organizational week | Richard | Anaconda, Jupyter, Git |
| W2 - 6 Apr | CRNs and simulating them with Bioscrape | William | Bioscrape |
| W3 - 13 Apr | Model reduction in bioscrape via non-mass-action propensities and rules | Ayush | Bioscrape |
| W4 - 20 Apr | BioCRNpyler for generating large CRN models from parts | William | BioCRNpyler |
| W5 - 27 Apr | Compartments as orthogonal CRNs connected by diffusion reactions and SubSBML | Ayush | Sub-SBML |
| W6 - 4 May | Spatial systems and signalling | Cindy | Gro |
| W7 - 11 May | Cells and Growth/death regulation | Cindy | Gro |
| W8 - 18 May | System ID: Bioscrape inference tools | Ayush | Bioscrape Inference |
| W9 - 25 May | Bioscrape Lineages as a well-mixed version of GRO | William | Bioscrape Lineages |
| W10 - 1 Jun | Advanced: Automated Model Reduction | Ayush | Auto-Reduce |
