BE 240, Spring 2020
Open Source Tools for Biological Circuit Design
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.
|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|
This class is graded pass/fail. To pass the class, you must participate in at least 80% of the lectures and recitations and submit a final project report consisting of a Jupyter notebook demonstrating the use of two or more of the tools in the class on a problem of interest to your research.
Collaboration is encouraged in figuring out how to use all of the tools of this course. The final project report should represent your individual understanding of how to apply the tools demonstrated in this course to a problem of interest to your research. Obtaining feedback and advice from the instructors, course participants, or others on the final project is allowed, but the final code included in the project should be written up individually, citing any sources of code snippets that are included in the notebook.