SBtools Bootcamp, June 2020

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Open Source Tools for Biological Circuit Design


  • Richard Murray (CDS/BE),
  • Lecturers: John Marken (BE), Ayush Pandey (CDS), William Poole (CNS), Rory Williams (BE)
  • TAs: Liana Merk, Manisha Kapasiawala, Ankita Roychoudhury, Sophie Walton

Class meeting times

  • 16-19 June, 8:30a-12:00p PDT

This is the course homepage for the Synthetic Biology (Modeling and Analysis) Tools [SBtools] bootcamp.

This bootcamp 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.

Lecture Schedule

Each day of the course will cover a different topic and/or tool. The class sessions will contain a mixture of lecture, hands-on demonstrations, and participatory exercises.

Date Topic Instructors Tools Notes
L1 - 16 Jun Chemical reactions, mass action → BioCRNPyler (species, reactions) Ayush, John, Ankita, Sophie Anaconda, Jupyter, GitHub, BioCRNpyler, Bioscrape
L2 - 17 Jun ODEs, Hill functions → BioCRNPyler (species, reactions) Ayush, John, Ankita, Sophie BioCRNpyler, Bioscrape Core processes: transcription, translation → BioCRNPyler (mixtures)
L3 - 18 Jun Intro to SBML and non-mass-action propensities & rules in bioscrape Rory, William, Liana, Manisha BioCRNpyler, Bioscrape
L4 - 19 Jun Genetic circuits → BioCRNPyler (components, mechanisms) Rory, William, Liana, Manisha BioCRNpyler, Bioscrape
TBD Compartments as orthogonal CRNs connected by diffusion reactions and SubSBML Ayush Sub-SBML
TBD Bioscrape Lineages as a well-mixed version of gro William Bioscrape Lineages
TBD System ID: Bioscrape inference tools Ayush Bioscrape Inference

Course Preparation

The course will rely on working knowledge of Python. Participants who are not familiar with using Python should consider taking the BE 203 bootcamp, offered by Justin Bois.