Build-a-cell Chemical Reaction Network (CRN) modeling tutorials
The Build-a-Cell CRN tutorial series is done.
Watch the tutorial series on YouTube
Due to Covid-19, many of us cannot enter the lab as often or as consistently as we would like. Modeling provides a lab-free alternative method to test hypothesis and understand experimental data.
This workshop series is an introduction to chemical reaction network (CRN) modeling for synthetic and systems biology using a suite of python software tools that make model building, exploration, and simulation easy and accessible.
CRN models are one of the most common models in biology and take the form of networks of familiar chemical reactions such as A + B --> C; importantly, this modeling formalism is incredibly expressive and can represent many core biochemical processes such as transcription, translation, genetic regulation, metabolism, and transport between compartments.
The software tools introduced in this series allow for sophisticated models to be easily built (BioCRNpyler), simulated & parameterized (Bioscrape), and combined together into systems level models (SubSBML and Vivarium). These tools require only the most rudimentary scripting experience in python and no modeling or mathematical background will be assumed.
Each workshop will consist of a 45 minute lecture followed by a 45 minutes hands on tutorial in small breakout groups.
You must RSVP to attend this workshop and attendance will be capped at 30 people.
If you are interested in the topics but cannot attend, please let us know in the RSVP form as well in case we run this workshop again.
Core Organizers [the BioCRNpyler Team]: William Poole (Caltech), Ayush Pandey (Caltech), Andrey Shur (Caltech), and Zoltan Tuza (Imperial College London). The Vivarium Team [will take the lead on lecture 6]: Eran Agmon (Stanford) and Ryan Spangler (Currently Stanford, but soon the Allen Cell Institute) TAs: Sam Clamons (Caltech), Matthieu Kratz (Caltech), Manisha Kapasiawala (Caltech) & more TBA.
Each workshop will be on Thursday 8.30AM-10AM US Pacific time. Please double check time zones!
Syllabus
[Thr October 8th 8:30-10AM Pacific Time] An Introduction to Chemical Reaction Network Modeling:
this lecture will provide an overview of what a CRN model is, how they are simulated deterministically, and how to build simple models using BioCRNpyler. At the end of the lecture, CRN compilation will be introduced as a more efficient way to organize and build models. The workshop will provide hands-on experience building and simulating simple CRN models related to enzyme kinetics and metabolism.
[Thr October 15th 8:30-10AM Pacific Time] Chemical Reaction Network Compilation using BioCRNpyler:
this lecture will build on the idea of compiling CRNs from simple specifications with specific emphasis on building models of synthetic genetic circuits that include transcription, translation, and genetic regulation. The workshop will provide hands-on experience using BioCRNpyler to compare models of the same genetic regulatory network with different underlying assumptions about how transcription and translation function.
[Thr October 22nd 8:30-10AM Pacific Time] Systems with Multiple Compartments and Transport:
this lecture will introduce CRN models of transport and show how multiple compartments can be modeled and linked together in the CRN framework. The SubSBML package will be introduced as a tool for combining individual CRN models together to produce more complex systems level models across multiple compartments. The workshop will provide hands-on experience using SubSBML to combine multiple models together.
[Thr October 29th 8:30-10AM Pacific Time] Stochastic Simulation and Small Volume Effects:
this lecture will introduce stochastic simulation of CRNs and examine how small copy number, division, and volume effect CRN models using the Bioscrape Lineage package. Additionally, analysis of stochastic simulation data will be discussed. The workshop will provide hands-on experience building and analyzing stochastic models.
[Thr November 5th 8:30-10AM Pacific Time] Parameter Inference:
this lecture will give a brief overview of Bayesian parameter inference and how it can be used to find CRN parameters from data. The Bioscrape Inference package will be introduced as a useful tool parameterizing CRN models from diverse data sets. The workshop will provide hands-on experience using this package.
[Thr November 12th 8:30-10AM Pacific Time] Combining Diverse Models using Vivarium:
This workshop will give an introduction to the Vivarium software package which is a sophisticated framework to combine models together and conducting massive simulations. In the workshop, participants will have the opportunity to combine CRN models from previous tutorials in order to produce large systems level models.