DiffEqRxn : A Faster Way To Write Mass Action Kinetics!

• Installation
  • Via Github + Cabal.
  • Via Nix Flakes (Windows WSL, MacOS, Linux)
• A Single Source Of Truth
  • Defining a forwards chemical reaction.
  • Defining a reversible chemical reaction.
  • Moving forwards.
• Holes in the Model (void)
  • Chemicals From “Nowhere”
  • Rules for Using void
  • void behavior
  • Getting chemicals from the void
  • Moving chemicals into the void
• Non Linearity In The System (Macros)
  • Macros
  • Macro Limitations
• Computing Parameters
  • Implicit Parameters
  • Computed Parameters
• Exporting (CLI)
  • Exporting To Julia
  • The Export Subcommand
• Editor Support
  • Helix Editor

What is DiffEqRxn?

It’s a way to represent a mass action model textually and then export equivalent forms to typesetters and programming languages.

Why create DiffEqRxn?

Mass action kinetics have a lot of repetition and tediously updated equations. What’s more is that all of this work needs to be repeated multiple times across languages and typesetters and I have a couple of notable skill issues when writing them.

1. The amount of tedium means that often global variables sneak into the equations.

2. Copying the model into a language from a typeset definition often leads to a simple typo which subtley bugs the model with no immediate way to spot it.

3. It’s hard to see the dynamics of the system immediately just from the equations; while possible, I get lost in the sea of symbols that define the models.

4. Tedium leads to shortcuts

5. Computers do tedious things. Humans do creative things.

Use Cases.

This program was developed for use with systems biology where reactions are often expressed as a set of differential equations, and our use cases uses it for modeling circadian systems and light entrainment.