Reactamole: A Functional Reactive Molecular Programming DSL

Reactamole is a domain-specific language for molecular programming that utilizes reactive functional programming principles. Reactamole observes a direct correspondence between signal functions in a reactive functional program (FRP) and chemical reaction networks (CRNs) in a molecular program. This correspondence allows us to directly translate the core combinators of (arrowized) FRP to CRNs. Because Reactamole is embedded in the Haskell programming language, takes advantage of Haskell's rich type system to ensure the well-formedness of the resulting chemical reaction networks.

Installation

Reactamole is implemented as a Haskell Stack project and as such requires a Haskell toolchain (namely stack) to build and run.

1. Download ghcup (https://www.haskell.org/ghcup) to install Haskell and its toolchain.
2. stack build to build the project.
3. stack repl to run Reactamole in GHCi.
4. stack haddock --haddock-arguments "-o docs" to build API documentation (deposited in /docs).

The included Makefile also includes shortcuts for these commands if you are unfamiliar with working within the Haskell ecosystem.

Running Examples

The Bio.Reactamole.Examples module contains a number of example molecular programs for you to explore. You can use the functions from Bio.Reactamole.Export to export these Reactamole programs as ODEs or collections of reactions. Here is an example of their usage:

$> stack repl
...
GHCi, version 8.8.4: https://www.haskell.org/ghc/  :? for help
...
Ok, 10 modules loaded.
Loaded GHCi configuration from /private/var/folders/rj/4hpzks9x6m3bvbdbvqbs3ndm0000gn/T/haskell-stack-ghci/38c8115e/ghci-script
λ> import Bio.Reactamole
λ> import Bio.Reactamole.Examples
λ> :t srLatch
srLatch :: CRN (Bool, Bool) (Bool, Bool)
λ> toIVP srLatch
INPUT:
  Tuple(Bool(x0, x1), Bool(x2, x3))

OUTPUT:
  Tuple(Bool(x4, x5), Bool(x6, x7))

EQUATIONS:
  dx4/dt = [-1.0e-2*x0*x4*x6,+1.0e-2*x1*x5,+3.0e-2*x4^2*x5,-3.0e-2*x4*x5^2,+1.0e-2*x5*x7]
  dx5/dt = [+1.0e-2*x0*x4*x6,-1.0e-2*x1*x5,-3.0e-2*x4^2*x5,+3.0e-2*x4*x5^2,-1.0e-2*x5*x7]
  dx6/dt = [-1.0e-2*x2*x4*x6,+1.0e-2*x3*x7,+1.0e-2*x5*x7,+3.0e-2*x6^2*x7,-3.0e-2*x6*x7^2]
  dx7/dt = [+1.0e-2*x2*x4*x6,-1.0e-2*x3*x7,-1.0e-2*x5*x7,-3.0e-2*x6^2*x7,+3.0e-2*x6*x7^2]

INITIAL CONDITIONS:
  x4(0) = 0.0
  x5(0) = 1.0
  x6(0) = 0.0
  x7(0) = 1.0

λ> toRxns srLatch
INPUT:
  Tuple(Bool(x0, x1), Bool(x2, x3))

OUTPUT:
  Tuple(Bool(x4, x5), Bool(x6, x7))

REACTIONS:
  x0 + x4 + x6 --{1.0e-2}-> x0 + x6 + x5
  x1 + x5 --{1.0e-2}-> x1 + x4
  x2 + x4 + x6 --{1.0e-2}-> x2 + x4 + x7
  x3 + x7 --{1.0e-2}-> x3 + x6
  x4 + x4 + x5 --{3.0e-2}-> x4 + x4 + x4
  x4 + x5 + x5 --{3.0e-2}-> x5 + x5 + x5
  x5 + x7 --{1.0e-2}-> x4 + x6
  x6 + x6 + x7 --{3.0e-2}-> x6 + x6 + x6
  x6 + x7 + x7 --{3.0e-2}-> x7 + x7 + x7

INITIAL CONDITIONS:
  x4(0) = 0.0
  x5(0) = 1.0
  x6(0) = 0.0
  x7(0) = 1.0

Publication

Titus H. Klinge, James I. Lathrop, Peter-Michael Osera, and Allison Rogers. Reactamole: Functional Reactive Molecular Programming. 27th International Conference on DNA Computing and Molecular Programming (DNA '27). September, 2021, Oxford, UK.