License: Creative Commons Attribution 4.0 International license (CC BY 4.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.DNA.27.10
URN: urn:nbn:de:0030-drops-146775
URL: https://drops.dagstuhl.de/opus/volltexte/2021/14677/
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Klinge, Titus H. ; Lathrop, James I. ; Osera, Peter-Michael ; Rogers, Allison

Reactamole: Functional Reactive Molecular Programming

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LIPIcs-DNA-27-10.pdf (1 MB)


Abstract

Chemical reaction networks (CRNs) are an important tool for molecular programming, a field that is rapidly expanding our ability to deploy computer programs into biological systems for a variety of applications. However, CRNs are also difficult to work with due to their massively parallel nature, leading to the need for higher-level languages that allow for easier computation with CRNs. Recently, research has been conducted into a variety of higher-level languages for deterministic CRNs but modeling CRN parallelism, managing error accumulation, and finding natural CRN representations are ongoing challenges.
We introduce Reactamole, a higher-level language for deterministic CRNs that utilizes the functional reactive programming (FRP) paradigm to represent CRNs as a reactive dataflow network. Reactamole equates a CRN with a functional reactive program, implementing the key primitives of the FRP paradigm directly as CRNs. The functional nature of Reactamole makes reasoning about molecular programs easier, and its strong static typing allows us to ensure that a CRN is well-formed by virtue of being well-typed. In this paper, we describe the design of Reactamole and how we use CRNs to represent the common datatypes and operations found in FRP. We also demonstrate the potential of this functional reactive approach to molecular programming by giving an extended example where a CRN is constructed using FRP to modulate and demodulate an amplitude modulated signal.

BibTeX - Entry

@InProceedings{klinge_et_al:LIPIcs.DNA.27.10,
  author =	{Klinge, Titus H. and Lathrop, James I. and Osera, Peter-Michael and Rogers, Allison},
  title =	{{Reactamole: Functional Reactive Molecular Programming}},
  booktitle =	{27th International Conference on DNA Computing and Molecular Programming (DNA 27)},
  pages =	{10:1--10:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-205-1},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{205},
  editor =	{Lakin, Matthew R. and \v{S}ulc, Petr},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/opus/volltexte/2021/14677},
  URN =		{urn:nbn:de:0030-drops-146775},
  doi =		{10.4230/LIPIcs.DNA.27.10},
  annote =	{Keywords: Chemical Reaction Network, Functional Reactive Programming, Domain Specific Language}
}

Keywords: Chemical Reaction Network, Functional Reactive Programming, Domain Specific Language
Collection: 27th International Conference on DNA Computing and Molecular Programming (DNA 27)
Issue Date: 2021
Date of publication: 08.09.2021
Supplementary Material: Software (Source Code): https://github.com/digMP/haskell-reactamole archived at: https://archive.softwareheritage.org/swh:1:dir:9f8a912be45038fedf03c9dd6bf74a6a20f29aff


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