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Reactamole: Functional Reactive Molecular Programming

Authors Titus H. Klinge, James I. Lathrop, Peter-Michael Osera, Allison Rogers

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Author Details

Titus H. Klinge
  • Drake University, Des Moines, IA, USA
James I. Lathrop
  • Iowa State University, Ames, IA, USA
Peter-Michael Osera
  • Grinnell College, Grinnell, IA, USA
Allison Rogers
  • Grinnell College, Grinnell, IA, USA

Funding

  • Lathrop, James I.: This research was supported in part by NSF grants 1545028, 1900716, and 1909688.
  • Osera, Peter-Michael: This research was supported in part by NSF grants 1651817 and 2049911.

Acknowledgements

We thank the four anonymous reviewers for their feedback on this paper and Noah Susag for his contributions to the Reactamole code.

Cite AsGet BibTex

Titus H. Klinge, James I. Lathrop, Peter-Michael Osera, and Allison Rogers. Reactamole: Functional Reactive Molecular Programming. In 27th International Conference on DNA Computing and Molecular Programming (DNA 27). Leibniz International Proceedings in Informatics (LIPIcs), Volume 205, pp. 10:1-10:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
https://doi.org/10.4230/LIPIcs.DNA.27.10

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.

Subject Classification

ACM Subject Classification
  • Software and its engineering → Functional languages
  • Software and its engineering → Data flow languages
Keywords
  • Chemical Reaction Network
  • Functional Reactive Programming
  • Domain Specific Language

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References

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