On Chemical Reaction Network Design by a Nested Evolution Algorithm

International audienceOne goal of synthetic biology is to implement useful functions with biochemical reactions, either by reprogramming living cells or programming artificial vesicles. In this perspective, we consider Chemical Reaction Networks (CRN) as a programming language, and investigate the CRN program synthesis problem. Recent work has shown that CRN interpreted by differential equations are Turing-complete and can be seen as analog computers where the molecular concentrations play the role of information carriers. Any real function that is computable by a Turing machine in arbitrary precision can thus be computed by a CRN over a finite set of molecular species. The proof of this result gives a numerical method to generate a finite CRN for implementing a real function presented as the solution of a Polynomial Initial Values Problem (PIVP). In this paper, we study an alternative method based on artificial evolution to build a CRN that approximates a real function given on finite sets of input values. We present a nested search algorithm that evolves the structure of the CRN and optimizes the kinetic parameters at each generation. We evaluate this algorithm on the Heaviside and Cosine functions both as functions of time and functions of input molecular species. We then compare the CRN obtained by artificial evolution both to the CRN generated by the numerical method from a PIVP definition of the function, and to the natural CRN found in the BioModels repository for switches and oscillators

Automatic Optimization of Python Skeletal Parallel Programs

International audienceSkeletal parallelism is a model of parallelism where parallel constructs are provided to the programmer as usual patterns of parallel algorithms. High-level skeleton libraries often offer a global view of programs instead of the common Single Program Multiple Data view in parallel programming. A program is written as a sequential program but operates on parallel data structures. Most of the time, skeletons on a parallel data structure have counterparts on a sequential data structure. For example, the map function that applies a given function to all the elements of a sequential collection (e.g., a list) has a map skeleton counterpart that applies a sequential function to all the elements of a distributed collection. Two of the challenges a programmer faces when using a skeleton library that provides a wide variety of skeletons are: which are the skeletons to use, and how to compose them? These design decisions may have a large impact on the performance of the parallel programs. However, skeletons, especially when they do not mutate the data structure they operate on, but are rather implemented as pure functions , possess algebraic properties that allow to transform compositions of skeletons into more efficient compositions of skeletons. In this paper, we present such an automatic transformation framework for the Python skeleton library PySke and evaluate it on several example applications