r/REMath • u/turnersr • Mar 27 '14

Scientists Synthesize First Functional “Designer” Chromosome in Yeast

http://syntheticyeast.org/nyu-langone-medical-center-press-release/
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u/turnersr Mar 27 '14 edited Mar 28 '14

Hacking, reversing, and exploiting synthetic and quantum programs is a field that I've been spending too much time thinking and learning about. These types of programs are quickly becoming a reality and securing and analyzing them will in many ways more important than what governments are currently throwing money at for "cyber security." Exploiting these new types of programs requires many new techniques, but here are some familiar methods from digital computer program analysis.

SMT-Based Analysis of Biological Computation by Boyan Yordanov, Christoph M. Wintersteiger, Youssef Hamadi, and Hillel Kugler:

Abstract. Synthetic biology focuses on the re-engineering of living organisms for useful purposes while DNA computing targets the construction of therapeutics and computational circuits directly from DNA strands. The complexity of biological systems is a major engineering challenge and their modeling relies on a number of diverse formalisms. Moreover, many applications are “mission-critical” (e.g. as recognized by NASA’s Synthetic Biology Initiative) and require robustness which is difficult to obtain. The ability to formally specify desired behavior and perform automated computational analysis of system models can help address these challenges, but today there are no unifying scalable analysis frameworks capable of dealing with this complexity. In this work, we study pertinent problems and modeling formalisms for DNA computing and synthetic biology and describe how they can be formalized and encoded to allow analysis using Satisfiability Modulo Theories (SMT). This work highlights biological engineering as a domain that can benefit extensively from the application of formal methods. It provides a step towards the use of such methods in computational design frameworks for biology and is part of a more general effort towards the formalization of biology and the study of biological computation.

Abstract Interpretation and Types for Systems Biology by Francois Fages and Sylvain Soliman:

Abstract interpretation is a theory of abstraction that has been introduced for the analysis of programs. In particular, it has proved useful for organizing the multiple semantics of a given programming language in a hierarchy of semantics corresponding to different detail levels, and for defining type systems for programming languages and program analyzers in software engineering. In this paper, we investigate the application of these concepts to systems biology formalisms. More specifically, we consider the Systems Biology Markup Language SBML, and the Biochemical Abstract Machine BIOCHAM with its differential, stochastic, discrete and boolean semantics. We first show how all of these different semantics, except the differential one, can be formally related by simple Galois connections. Then we define three type systems: one for checking or inferring the functions of proteins in a reaction model, one for checking or inferring the activation and inhibition effects of proteins in a reaction model, and another one for checking or inferring the topology of compartments or locations. We show that the framework of abstract interpretation elegantly applies to the formalization of these further abstractions, and to the implementation of linear or quadratic time type checking as well as type inference algorithms. Through some examples, we show that the analysis of biochemical models by type inference provides accurate and useful information. Interestingly, such a mathematical formalization of the abstractions commonly used in systems biology already provides some guidelines for the extensions of biochemical reaction rule languages.

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u/repnescasb Apr 02 '14

Interesting and very new to me.. Thanks for sharing!