The κ-Lattice: Decidability Boundaries for Qualitative Analysis in Biological Languages

Delzanno, Giorgio; Giusto, Cinzia Di; Gabbrielli, Maurizio; Laneve, Cosimo; Zavattaro, Gianluigi

doi:10.1007/978-3-642-03845-7_11

Cited by 16 publications

(14 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In general, as the Kappacalculus is Turing complete, the problem of checking whether a Kappa model can generate only finitely many complexes is undecidable. Nevertheless, there are fragments of Kappa for which this problem turns out to be decidable [16], and also techniques -based on abstract interpretation-which are capable of computing an over-approximation of the set of reachable complexes [12] that can be used to prove, in some cases, that this set is finite.…”

Section: Resultsmentioning

confidence: 99%

“…We will discuss in the Conclusions that, despite in Kappa the problem of checking finiteness of the generable complexes is undecidable, there are interesting fragments of Kappa in which this problem is decidable [16] and abstract interpretation techniques that over-approximate the set of all possible complexes [12].…”

Section: Definition 9 (Chemical Reaction Network)mentioning

confidence: 99%

See 1 more Smart Citation

Complex Functional Rates in Rule-Based Languages for Biochemistry

Versari

Zavattaro

2012

Lecture Notes in Computer Science

Self Cite

View full text Add to dashboard Cite

Rule-based languages (like, for example, Kappa, BioNetGen, and BioCham) have emerged as successful models for the representation, analysis, and simulation of bio-chemical systems. In particular Kappa, although based on reactions, differs from traditional chemistry as it allows for a graph-like representation of complexes. It follows the "don't care, don't write" approach: a rule contains the description of only those parts of the complexes that are actually involved in a reaction. Hence, given any possible combination of complexes that contain the reactants, such complexes can give rise to the reaction. In this paper we address the problem of extending the "don't care, don't write" approach to cases in which the actual structure of the complexes involved in the reaction could affect it (for instance, the mass of the complexes could influence the rate). The solutions that we propose is κF , an extension of the Kappa-calculus in which rates are defined as functions of the actually involved complexes.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Definition 9 (Chemical Reaction Network)mentioning

confidence: 99%

Complex Functional Rates in Rule-Based Languages for Biochemistry

Versari

Zavattaro

2012

Lecture Notes in Computer Science

Self Cite

View full text Add to dashboard Cite

show abstract

“…In principle the ideas presented and further directions are clearly expressible and testable in Maude or another tool for implementing term rewriting systems, or the kappa-calculus [26,31,40,44]. Recent work involves programming a blob simulator, and execution visualiser.…”

Section: What Can Be Done In the Blob World?mentioning

confidence: 99%

“…We take a very simplified view of a (macro-)molecule and its interactions, with abstraction level similar to the Kappa model [40,26,44]. To avoid misleading de-tail questions about real molecules we use the generic term "blob" for an abstract molecule.…”

Section: The Blob Model Of Programmed Universal Computationmentioning

confidence: 99%

Computational Biology: A Programming Perspective

Hartmann

Jones

Simonsen

et al. 2011

Formal Modeling: Actors, Open Systems, Biological Systems

View full text Add to dashboard Cite

Abstract. Computation via biological devices has been the subject of close scrutiny since von Neumann's early work some 60 years ago. In spite of the many relevant works in this field, the notion of programming biological devices seems to be, at best, ill-defined. While many devices are claimed or proved to be computationally universal in some sense, the full step to a bona fide programming language is rarely taken, and one question is noticeable by its absence: If the device is universal, where are the programs?We begin with an extensive review of the literature on programmingrelated biocomputing; and briefly identify some strengths and shortcomings from a programming perspective. To show concretely what one could see as programming in biocomputing, we outline (from recent work) a computation model and a small programming language that are biologically more plausible than existing silicon-inspired models. Whether or not the model is biologically plausible in an absolute sense, we believe it sets a standard for a biological device that can be both universal and programmable. ContextThe terms "biocomputing" and "systems biology", taken in their broadest senses, span many fields and areas of research: biology, chemistry, physics, mathematics, electrical engineering and computer science among others. Two major subareas:-Computer modeling of biological and biomolecular processes -Biological hardware for computationThe terms "biomolecular computation" and "biomolecular computational model" occur with both meanings in the literature (see Section 4), sometimes referring to the one and sometimes the other subarea. This paper emphasises the second. More precisely: we take a synthetic viewpoint, concerned with building things as in the engineering and computer sciences. This is in contrast to the inevitable and ubiquitous analytic viewpoint common to the natural sciences, concerned with finding out how naturally evolved things work. We ask: What can be done or built or constructed; and not: how does nature work? (Caveat: just as in engineering, one will need to understand nature's cause-and-effect sufficiently well to be able to modulate it, i.e., to use nature to effectively serve our purposes.) A Theme: Biological Problem-SolvingOur main aim is thus to use the biological world as a computational medium. From a programming perspective, the main goal is problem-solving by writing programs. This section thus refers to solving problems by biology, not solving problems about biology or in biology.Given: a computational problem. To find: a biological solution. Further, problem-solving by a program means finding a general solution (and not just one run of one algorithm on one input data instance).A top-down approach is to devise a model of computation that -satisfies requirements for computer science/engineering -that could conceivably be realised in a biological medium -in which programs are clearly visible, and programming can be done -is a framework in which it is possible, at least in principle, to say when a problem has be...

show abstract

“…Parameterized verification of combinations of automata-and graph-based models of distributed systems has been studied, e.g. in [10,4,15,16,13,12]. In [5] we applied graphbased transformations to model intermediate evaluations of non-atomic mutual exclusion protocols with universally quantified conditions.…”

Section: Conclusion and Related Workmentioning

confidence: 99%

Parameterized Verification of Graph Transformation Systems with Whole Neighbourhood Operations

Delzanno

Stückrath

2014

Lecture Notes in Computer Science

Self Cite

View full text Add to dashboard Cite

We introduce a new class of graph transformation systems in which rewrite rules can be guarded by universally quantified conditions on the neighbourhood of nodes. These conditions are defined via special graph patterns which may be transformed by the rule as well. For the new class for graph rewrite rules, we provide a symbolic procedure working on minimal representations of upward closed sets of configurations. We prove correctness and effectiveness of the procedure by a categorical presentation of rewrite rules as well as the involved order, and using results for well-structured transition systems. We apply the resulting procedure to the analysis of the Distributed Dining Philosophers protocol on an arbitrary network structure.

show abstract

The κ-Lattice: Decidability Boundaries for Qualitative Analysis in Biological Languages

Cited by 16 publications

References 35 publications

Complex Functional Rates in Rule-Based Languages for Biochemistry

Complex Functional Rates in Rule-Based Languages for Biochemistry

Computational Biology: A Programming Perspective

Parameterized Verification of Graph Transformation Systems with Whole Neighbourhood Operations

Contact Info

Product

Resources

About