ASP for Construction and Validation of Regulatory Biological Networks

Rocca, Alexandre; Mobilia, Nicolas; Fanchon, Éric; Ribeiro, Tony; Trilling, Laurent; Inoue, Katsumi

doi:10.1002/9781119005223.ch5

Cited by 4 publications

(8 citation statements)

References 24 publications

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“…In this section, a short overview of Answer Set Programming (ASP) syntax and semantics is given (for an in-depth description see [ 28 – 30 ]). ASP is a form of declarative programming using logical semantics [ 29 ] which has been successfully applied to model biological networks [ 11 – 13 , 15 , 16 , 20 , 21 ]. An ASP program is a finite set of rules and looks very similar to a Prolog program.…”

Section: Preliminariesmentioning

confidence: 99%

“…Rocca et al [ 21 ] proposed two possible routes to validate biological networks using different methods. The first method discussed uses the Boolean method to validate the consistency of the networks.…”

Section: Related Workmentioning

confidence: 99%

“…An increasing number of references can be found in the literature with the successful application of ASP to model and reason over biological networks [ 12 , 15 – 21 ]. In comparison with other problem solving paradigms, the ASP declarative language is easy to model and does not require the development of sophisticated algorithms.…”

Section: Introductionmentioning

confidence: 99%

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Repairing Boolean logical models from time-series data using Answer Set Programming

Lemos

Lynce

Monteiro

2019

Algorithms Mol Biol

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BackgroundBoolean models of biological signalling-regulatory networks are increasingly used to formally describe and understand complex biological processes. These models may become inconsistent as new data become available and need to be repaired. In the past, the focus has been shed on the inference of (classes of) models given an interaction network and time-series data sets. However, repair of existing models against new data is still in its infancy, where the process is still manually performed and therefore slow and prone to errors.ResultsIn this work, we propose a method with an associated tool to suggest repairs over inconsistent Boolean models, based on a set of atomic repair operations. Answer Set Programming is used to encode the minimal repair problem as a combinatorial optimization problem. In particular, given an inconsistent model, the tool provides the minimal repairs that render the model capable of generating dynamics coherent with a (set of) time-series data set(s), considering either a synchronous or an asynchronous updating scheme.ConclusionsThe method was validated using known biological models from different species, as well as synthetic models obtained from randomly generated networks. We discuss the method’s limitations regarding each of the updating schemes and the considered minimization algorithm.Electronic supplementary materialThe online version of this article (10.1186/s13015-019-0145-8) contains supplementary material, which is available to authorized users.

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Section: Preliminariesmentioning

confidence: 99%

Section: Related Workmentioning

confidence: 99%

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Repairing Boolean logical models from time-series data using Answer Set Programming

Lemos

Lynce

Monteiro

2019

Algorithms Mol Biol

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“…If we execute the ASP program detailed above (lines [11][12][13][14][15][16][17], alongside with the description of the PH model given in Example 2 (lines 1-8), we obtain two answer sets that match the expected result:…”

Section: Example 3 (Fixed Points Enumeration)mentioning

confidence: 99%

“…However, the limitation of the method above is that the user has to decide upstream the number of computed steps that should be sufficient to reach all the goals. It is a main disadvantage which is shared for instance by the method proposed in [13]. One solution is then to use an incremental computation mode, which is especially tackled by the incremental solver of CLINGO [12].…”

Section: B Reachability Verificationmentioning

confidence: 99%

Exhaustive analysis of dynamical properties of Biological Regulatory Networks with Answer Set Programming

Abdallah

Folschette

Roux

et al. 2015

2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

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International audienceThe combination of numerous simple influences between the components of a Biological Regulatory Network (BRN) often leads to behaviors that cannot be grasped intuitively. They thus call for the development of proper mathematical methods to delineate their dynamical properties. As a consequence , formal methods and computer tools for the modeling and simulation of BRNs become essential. Our recently introduced discrete formalism called the Process Hitting (PH), a restriction of synchronous automata networks, is notably suitable to such study. In this paper, we propose a new logical approach to perform model-checking of dynamical properties of BRNs modeled in PH. Our work here focuses on state reachability properties on the one hand, and on the identification of fixed points on the other hand. The originality of our model-checking approach relies in the exhaustive enumeration of all possible simulations verifying the dynamical properties thanks to the use of Answer Set Programming

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