Biochemical reaction networks are one of the most widely used formalism in systems biology to describe the molecular mechanisms of high-level cell processes. However modellers also reason with influence diagrams to represent the positive and negative influences between molecular species and may find an influence network useful in the process of building a reaction network. In this paper, we introduce a formalism of influence networks with forces, and equip it with a hierarchy of Boolean, Petri net, stochastic and differential semantics, similarly to reaction networks with rates […]
Sat, Dec 1, 2018
In Systems Biology, modelers develop more and more reaction-based models to describe the mechanistic biochemical reactions underlying cell processes. They may also work, however, with a simpler formalism of influence graphs, to merely describe the positive and negative influences between molecular species. The first approach is promoted by reaction model exchange formats such as SBML, and tools like CellDesigner, while the second is supported by other tools that have been historically developed to reason about boolean gene regulatory networks […]
Thu, Sep 1, 2016
Fri, Apr 1, 2016
Constraint programming is traditionally viewed as the combination of two components: a constraint model and a search procedure. In this paper we show that tree search procedures can be fully inter-nalized in the constraint model with a fixed enumeration strategy. This approach has several advantages: 1) it makes search strategies declarative, and modeled as constraint satisfaction problems; 2) it makes it possible to express search strategies in existing front-end modeling languages supporting reified constraints without any extension ; 3) it opens up constraint propagation algorithms to search constraints and to the implementation of novel search procedures based on constraint propagation […]
Wed, Jul 1, 2015
In this paper we study the problem of deciding the existence of a subgraph epimorphism between two graphs. Our interest in this variant of graph matching problem stems from the study of model reductions in systems biology, where large systems of biochemical reactions can be naturally represented by bipartite digraphs of species and reactions. In this setting, model reduction can be formalized as the existence of a sequence of vertex deletion and merge operations that transforms a first reaction graph into a second graph […]
Wed, Jan 1, 2014
Mon, Oct 1, 2012
Petri-nets are a simple formalism for modeling concurrent computation. Recently, they have emerged as a powerful tool for the modeling and analysis of biochemical reaction networks, bridging the gap between purely qualitative and quantitative models. These networks can be large and complex, which makes their study difficult and computationally challenging […]
Tue, May 1, 2012