• Publications
  • Influence
Constraint Logic Programming
From the combination of knowledge and actions, someone can improve their skill and ability. It will lead them to live and work much better. This is why, the students, workers, or even employersExpand
  • 554
  • 21
  • PDF
BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge
TLDR
BIOCHAM provides tools and languages for describing protein networks with a simple and straightforward syntax, and for integrating biological properties into the model. Expand
  • 241
  • 17
  • PDF
Modelling and querying interaction networks in the biochemical abstract machine BIOCHAM
TLDR
We present a formal modelling environment for network biology, called the Biochemical Abstract Machine (BIOCHAM), which delivers precise semantics to biomolecular interaction maps. Expand
  • 164
  • 15
  • PDF
Linear Concurrent Constraint Programming: Operational and Phase Semantics
TLDR
In this paper we give a logical semantics for the class CC of concurrent constraint programming languages and for its extension LCC based on linear constraint systems. Expand
  • 72
  • 10
  • PDF
Machine Learning Biochemical Networks from Temporal Logic Properties
TLDR
We show how the temporal logic language can be turned into a specification language. Expand
  • 129
  • 7
  • PDF
The Biochemical Abstract Machine BIOCHAM
TLDR
In this article we present the Biochemical Abstract Machine BIOCHAM and advocate its use as a formal modeling environment for networks biology. Expand
  • 92
  • 7
  • PDF
Formal Cell Biology in Biocham
TLDR
We consider systems of biochemical reactions with kinetic expressions, as written in the Systems Biology Markup Language (SBML), and interpreted in the Biochemical Abstract Machine (Biocham) at different levels of abstraction, by either an asynchronous boolean transition system. Expand
  • 74
  • 4
  • PDF
Abstract interpretation and types for systems biology
TLDR
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. Expand
  • 71
  • 3
  • PDF
CLPGUI: A Generic Graphical User Interface for Constraint Logic Programming
TLDR
We propose CLPGUI, a generic graphical user interface for visualizing and controlling the execution of constraint logic programs. Expand
  • 31
  • 3
  • PDF
A general computational method for robustness analysis with applications to synthetic gene networks
TLDR
We propose a general definition of robustness that applies to any biological function expressible in temporal logic LTL (linear temporal logic), and to broad model classes and perturbation types. Expand
  • 102
  • 2
  • PDF