Computational modeling, formal analysis, and tools for systems biology
E Bartocci, P Lió - PLoS computational biology, 2016 - journals.plos.org
As the amount of biological data in the public domain grows, so does the range of modeling
and analysis techniques employed in systems biology. In recent years, a number of …
and analysis techniques employed in systems biology. In recent years, a number of …
Biochemical systems theory: a review
EO Voit - International Scholarly Research Notices, 2013 - Wiley Online Library
Biochemical systems theory (BST) is the foundation for a set of analytical andmodeling tools
that facilitate the analysis of dynamic biological systems. This paper depicts major …
that facilitate the analysis of dynamic biological systems. This paper depicts major …
Robust satisfaction of temporal logic over real-valued signals
We consider temporal logic formulae specifying constraints in continuous time and space on
the behaviors of continuous and hybrid dynamical system admitting uncertain parameters …
the behaviors of continuous and hybrid dynamical system admitting uncertain parameters …
Petri nets for systems and synthetic biology
We give a description of a Petri net-based framework for modelling and analysing
biochemical pathways, which unifies the qualitative, stochastic and continuous paradigms …
biochemical pathways, which unifies the qualitative, stochastic and continuous paradigms …
A bayesian approach to model checking biological systems
Recently, there has been considerable interest in the use of Model Checking for Systems
Biology. Unfortunately, the state space of stochastic biological models is often too large for …
Biology. Unfortunately, the state space of stochastic biological models is often too large for …
Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project
M Hucka, A Finney, BJ Bornstein, SM Keating… - Systems biology, 2004 - IET
Biologists are increasingly recognising that computational modelling is crucial for making
sense of the vast quantities of complex experimental data that are now being collected. The …
sense of the vast quantities of complex experimental data that are now being collected. The …
Dizzy: stochastic simulation of large-scale genetic regulatory networks
We describe Dizzy, a software tool for stochastically and deterministically modeling the
spatially homogeneous kinetics of integrated large-scale genetic, metabolic, and signaling …
spatially homogeneous kinetics of integrated large-scale genetic, metabolic, and signaling …
A general computational method for robustness analysis with applications to synthetic gene networks
Motivation: Robustness is the capacity of a system to maintain a function in the face of
perturbations. It is essential for the correct functioning of natural and engineered biological …
perturbations. It is essential for the correct functioning of natural and engineered biological …
Robustness analysis and tuning of synthetic gene networks
Motivation: The goal of synthetic biology is to design and construct biological systems that
present a desired behavior. The construction of synthetic gene networks implementing …
present a desired behavior. The construction of synthetic gene networks implementing …
A unifying framework for modelling and analysing biochemical pathways using Petri nets
We give a description of a Petri net-based framework for modelling and analysing
biochemical pathways, which unifies the qualitative, stochastic and continuous paradigms …
biochemical pathways, which unifies the qualitative, stochastic and continuous paradigms …