Transactions on Computational Systems Biology XII
Special Issue on Modeling Methodologies
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78 Result(s)
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Open Access This content is freely available online to anyone, anywhere at any time.
Article
Snazer: the simulations and networks analyzer
Networks are widely recognized as key determinants of structure and function in systems that span the biological, physical, and social sciences. They are static pictures of the interactions among the component...
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Book
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Chapter
Modelling Self-assembly in BlenX
The process through which disordered components spontaneously arrange themselves into patterns is called self-assembly. Molecular self-assembly describes the process by which molecules adopt a defined arrangem...
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Chapter
Programming Biology in BlenX
We introduce a programming language called BlenX. It has been specifically designed and implemented to model and simulate biological systems and is strongly inspired to process calculi. We describe all the fea...
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Open Access This content is freely available online to anyone, anywhere at any time.
Article
Elucidation of functional consequences of signalling pathway interactions
A great deal of data has accumulated on signalling pathways. These large datasets are thought to contain much implicit information on their molecular structure, interaction and activity information, which prov...
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Open Access This content is freely available online to anyone, anywhere at any time.
Article
Narrative-based computational modelling of the Gp130/JAK/STAT signalling pathway
Appropriately formulated quantitative computational models can support researchers in understanding the dynamic behaviour of biological pathways and support hypothesis formulation and selection by "in silico" ...
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Book
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Chapter and Conference Paper
BlenX Static and Dynamic Semantics
We introduce a new programming language called BlenX. It is strongly inspired to process calculi and it is an evolution of Beta-binders. It has been specifically designed and implemented to model and simulate bio...
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Chapter
Process Calculi Abstractions for Biology
Several approaches have been proposed to model biological systems by means of the formal techniques and tools available in computer science. To mention just a few of them, some representations are inspired by ...
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Chapter and Conference Paper
BlenX4Bio – BlenX for Biologists
We introduce BlenX4Bio, a high-level interface for the programming language BlenX. BlenX4Bio allows biologists to write BlenX programs without having any programming skills. The main elements of a biological mode...
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Book and Conference Proceedings
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Book
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Chapter and Conference Paper
The BlenX Language: A Tutorial
This paper presents a new programming language, BlenX. BlenX is inspired to the process calculus Beta-binders and it is intended for modelling any system whose basic step of computation is an interaction between ...
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Book
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Chapter and Conference Paper
A Stochastic Semantics for BioAmbients
We consider BioAmbients, a calculus for specifying biological entities and for simulating and analysing their behaviour. We extend BioAmbients to take quantitative information into account by defining a stocha...
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Chapter
Computational Thinking in Biology
The paper presents a new approach based on process calculi to systems modeling suitable for biological systems. The main characteristic of process calculi is a linguistic description level to define incrementa...
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Chapter and Conference Paper
An Automated Translation from a Narrative Language for Biological Modelling into Process Algebra
The aim of this work is twofold. First, we propose an high level textual modelling language, which is meant to be biologically intuitive and hence easily usable by life scientists in modelling intra-cellular s...
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Chapter and Conference Paper
Modeling Static Biological Compartments with Beta-binders
We investigate the modeling of biological systems with static compartments through Beta-binders, a recently developed process calculus. Biological entities are represented as bio-processes and the calculus is ...
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Chapter and Conference Paper
A Formal and Integrated Framework to Simulate Evolution of Biological Pathways
This paper presents a formal approach to the study of evolution of biological pathways. The basic idea is to use the Beta Workbench to model and simulate pathway in connection with evolutionary algorithms to i...
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Book and Conference Proceedings
