10 Result(s)
within
Federica Ciocchetta
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Chapter
A Hierarchy of Networks Spanning from Individual Organisms to Ecological Landscapes
Living systems are hierarchically organised. A number of components are linked by the multiplicity of interactions at each level (from organisms to species to ecosystems). This kind of compositional and hierar...
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Chapter
Modelling and Analysis of the NF-κB Pathway in Bio-PEPA
In this work we present a Bio-PEPA model describing the Nuclear Factor κB (NF-κB) signalling pathway. In particular our model focuses on the dynamic response of NF-κB to an external stimulus. Each biochemical spe...
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Chapter and Conference Paper
Modelling Biological Clocks with Bio-PEPA: Stochasticity and Robustness for the Neurospora crassa Circadian Network
Circadian clocks are biochemical networks, present in nearly all living organisms, whose function is to regulate the expression of specific mRNAs and proteins to synchronise rhythms of metabolism, physiology a...
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Chapter
Bio-PEPA with Events
In this work we present an extension of Bio-PEPA, a language recently defined for the modelling and analysis of biochemical systems, to handle events. Events are constructs that represent changes in the system du...
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Chapter and Conference Paper
Integrated Analysis from Abstract Stochastic Process Algebra Models
Bio-PEPA is a novel stochastic process algebra which has been recently developed for modelling biochemical pathways [5,6]. In Bio-PEPA a reagent-centric style of modelling is adopted, and a variety of analysis...
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Chapter and Conference Paper
Process Algebras in Systems Biology
In this chapter we introduce process algebras, a class of formal modelling techniques developed in theoretical computer science, and discuss their use within systems biology. These formalisms have a number of ...
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Chapter and Conference Paper
The BlenX Language with Biological Transactions
An extension of the BlenX language with biological transactions, called TBlenX, is presented. The aim of this extension is to model a sequence of elementary actions as if it were atomic. This extension is useful ...
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Chapter and Conference Paper
Modelling Yeast Pre-rRNA Processing
In this paper we present a quantified model concerning the synthesis of pre-rRNAs. The chemical kinetics simulation software Dizzy has been chosen as both the modelling and simulation framework of our study. W...
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Chapter and Conference Paper
Modeling Kohn Interaction Maps with Beta-Binders: An Example
We represent a subset of the mammalian cell cycle Kohn interaction map using Beta-binders, a formalism inspired to the pi-calculus and enriched with binders that allow the description of enclosing surfaces equ...
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Chapter and Conference Paper
Combining Supervised and Unsupervised Methods to Support Early Diagnosis of Hepatocellular Carcinoma
The early diagnosis of Hepatocellular Carcinoma (HCC) is extremely important for effective treatment and improvements in diagnosis are indispensable, particularly concerning the differentiation between “early”...
