27 research outputs found
Modular Verification of Biological Systems
Systems of interest in systems biology (such as metabolic pathways, signalling pathways and gene regulatory networks) often consist of a huge number of components interacting in different ways, thus exhibiting very complex behaviours. In biology, such behaviours are usually explored by means of simulation techniques applied to models defined on the basis of system observation and of hypotheses on its functioning.
Model checking has also been recently applied to the analysis of biological systems. This analysis technique typically relies on a state space representation whose size, unfortunately, makes the analysis often intractable for realistic models. A method for trying to avoid the state space explosion problem is to consider a decomposition of the system, and to apply a modular verification technique.
In particular, properties to be verified often concern only a small portion of the modelled system rather than the system as a whole. Hence, for each property it would be useful to be able to isolate a minimal fragment of the model that is necessary to verify such a property.
In this thesis we introduce a modular verification technique in which the system of interest is described by means of an automata-based formalism, called sync-programs, that supports modular construction. Our modular verification technique is based on results of Grumberg et al.~and on their application to the theory of concurrent systems proposed by Attie and Emerson. In particular, we adapt Attie and Emerson's approach to deal with biological systems by allowing automata to synchronise by performing transitions simultaneously.
Modular verification allows qualitative aspects of systems to be analysed with the guarantee that properties proved to hold in a suitable model fragment also hold in the whole model. The correctness of the verification technique is proved. The class of properties preserved is ACTL, the universal fragment of temporal logic CTL. The preservation holds only for positive answers and negative answers are not necessarily preserved.
In order to verify properties we use the NuSMV model checker, which is a well-established and efficient instrument. We provide a formal translation of sync-programs to simpler automata, which can be given as input to NuSMV. We prove the correspondence of the verification problems.
We show the application of our verification technique in some biological case studies. We compare the time required to verify the property on the whole model with the time needed to verify the same property by only considering those modules which are involved in the behaviour of the system related to the property.
In order to handle modelling and verification of more realistic biological scenarios, we propose also a dynamic version of our formalism. It allows entities to be created dynamically, in particular by other already running entities, as it often happens in biological systems. Moreover, multiple copies of the same entities can be present at the same time in a system. We show a correspondence of our model with Petri Nets. This has a consequence that tools developed for Petri Nets could be used also for dynamic sync-programs. Modular verification allows properties expressed as DACTL- formulae (dynamic version of ACTL-) to be verified on a portion of the model.
The results of analysis of the case study of the MAP kinase cascade activated by surface and internalised EGF receptors, which consists of 143 species and 80 reactions, suggest applicability and scalability of the approach.
The results raise the prospect of rendering tractable problems that are currently intractable in the verification of biological systems. In addition, we expect that the techniques developed in the thesis could be applied with profit not only to models of biological systems, but more generally to models of concurrent systems
Investigating modularity in the analysis of process algebra models of biochemical systems
Compositionality is a key feature of process algebras which is often cited as
one of their advantages as a modelling technique. It is certainly true that in
biochemical systems, as in many other systems, model construction is made
easier in a formalism which allows the problem to be tackled compositionally.
In this paper we consider the extent to which the compositional structure which
is inherent in process algebra models of biochemical systems can be exploited
during model solution. In essence this means using the compositional structure
to guide decomposed solution and analysis.
Unfortunately the dynamic behaviour of biochemical systems exhibits strong
interdependencies between the components of the model making decomposed
solution a difficult task. Nevertheless we believe that if such decomposition
based on process algebras could be established it would demonstrate substantial
benefits for systems biology modelling. In this paper we present our
preliminary investigations based on a case study of the pheromone pathway in
yeast, modelling in the stochastic process algebra Bio-PEPA
QUALITATIVE AND QUANTITATIVE FORMAL MODELING OF BIOLOGICAL SYSTEMS
Nella tesi si sviluppa un formalismo basato su riscrittura di termini e lo si propone come strumento per la descrizione di sistemi biologici. Tale formalismo, chiamato calculus of looping sequences (cls) consente di descrivere proteine, dna e membrane come termini, e interazioni tra questi elementi come regole di riscrittura.
Diverse varianti di cls sono studiate al fine di descrivere diversi aspetti dei sistemi biologici, inoltre vengono definite equivalenze sul comportamento dei sistemi (bisimulazioni) e una versione stocastica del formalismo che consente di sviluppare strumenti di simulazione
Hands-on Science: brightening our future
Light, either sunlight or coming from the moon or the stars, emitted by the fireflies or
the bulbs in our room or coming out of our TV screen, is not only one of the first main
vehicles of contact with the world around us but also adds beauty and fascination to
our lives. Blessing all of us, it is definitely one of the corner stones of the structure of
our modern world and crucial to its development. The book herein aims to contribute to an effective implementation of a sound
widespread scientific literacy and effective Science Education in our schools and at
all levels of society
Meta-stochastic simulation for systems and synthetic biology using classification
PhD ThesisTo comprehend the immense complexity that drives biological systems, it is necessary
to generate hypotheses of system behaviour. This is because one can observe the
results of a biological process and have knowledge of the molecular/genetic components,
but not directly witness biochemical interaction mechanisms. Hypotheses
can be tested in silico which is considerably cheaper and faster than “wet” lab trialand-
error experimentation. Bio-systems are traditionally modelled using ordinary
differential equations (ODEs). ODEs are generally suitable for the approximation of
a (test tube sized) in vitro system trajectory, but cannot account for inherent system
noise or discrete event behaviour. Most in vivo biochemical interactions occur within
small spatially compartmentalised units commonly known as cells, which are prone
to stochastic noise due to relatively low intracellular molecular populations.
Stochastic simulation algorithms (SSAs) provide an exact mechanistic account of the
temporal evolution of a bio-system, and can account for noise and discrete cellular
transcription and signalling behaviour. Whilst this reaction-by-reaction account of
system trajectory elucidates biological mechanisms more comprehensively than ODE
execution, it comes at increased computational expense. Scaling to the demands
of modern biology requires ever larger and more detailed models to be executed.
Scientists evaluating and engineering tissue-scale and bacterial colony sized biosystems
can be limited by the tractability of their computational hypothesis testing
techniques.
This thesis evaluates a hypothesised relationship between SSA computational performance
and biochemical model characteristics. This relationship leads to the possibility
of predicting the fastest SSA for an arbitrary model - a method that can provide
computational headroom for more complex models to be executed. The research
output of this thesis is realised as a software package for meta-stochastic simulation
called ssapredict. Ssapredict uses statistical classification to predict SSA performance,
and also provides high performance stochastic simulation implementations to the
wider community.Newcastle University & University of Nottingham Computing Science
department
Exploration of scalable industrial platforms for the commercial production of active molecules from microalgae cell walls
Food, nutraceutical, cosmeceutical, pharmaceutical and biomedical industries are putting significant effort into looking for new natural ingredients [1,2]. Microalgae have been recognised as potential sources of high-value chemicals, with most attention focused on antioxidants, pigments and specialty oils [3]. An under-exploited group of biochemicals produced by microalgae are extracellular polymeric substances (EPS) with hyaluronan (HA) representing one of them. Current industrial production methodologies for HA leave opportunities for the establishment of improved routes with higher molecular mass, enhanced biophysical properties, lower production costs and non-bacterial nor animal origins as key unique selling points. At present, incumbent platforms are either based upon Streptococcus spp. (pathogen) bacterial fermentation, modified (GM) Bacillus subtilis or derived from animal tissues.
Furthermore, the extraction of various economically exploitable cell components from microalgal biomass is at the core of a successful microalgal biorefinery approach, and it remains a current bottleneck for the economic feasibility of microalgal biotechnological processes [4]. Cell disruption is often required to break down the hard and complicated microalgal cell walls in order to retrieve microalgal constituents such as proteins, lipids, and polysaccharides. Viral enzymes may play a beneficial role in this scenario and might be used to facilitate genetic engineering by overcoming the cell wall barrier or for biorefinery purposes.
This project's hypothesis was that it was feasible for microalgae to produce HA. The objectives included investigating a stress-induced platform for the possible production of HA, learning how Chlorovirus/C. varibilis infection leads to HA formation, improving the HA production for the latter platform and looking into intriguing enzymes that can break down polysaccharides.
This PhD project focused on exploring, characterizing and developing new platforms in order to achieve profitable industrial production of valuable compounds from microalgae and identify viral enzymes that could help with the processing of Chlorella cells for multiple applications. Two platforms were successfully explored for the production of valuable polysaccharides, and multiple enzymes were identified, produced, characterised and evaluated for Chlorella cell wall digestion to enable possible biorefinery approaches of a non-domesticated Chlorella vulgaris strain
A novel approach to dynamic flux balance analysis that accounts for the dynamic transfer of information by internal metabolites
Understanding the dynamics of information feedback amongst components of complex biological systems is crucial to the success of engineering desirable metabolic phenotypes. Flux Balance Analysis (FBA) is a structural metabolic modelling procedure that allows for local topological constraints to be related to steady-state global behaviors of metabolic systems. A vast majority of biological systems of interest, such as microbial communities, however do not exist under steady-state conditions. Therefore, extending FBA methods to the dynamical setting has been a major challenge to metabolic modelling. In dynamic FBA (dFBA), the representation of feedback dynamics is made possible by combining the methods of FBA with those of Ordinary Differential Equations (ODE). Although numerous dFBA models have been constructed to date, very little effort has gone into the theoretical analysis of how static FBA models and dynamic ODE models should be combined in dFBA. To develop a better understanding of the mathematical structure of dFBA, we investigate the properties of FBA. In order to predict time-derivatives of population growth, every dFBA model must make the assumption that the underlying metabolic network modeled via FBA optimizes a phenotypic function of growth rate. We show however, that under certain circumstances, this requirement introduces a rigid correspondence between growth rate, and a related quantity, the growth yield. The consequence of this is that the dFBA models become rigid in its predictions, effectively becoming a near-static representation of metabolism. In this thesis, we show that this tight correspondence between yield and rate may be broken by combining two inversely related approaches to formulating the FBA problem
Classification and detection of Critical Transitions: from theory to data
From population collapses to cell-fate decision, critical phenomena are abundant in complex real-world systems. Among modelling theories to address them, the critical transitions framework gained traction for its purpose of determining classes of critical mechanisms and identifying generic indicators to detect and alert them (“early warning signals”). This thesis contributes to such research field by elucidating its relevance within the systems biology landscape, by providing a systematic classification of leading mechanisms for critical transitions, and by assessing the theoretical and empirical performance of early warning signals. The thesis thus bridges general results concerning the critical transitions field – possibly applicable to multidisciplinary contexts – and specific applications in biology and epidemiology, towards the development of sound risk monitoring system