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The Bio-PEPA Tool Suite

Federica Ciocchetta, Adam Duguid, Stephen Gilmore, Maria Luisa Guerriero, Jane Hillston
2009 2009 Sixth International Conference on the Quantitative Evaluation of Systems  
Stephen Gilmore and Maria Luisa Guerriero are supported by the EPSRC grant EP/E031439/1 "Stochastic Process Algebra for Biochemical Signalling Pathway Analysis".  ...  Acknowledgements: Jane Hillston is supported by the Engineering and Physical Sciences Research Council (EP-SRC) Advanced Research Fellowship and research grant EP/C543696/1 "Process Algebra Approaches  ...  The Bio-PEPA Workbench The Bio-PEPA Workbench is a lightweight modelling tool whose primary function is to compile Bio-PEPA models into other formats for analysis by a suite of other tools.  ... 
doi:10.1109/qest.2009.27 dblp:conf/qest/CiocchettaDGGH09 fatcat:rzsxvrnv45ftben3wvqu6i2svm

Design and development of software tools for Bio-PEPA

Adam Duguid, Stephen Gilmore, Maria Luisa Guerriero, Jane Hillston, Laurence Loewe
2009 Proceedings of the 2009 Winter Simulation Conference (WSC)  
This paper surveys the design of software tools for the Bio-PEPA process algebra.  ...  Further, by providing mappings to a range of different analysis tools the Bio-PEPA language allows modellers to compare analysis results which have been computed using independent numerical analysers,  ...  Laurence Loewe is supported by the Centre for Systems Biology at Edinburgh.  ... 
doi:10.1109/wsc.2009.5429725 dblp:conf/wsc/DuguidGGHL09 fatcat:vpmsziaa5zb4bkcswi42edkw5a

SBML for optimizing decision support's tools

Dalila Hamami, Baghdad Atmani
2013 arXiv   pre-print
In this paper, we present a new approach: the passage of an epidemic model realized in Bio-PEPA to a narrative language using the basics of SBML language.  ...  Many theoretical works and tools on epidemiological field reflect the emphasis on decision-making Tools by both public health and the scientific community, which continues to increase.  ...  Bio-PEPA (Biological Performance Evaluation of Process Algebras) Bio-PEPA is a tool, method and language based on process algebra.  ... 
arXiv:1311.3837v1 fatcat:jkohxc3zrrc53pcjchiaof7qva

VERIFICATION AND TESTING OF BIOLOGICAL MODELS

Allan Clark, Jane Hillston, Stephen Gilmore, Peter Kemper
2010 Proceedings of the 2010 Winter Simulation Conference  
Modern modeling environments like Bio-PEPA support both types of simulation within a single modeling formalism.  ...  In this paper, we describe relevant steps in the verification and testing of a TNFa-mediated NF-kB signal transduction pathway model and discuss to what extent automated techniques help a practitioner  ...  Stephen Gilmore and Jane Hillston are supported by the Centre for Systems Biology at Edinburgh.  ... 
doi:10.1109/wsc.2010.5679126 dblp:conf/wsc/ClarkHGK10 fatcat:ljexuf6wfzcjdjswczjla3vn24

PEPA'd Oysters: Converting Dynamic Energy Budget Models to Bio-PEPA, Illustrated by a Pacific Oyster Case Study

Erin Scott, Andrew Hoyle, Carron Shankland
2013 Electronical Notes in Theoretical Computer Science  
Experience with this specific model allows us to propose a generic scheme for translation between the widely-used DEB theory and Bio-PEPA.  ...  We present a Bio-PEPA (Biochemical-Performance Evaluation Process Algebra) computational model for the Pacific oyster, derived from a DEB (Dynamic Energy Budget) mathematical model.  ...  The authors thank the Bio-PEPA Plug-in development team at the University of Edinburgh, particularly Allan Clark, for help with the tool.  ... 
doi:10.1016/j.entcs.2013.07.014 fatcat:hzytaoiiuvhoncnat3cphvdpki

Analysing Robot Swarm Decision-Making with Bio-PEPA [chapter]

Mieke Massink, Manuele Brambilla, Diego Latella, Marco Dorigo, Mauro Birattari
2012 Lecture Notes in Computer Science  
Bio-PEPA is well suited for swarm robotics systems, because it lends itself well to modelling distributed scalable systems and their space-time characteristics.  ...  We demonstrate the validity of Bio-PEPA by modelling collective decision-making in a swarm robotics system and we evaluate the result of different analyses.  ...  Based on the Bio-PEPA syntax, the underlying ODE model can be generated automatically and in a systematic way [10] using the Bio-PEPA tool suite [4] .  ... 
doi:10.1007/978-3-642-32650-9_3 fatcat:7v6gpplxtvdrpnu3xrqt5zjnny

On the use of Bio-PEPA for modelling and analysing collective behaviours in swarm robotics

Mieke Massink, Manuele Brambilla, Diego Latella, Marco Dorigo, Mauro Birattari
2013 Swarm Intelligence  
Bio-PEPA is well suited for swarm robotics systems: by using Bio-PEPA it is possible to model distributed systems and their spacetime characteristics in a natural way.  ...  In this paper we analyse a swarm robotics system using Bio-PEPA. Bio-PEPA is a process algebra language originally developed to analyse biochemical systems.  ...  The Bio-PEPA tool suite relies on an implementation of Gillespie's stochastic simulation algorithm (Gillespie 1977) .  ... 
doi:10.1007/s11721-013-0079-6 fatcat:yofvrx2hu5fh5kyfi57fqnfpje

Stochastic Process Algebra and Stability Analysis of Collective Systems [chapter]

Luca Bortolussi, Diego Latella, Mieke Massink
2013 Lecture Notes in Computer Science  
We show how Stochastic Process Algebra (SPA) can be combined with numeric analysis tools for the analysis of emergent behavioural aspects of such systems.  ...  The analysis also shows some surprising aspects of the crowd model itself.  ...  This research has been partially funded by the EU-IP project ASCENS (nr. 257414), the EU-FET project QUANTICOL (nr. 600708) and the Italian MIUR-PRIN project CINA.  ... 
doi:10.1007/978-3-642-38493-6_1 fatcat:jpr5nm4r3jht7hyrrm7yold76i

A compartmental model of the cAMP/PKA/MAPK pathway in Bio-PEPA

Federica Ciocchetta, Adam Duguid, Maria Luisa Guerriero
2009 Electronic Proceedings in Theoretical Computer Science  
Here we present a Bio-PEPA compartmental model of the cAMP/PKA/MAPK pathway.  ...  We analyse the system using the Bio-PEPA Eclipse Plug-in and we show the correctness of our model by comparison with an existing ODE model.  ...  At the time of writing this paper, Federica Ciocchetta was a research fellow at the University of Edinburgh, supported by the EPSRC grant EP/C543696/1 "Process Algebra Approaches to Collective Dynamics  ... 
doi:10.4204/eptcs.11.5 fatcat:mblsnmskzvhivmsjaic6ibnn4a

From Simulated Model By Bio-Pepa to Narrative Language Through SBML

Dalila Hamami, Baghdad Atmani
2014 International Journal of Control Theory and Computer Modeling  
In this paper, we present a new approach consisting on the passage of an epidemic model realized in Bio-PEPA to a narrative language using the basics of SBML language.  ...  Many theoretical works and tools on epidemiological field reflect the emphasis on decision-making tools by both public health and the scientific community, which continues to increase.  ...  Bio-PEPA (Biological Performance Evaluation of Process Algebras) Bio-PEPA is a tool, method and language based on process algebra.  ... 
doi:10.5121/ijctcm.2014.4203 fatcat:q3phaxhyxrhqrphzsvsjm6ovcy

On verifying Bio-PEPA models

Allan Clark, Stephen Gilmore, Maria Luisa Guerriero, Peter Kemper
2010 Proceedings of the 8th International Conference on Computational Methods in Systems Biology - CMSB '10  
by the Bio-PEPA tool.  ...  In this paper, we discuss a variety of steps that contribute to this verification process, using the Bio-PEPA process algebra as a modelling language and describing the verification steps that are supported  ...  Stephen Gilmore and Maria Luisa Guerriero are supported by the Centre for Systems Biology at Edinburgh.  ... 
doi:10.1145/1839764.1839769 dblp:conf/cmsb/ClarkGGK10 fatcat:gwuchukhcfdhpdbdxozo4nfr3i

Scalable context-dependent analysis of emergency egress models

M. Massink, D. Latella, A. Bracciali, M. D. Harrison, J. Hillston
2011 Formal Aspects of Computing  
The design of such systems and the analysis of collective dynamic behaviour of people within them is a challenging problem.  ...  The proposed approach encompasses both the agent modelling viewpoint, as system behaviour emerges from specific (discrete) agent interaction, and the population viewpoint, when classes of homogeneous individuals  ...  the PEPA and Bio-PEPA tools and discussion on precursor models of the one here presented.  ... 
doi:10.1007/s00165-011-0188-1 fatcat:zcqefzjll5arhdxzlgaznqtdwq

Modelling Non-linear Crowd Dynamics in Bio-PEPA [chapter]

Mieke Massink, Diego Latella, Andrea Bracciali, Jane Hillston
2011 Lecture Notes in Computer Science  
We revisit this case study providing an elegant stochastic process algebraic model in Bio-PEPA amenable to several forms of analyses, among which simulation and fluid flow analysis.  ...  Emergent phenomena occur due to the pattern of non-linear and distributed local interactions between the elements of a system over time.  ...  The authors would like to thank Stephen Gilmore, Maria Luisa Guerriero, Allan Clark and Adam Duguid (University of Edinburgh) for their support with the Bio-PEPA plug-in, Richard Hayden and Jeremy Bradley  ... 
doi:10.1007/978-3-642-19811-3_8 fatcat:3qma2nvfjjh2rd76tfawm6nifi

Decision Support based on Bio-PEPA Modeling and Decision Tree Induction

Dalila Hamami, Atmani Baghdad, Carron Shankland
2017 International Journal of Information Systems in the Service Sector  
By using decision tree induction, the enhanced Bio-PEPA model shows considerable improvement over the initial model with regard to the simulated results matching observed data.  ...  In this paper, the authors propose an innovative structured approach combining decision tree induction with Bio-PEPA computational modelling, and illustrate the approach through application to tuberculosis  ...  By using Bio-PEPA modelling and simulation tools, we were able not only to validate the usefulness of extracting rules for the epidemiological study, but also to design the patterns which help to identify  ... 
doi:10.4018/ijisss.2017040104 fatcat:nm4w3eubdrelzhv4th3p2qbfvi

Probabilistic Programming Process Algebra [chapter]

Anastasis Georgoulas, Jane Hillston, Dimitrios Milios, Guido Sanguinetti
2014 Lecture Notes in Computer Science  
However, handling data and uncertainty in a statistically meaningful way is an open problem in formal modelling, severely hampering the usefulness of these elegant tools in many real world applications  ...  Formal modelling languages such as process algebras are widespread and effective tools in computational modelling.  ...  BB/I014713/1 and the European Research Council through grant MLCS306999.  ... 
doi:10.1007/978-3-319-10696-0_21 fatcat:vkqzg5d5dzafpoon73oi2xd4ze
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