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Bio-PEPA

swMATH ID: 1361
Software Authors: Federica Ciocchetta, Maria Luisa Guerriero, Vashti Galpin, Jane Hillston, Giulio Caravagna, Allan Clark, Andrea Degasperi, Adam Duguid, Kanimozhi Ellavarason, Stephen Gilmore, Laurence Loewe, Dimitrios Milios
Description: In this work we present Bio-PEPA, a process algebra for the modelling and the analysis of biochemical networks. It is a modification of PEPA, originally defined for the performanceanalysis of computer systems, in order to handle some features of biological models, suchas stoichiometry and the use of general kinetic laws. Bio-PEPA may be seen as an intermediate, formal, compositional representation of biological systems, on which different kindsof analysis can be carried out. Bio-PEPA is enriched with some notions of equivalence.Specifically, the isomorphism and strong bisimulation for PEPA have been considered andextended to our language. Finally, we show the translation of a biological model into thenew language and we report some analysis results.
Homepage: http://homepages.inf.ed.ac.uk/jeh/Bio-PEPA/biopepa.html
Programming Languages: Java
Operating Systems: Windows, Mac OS X, and Linux
Dependencies: Eclipse 3.5 Carbon version
Keywords: Process Algebras; Biochemical Networks; Modelling; Analysis
Related Software: PEPA; PRISM; BIOCHAM; BioNetGen; BlenX; LBS; Bio-PEPAd; SpiCO; COPASI; MRMC; BioModels; NFsim; PALOMA; ERODE; z3; ARACNE; KEGG; BioBayes; PARAM; PMTK
Referenced in: 91 Publications
Further Publications: http://homepages.inf.ed.ac.uk/jeh/Bio-PEPA/References.html
all top 5

Referenced by 156 Authors

8 Hillston, Jane
7 Calder, Muffy
7 Milazzo, Paolo
6 Bortolussi, Luca
6 Ciocchetta, Federica
6 Maggiolo-Schettini, Andrea
6 Tribastone, Mirco
4 Aderhold, Andrej
4 Degasperi, Andrea
4 Galpin, Vashti
4 Grzegorczyk, Marco
4 Husmeier, Dirk
4 Tschaikowski, Max
4 Vandin, Andrea
3 Barbuti, Roberto
3 Brim, Luboš
3 Caravagna, Giulio
3 Chiarugi, Davide
3 Ciobanu, Gabriel
3 Falaschi, Moreno
3 Merelli, Emanuela
3 Olarte, Carlos
3 Pardini, Giovanni
3 Priami, Corrado
3 Šafránek, David
2 Angius, Alessio
2 Back, Ralph-Johan
2 Boreale, Michele
2 Cardelli, Luca
2 Ding, Jie
2 Hermith, Diana
2 Horváth, András
2 Júlvez, Jorge
2 Kwiatkowska, Marta Z.
2 Lhoussaine, Cédric
2 Lin, Zhigui
2 Loreti, Michele
2 Petre, Ion
2 Piazza, Carla
2 Šalagovič, Jakub
2 Sanguinetti, Guido
2 Tini, Simone
2 Troina, Angelo
2 Troják, Matej
2 Uhrmacher, Adelinde M.
1 Aman, Bogdan
1 Andrei, Oana
1 Andronikos, Theodore
1 Antoniotti, Marco
1 Baier, Christel
1 Balbo, Gianfranco
1 Ballarini, Paolo
1 Barbot, Benoît
1 Bartocci, Ezio
1 Beccuti, Marco
1 Benkirane, Soufiene
1 Bibbona, Enrico
1 Breitling, Rainer
1 Busi, Nadia
1 Buti, Federico
1 Cacciagrano, Diletta Romana
1 Cannata, Nicola
1 Casagrande, Alberto
1 Castiglioni, Valentina
1 Červený, Jan
1 Češka, Milan
1 Colvin, Robert J.
1 Coppo, Mario
1 Corradini, Flavio
1 Credi, A.
1 Damiani, Ferruccio
1 de Alfaro, Luca
1 de Vink, Erik P.
1 Děd, T.
1 Del Tedesco, Filippo
1 Donaldson, Robin A.
1 d’Onofrio, Alberto
1 Drábik, Peter
1 Drocco, Maurizio
1 Forejt, Vojtěch
1 Garavelli, Marco
1 Gast, Nicolas
1 Giannakis, Konstantinos
1 Gilbert, David
1 Gori, Roberta
1 Grassi, Elena
1 Gu, Hong
1 Guerriero, Maria Luisa
1 Hagihara, Shigeki
1 Heiner, Monika
1 Henzinger, Thomas A.
1 Hsu, David Y.
1 Huynh-Thu, Vân Anh
1 Iacobelli, Giulio
1 Ichinose, Takuma
1 Ito, Sohei
1 Izumi, Naoko
1 Jobstmann, Barbara
1 John, Mathias
1 Klement, M.
...and 56 more Authors

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