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 Standard Articles 1 Publication describing the Software, including 1 Publication in zbMATH Year Bio-PEPA: A framework for the modelling and analysis of biological systems. Zbl 1173.68041Ciocchetta, Federica; Hillston, Jane 2009 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 all top 5 Referenced in 15 Serials 24 Theoretical Computer Science 4 Information and Computation 3 Natural Computing 3 Lecture Notes in Computer Science 2 Discrete Event Dynamic Systems 2 Statistical Applications in Genetics and Molecular Biology 2 Journal of Logical and Algebraic Methods in Programming 1 Applied Mathematics Letters 1 Computational Statistics 1 Applied Mathematical Modelling 1 Electronic Notes in Theoretical Computer Science 1 Logical Methods in Computer Science 1 Statistics and Computing 1 Methods in Molecular Biology 1 Journal of Membrane Computing all top 5 Referenced in 15 Fields 66 Computer science (68-XX) 65 Biology and other natural sciences (92-XX) 10 Probability theory and stochastic processes (60-XX) 6 Ordinary differential equations (34-XX) 4 General and overarching topics; collections (00-XX) 3 Mathematical logic and foundations (03-XX) 3 Numerical analysis (65-XX) 3 Systems theory; control (93-XX) 2 Commutative algebra (13-XX) 2 Partial differential equations (35-XX) 2 Statistics (62-XX) 1 Category theory; homological algebra (18-XX) 1 Mechanics of deformable solids (74-XX) 1 Fluid mechanics (76-XX) 1 Operations research, mathematical programming (90-XX) Referencing Publications by Year