References

  1. Yifei Bao, Adriana B. Compagnoni, Joseph Glavy & Tommy White (2010): Computational Modeling for the Activation Cycle of G-proteins by G-protein-coupled Receptors. In: MeCBIC'10, EPTCS 40, pp. 39–53. Available at http://dx.doi.org/10.4204/EPTCS.40.4.
  2. Ezio Bartocci, Flavio Corradini, Maria Rita Di Berardini, Emanuela Merelli & Luca Tesei (2010): Shape Calculus. A Spatial Mobile Calculus for 3D Shapes. Sci. Ann. Comp. Sci. 20, pp. 1–31. Available at http://www.info.uaic.ro/bin/Annals/Article?v=XX&a=0.
  3. Marco Bernardo & Roberto Gorrieri (1998): A tutorial on EMPA: A theory of concurrent processes with nondeterminism, priorities, probabilities and time. Theor. Comput. Sci. 202(1–2), pp. 1–54. Available at http://dx.doi.org/10.1016/S0304-3975(97)00127-8.
  4. F. Buti, D. Cacciagrano, F. Corradini, E. Merelli & L. Tesei (2010): BioShape: a spatial shape-based scale-independent simulation environment for biological systems. Procedia Computer Science 1(1), pp. 827–835. Available at http://dx.doi.org/10.1016/j.procs.2010.04.090.
  5. Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Ozan Kahramanoğulları & Andrew Phillips (2009): A process model of Rho GTP-binding proteins. Theor. Comput. Sci. 410(33), pp. 3166–3185. Available at http://dx.doi.org/10.1016/j.tcs.2009.04.029.
  6. Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Ozan Kahramanogullari & Andrew Phillips (2009): A Process Model of Actin Polymerisation. Electr. Notes Theor. Comput. Sci. 229(1), pp. 127–144. Available at http://dx.doi.org/10.1016/j.entcs.2009.02.009.
  7. Luca Cardelli & Philippa Gardner (2012): Processes in Space. Theor. Comput. Sci. 431, pp. 40–55. Available at http://dx.doi.org/10.1016/j.tcs.2011.12.051.
  8. Federica Ciocchetta & Jane Hillston (2009): Bio-PEPA: A framework for the modelling and analysis of biological systems. Theor. Comput. Sci. 410(33-34), pp. 3065–3084. Available at http://dx.doi.org/10.1016/j.tcs.2009.02.037.
  9. Adriana B. Compagnoni, Mariangiola Dezani-Ciancaglini, Paola Giannini, Karin Sauer, Vishakha Sharma & Angelo Troina (2012): Parallel BioScape: A Stochastic and Parallel Language for Mobile and Spatial Interactions. In: MeCBIC, pp. 101–106. Available at http://dx.doi.org/10.4204/EPTCS.100.7.
  10. Adriana B. Compagnoni, Vishakha Sharma, Yifei Bao, Matthew Libera, Svetlana Sukhishvili, Philippe Bidinger, Livio Bioglio & Eduardo Bonelli (2013): BioScape: A Modeling and Simulation Language for Bacteria-Materials Interactions. Electr. Notes Theor. Comput. Sci. 293, pp. 35–49. Available at http://dx.doi.org/10.1016/j.entcs.2013.02.017.
  11. Jane Hillston (2005): Process algebras for quantitative analysis. In: Logic in Computer Science, 2005. Proceedings. 20th Annual IEEE Symposium on. IEEE Computer Society, pp. 239–248. Available at http://dx.doi.org/10.1109/LICS.2005.35.
  12. Mathias John, Roland Ewald & Adelinde M. Uhrmacher (2008): A Spatial Extension to the π Calculus. ENTCS 194(3), pp. 133–148. Available at http://dx.doi.org/10.1016/j.entcs.2007.12.010.
  13. Damien Lacroix, Josep A Planell & Patrick J Prendergast (2009): Computer-aided design and finite-element modelling of biomaterial scaffolds for bone tisse engineering. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 367(1895), pp. 1993–2009. Available at http://dx.doi.org/10.1098/rsta.2009.0024.
  14. Vinod Mugathan, Andrew Phillips & Maria Vigliotti (2008): BAM: BioAmbient Machine. In: Application of Concurrency to System Design. IEEE Computer Society, pp. 45–49. Available at http://dx.doi.org/10.1109/ACSD.2008.4574594.
  15. Andrew Phillips & Luca Cardelli (2007): Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus. In: Computational Methods in Systems Biology, Lecture Notes in Computer Science 4695, pp. 184–199. Available at http://dx.doi.org/10.1007/978-3-540-75140-3_13.
  16. Corrado Priami (1995): Stochastic pi-Calculus. Comput. J. 38(7), pp. 578–589. Available at http://dx.doi.org/10.1093/comjnl/38.7.578.
  17. Corrado Priami, Aviv Regev, Ehud Y. Shapiro & William Silverman (2001): Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters 80(1), pp. 25–31. Available at http://dx.doi.org/10.1016/S0020-0190(01)00214-9.
  18. Vishakha Sharma, Adriana Compagnoni, Matthew Libera, Agnieszka K. Muszanska, Henk J. Busscher & Henny C. van der Mei (2013): Simulating Anti-adhesive and Antibacterial Bifunctional Polymers for Surface Coating Using BioScape. In: Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, BCB'13. ACM, pp. 613–613. Available at http://dx.doi.org/10.1145/2506583.2506646.
  19. Vishakha Sharma & Adriana B. Compagnoni (2013): Computational and mathematical models of the JAK-STAT signal transduction pathway. In: Agostino G. Bruzzone, Peter Kropf, Linda Ann Riley, Maryam Davoudpour & Adriano O. Solis: SummerSim. Society for Computer Simulation International / ACM DL, pp. 15. Available at http://dl.acm.org/citation.cfm?id=2557714.
  20. Jack R. Smith, Agnieszka Seyda, Norbert Weber, Doyle Knight, Sascha Abramson & Joachim Kohn (2004): Integration of Combinatorial Synthesis, Rapid Screening, and Computational Modeling in Biomaterials Development. Macromolecular Rapid Communications 25(1), pp. 127–140. Available at http://dx.doi.org/10.1002/marc.200300193.
  21. Kyriacos Zygourakis & Pauline A. Markenscoff (1996): Computer-aided design of bioerodible devices with optimal release characteristics: a cellular automata approach. Biomaterials 17(2), pp. 125–135. Available at http://dx.doi.org/10.1016/0142-9612(96)85757-7.

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