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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.