Constructing and visualizing chemical reaction networks from pi-calculus models

Formal Aspects of Computing

Volumn 25, Issue 5, 2013, Pages 723-742

  John, Mathias ^a   Schulz, Hans Jörg ^b   Schumann, Heidrun ^c   Uhrmacher, Adelinde M ^c   Unger, Andrea ^d  

^a UNIV LILLE   (France)

^b GRAZ UNIVERSITY OF TECHNOLOGY   (Austria)

^c UNIVERSITY OF ROSTOCK   (Germany)

^d GFZ GERMAN RESEARCH CENTRE FOR GEOSCIENCES   (Germany)

Author keywords

graph visualization; pi calculus; reaction networks; stochastic modeling

Indexed keywords

BIOCHEMICAL SYSTEMS; CHEMICAL REACTION NETWORKS; GRAPH VISUALIZATION; NETWORK COMPLEXITY; NETWORK VISUALIZATION; PI CALCULUS; REACTION NETWORK; STATES AND TRANSITIONS;

BIOCHEMISTRY; CALCULATIONS; CHEMICAL REACTIONS; COMPLEX NETWORKS; COMPUTER SIMULATION; MARKOV PROCESSES; SEMANTICS; STOCHASTIC SYSTEMS; VISUALIZATION;

STOCHASTIC MODELS;

EID: 84883055425     PISSN: 09345043     EISSN: 1433299X     Source Type: Journal    
DOI: 10.1007/s00165-011-0209-0     Document Type: Article

References (36)

1. Bonchev D, Buck GA (2005) Quantitative measures of network complexity. In: Bonchev D, Rouvray DH (eds) Complexity in chemistry, biology, and ecology. Springer, Berlin, pp 191-235
2. Byrd D (1999) A scrollbar-based visualization for document navigation. In: DL'99: proceedings of the fourth ACM conference on Digital libraries, pp 122-129
3. Cardelli L (2004) Brane calculi - interactions of biological membranes. In: Computational methods in systems biology, international conference, CMSB'04. LNCS, pp 257-278
4. Cardelli L (2008) From processes to ODEs by chemistry. In: (eds) In: IFIP Theoretical Computer Science. Springer, Berlin, pp 261-281
5. Cardelli L (2008) On process rate semantics. Theor Comput Sci 391(3): 190-215
6. Cardelli L, Caron E, Gardner P, Kahramanogullari O, Phillips A (2009) A process model of rho GTP-binding proteins. Theor Comput Sci 410(33-34): 3166-3185
7. Dwyer T, Eades P (2002) Visualising a fund manager flow graph with columns and worms. In IV'02: proceedings of the 6th international conference on information visualisation, pp 147-152
8. Diehl S, Görg C (2002) Graphs, they are changing - dynamic graph drawing for a sequence of graphs. In: GD'02: proceedings of the 10th international symposium on graph drawing, pp 23-31
9. Dematté L, Priami C, Romanel A (2008) Modelling and simulation of biological processes in BlenX. Sigmetrics Perform Eval Rev 35(4):32-39, 2008.
10. Eick SG, Karr AF (2002) Visual scalability. J Comput Graph Stat 11(1): 22-43
11. Faeder JR, Hlavacek WS, Reischl I, Blinov ML, Metzger H, Redondo A, Wofsy C, Goldstein B (2003) Investigation of early events in fcεri-mediated signaling using a detailed mathematical model. J Immunol 170(7): 3769-3781
12. Gillespie DT (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81(25): 2340-2361
13. Hlavacek WS, Faeder JR, Blinov ML, Perelson AS, Goldstein B (2003) The complexity of complexes in signal transduction. Biotechnol Bioeng 84(7): 783-794
14. John M, Lhoussaine C, Niehren J (2009) Dynamic compartments in the imperative pi-calculus. In: Degano P, Gorrieri R (eds) Computational methods in systems biology, international conference, CMSB'09. Lecture Notes in Computer Sience, vol 5688. Springer, Berlin, pp 235-250
15. John M, Lhoussaine C, Niehren J, Uhrmacher AM (2008) The attributed pi calculus. In: (eds) In: Computational methods in systems biology, international conference, CMSB'08 Lecture Notes in Computer Science, vol 5307. Springer, Berlin, pp 83-102
16. John M, Lhoussaine C, Niehren J, Uhrmacher AM (2010) The attributed pi-calculus with priorities. In: Transactions on computaional systems biology XII. Special issue on modeling methodologies. LNCS (lecture notes in bioinformatics), vol 5945. Springer, Berlin, pp 13-76
17. John M, Lhoussaine C, Niehren J, Versari C (2011) Biochemical reaction rules with constraints. In: Proceedings of the European symposium on programming, pp 338-357
18. Kuttler C, Lhoussaine C, Niehren J (2007) A stochastic pi calculus for concurrent objects. In: Anai H, Horimoto K, Kutsia T (eds) Second international conference on algebraic biology. Lecture notes in computer science, vol 4545. pp 232-246
19. Kuttler C (2006) Simulating bacterial transcription and translation in a stochastic pi-calculus. In: Transactions on computational systems biology 4220/2006:113-149
20. Leye S, John M, Uhrmacher AM (2010) A flexible architecture for performance experiments with the pi-calculus and its extensions. In: Lawson B (ed) 3rd international ICST conference on simulation tools and techniques, ICST. ICST/IEEE, Malaga, spain
21. Meyer R, Gorrieri R (2009) On the relationship between π-calculus and finite place/transition petri nets. In: Bravetti M, Zavattaro G (eds) CONCUR - concurrency theory, 20th international conference, vol 5710 in Lecture Notes in Computer Science. Springer, Berlin, pp 463-480
22. Robin Milner. Communicating and Mobile Systems: the π-calculus. Cambridge University Press, 1999.
23. Mazemondet O, John M, Maus C, Uhrmacher AM, Rolfs A (2009) Integrating diverse reaction types into stochastic models - a signaling pathway case study in the imperative pi-calculus. In: Rossetti MD, Hill RR, Johansson B, Dunkin A, Ingalls RG (eds) Winter simulation conference, Institute of Electrical and Electronics Engineers, Inc., USA, pp 932-943
24. Phillips A, Cardelli L (2007) Efficient, correct simulation of biological processes in the stochastic pi-calculus. In: Calder M, Gilmore S (eds) Computational methods in systems biology, international conference, CMSB'07. Lecture Notes in Computer Science, vol 4695. Springer, Berlin, pp 184-199
25. Phillips A, Cardelli L, Castagna G (2006) A graphical representation for biological processes in the stochastic pi-calculus. Trans Comput Syst Biol 7: 123-152
26. Phillips A (2009) Some 3D videos of SPiM simulations. http://research.microsoft.com/en-us/projects/spim/default.aspx. Accessed 05 OCT 2009.
27. Priami C (1995) Stochastic π-calculus. In: Comput J 6: 578-589
28. Priami C, Regev A, Shapiro EY, Silverman W (2001) Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Inf Process Lett 80(1): 25-31
29. Rao R, Card SK (1994) The table lens: merging graphical and symbolic representations in an interactive focus+context visualization for tabular information. In: ACM SIGCHI'94: proceedings of the ACM SIGCHI conference on human factors in computing systems, pp 111-117
30. Regev A (2003) Computational systems biology: a calculus for biomolecular knowledge. PhD thesis, Tel Aviv University, Tel Aviv
31. Regev A, Panina EM, Silverman W, Cardelli L, Shapiro E (2004) BioAmbients: an abstraction for biological compartments. Theor Comput Sci 325(1): 141-167
32. Schulz H, John M, Unger A, Schumann H (2008) Visual analysis of bipartite biological networks. In: VCBM'08: proceedings of the eurographics workshop on visual computing for biomedicine, pp 135-142
33. Tominski C, Abello J, Schumann H (2009) CGV - an interactive graph visualization system. Comput Graph 33(6): 660-678
34. Tymchyshyn O, Kwiatkowska MZ (2008) Combining intra- and inter-cellular dynamics to investigate intestinal homeostasis. In: Formal methods in systems biology. First international workshop, FMSB 2008, pp 63-76
35. Versari C, Busi N (2008) Efficient stochastic simulation of biological systems with multiple variable volumes. Electron Notes Theor Comput Sci 194(3): 165-180
36. Versari C (2007) A core calculus for a comparative analysis of bio-inspired calculi. In: European symposium on programming (ESOP'07), pp 411-425