Pathway analysis for BioAmbients

Journal of Logic and Algebraic Programming

Volumn 77, Issue 1-2, 2008, Pages 92-130

  Pilegaard, Henrik ^a   Nielson, Flemming ^a   Nielson, Hanne Riis ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

BioAmbients; Control flow analysis; Data flow analysis; Flow logic; LDL degradation pathway; Monotone frameworks; Pathway analysis; Process calculus; Static analysis; Systems Biology

Indexed keywords

CHEMOTHERAPY; COMPUTER SOFTWARE; DRUG DELIVERY; DRUG DOSAGE; FORMAL LOGIC; STATIC ANALYSIS;

BIOAMBIENTS; BIOLOGICAL PROCESSING; CAUSAL CONSEQUENCES; CONTROL FLOW ANALYSIS; DATA FLOW ANALYSIS; DRUG DESIGNS; FLOW LOGIC; FORMAL MODELING; LDL DEGRADATION PATHWAY; MODEL DEVELOPMENT; MODEL VALIDATIONS; MONOTONE FRAMEWORKS; PATHWAY ANALYSIS; PROCESS CALCULUS; PROGRAMMING LANGUAGES; STATIC ANALYSIS TECHNIQUES; SYSTEMS BIOLOGY;

MODAL ANALYSIS;

EID: 49349098457     PISSN: 15678326     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jlap.2008.05.006     Document Type: Article

References (41)

1. Alberts B., Johnson A., Lewis J., Raff M., Roberts K., and Walter P. Molecular Biology of The Cell. fourth ed. (2002), Garland Science
2. Berry G., and Boudol G. The chemical abstract machine. POPL'90: Proceedings of the 17th ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages (1990), ACM Press, New York, NY, USA 81-94
3. Blossey R., Cardelli L., and Phillips A. A compositional approach to the stochastic dynamics of gene networks. Trans. Comput. Syst. Biol. 3939 (2006) 99-122
4. Calder M., Gilmore S., and Hillston J. Modelling the influence of RKIP on the ERK signalling pathway using the stochastic process algebra PEPA. Transactions on Computational Systems Biology VII. Lecture Notes in Computer Science vol. 4230 (2006), Springer 1-23
5. Cardelli L. Bioware languages. In: Herbert A., and Jones K.S. (Eds). Computer Systems: Theory, Technology, and Applications - A Tribute to Roger Needham. Monographs in Computer Science (2004), Springer 59-65
6. Cardelli L. Brane calculi. In: Danos V., and Schachter V. (Eds). Computational Methods in Systems Biology (CMSB'04). Lecture Notes in Computer Science vol. 3082 (2005), Springer 257-280
7. Cardelli L., and Gordon A.D. Mobile ambients. Theor. Comput. Sci. 240 1 (2000) 177-213
8. Chiaverini M., and Danos V. A core modeling language for the working molecular biologist. Proc. of CMSB'03. Lecture Notes in Computer Science vol. 2602 (2003), Springer 166
9. Clarke E.M., Grumberg O., and Peled D.A. Model Checking (2000), MIT Press
10. Danos V., and Laneve C. Core formal molecular biology. European Symposium on Programming (ESOP03). Lecture Notes in Computer Science vol. 2618 (2004), Springer
11. Danos V., and Laneve C. Formal molecular biology. Theor. Comput. Sci. 325 1 (2004) 69-110
12. Vincent Danos, Sylvain Pradalier. Projective brane calculus, in: Proceedings of Computational Methods in Systems Biology (CMSB'04), 2004.
13. Jagannathan S., and Weeks S. A unified treatment of flow analysis in higher-order languages. POPL'95: Proceedings of the 22nd ACM SIGPLAN-SIGACT symposium on Principles of programming languages (1995), ACM Press, New York, NY, USA 393-407
14. Kam N., Harel D., Kugler H., Marelly R., Pnueli A., Hubbard E.J.A., and Stern M.J. Formal modeling of c. elegans development: a scenario based approach. Proceedings of CMSB 2003. Lecture Notes in Computer Science vol. 2602 (2003), Springer 4-20
15. Kaneko K. Life: An Introduction to Complex Systems Biology (Understanding Complex Systems) (2006), Springer-Verlag New York, Inc., Secaucus, NJ, USA
16. Kitano H. Systems biology: a brief overview. Science 295 5560 (2002) 1662-1664
17. Céline Kuttler. Modeling bacterial gene expression in a stochastic pi-calculus with concurrent objects, PhD Thesis, University of Lille 1, 2007.
18. Levi F., and Sangiorgi D. Mobile safe ambients. ACM Transactions on Programming Languages and Systems (TOPLAS'03) 25 1 (2003) 1-69
19. Lodish H., Berk A., Zipursky S.L., Matsudaira P., Baltimore D., and Darnell J.E. Molecular Cell Biology. fourth ed. (1999), W.H. Freeman and Company Fig. 24 reprinted with the permission of the publisher
20. Milner R. Communication and Concurrency (1989), Prentice-Hall, Inc., Upper Saddle River, NJ, USA
21. Milner R. Communicating and Mobile Systems: The π-Calculus (1999), Cambridge University Press
22. Nielson F., and Nielson H.R. Flow Logic: a multi-paradigmatic approach to static analysis. The Essense of Computation: Complexity, Analysis, Transformation. Lecture Notes in Computer Science vol. 2566 (2002), Springer 223-244
23. Nielson F., Nielson H.R., and Hankin C. Principles of Program Analysis (1999), Springer
24. Nielson F., Nielson H.R., and Pilegaard H. What is a free name in a process algebra?. Inform. Process. Lett. 103 5 (2007) 188-194
25. Flemming Nielson, Hanne Riis Nielson, Corrado Priami, Debora S. da Rosa. Control flow analysis for BioAmbients, in: Proceedings of the First Workshop on Concurrent Models in Molecular Biology (BioConcur 2003), Electronic Notes in Theoretical Computer Science, vol. 180, 2007, pp. 65-79.
26. Nielson F., Nielson H.R., and Seidl H. A succinct solver for ALFP. Nordic J. Comput. 9 (2002) 335-372
27. Nielson F., Nielson H.R., Sun H., Buchholtz M., Hansen R.R., Pilegaard H., and Seidl H. The succinct solver suite. Tools and Algorithms for the Construction and Analysis of Systems (TACAS'04). Lecture Notes in Computer Science vol. 2988 (2004), Springer 251-265
28. Hanne Riis Nielson, Flemming Nielson, Infinitary control flow analysis: a collecting semantics for closure analysis, in: POPL'1997: Proceedings of the 24th ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages, 1997, pp. 332-345.
29. Nielson H.R., and Nielson F. Flow logics for constraint based analysis. The Seventh International Conference on Compiler Construction (CC'98). Lecture Notes in Computer Science vol. 1383 (1998), Springer 109-127
30. Nielson H.R., and Nielson F. Data flow analysis for CCS. In: Reps T., and Sagiv M. (Eds). Festschrift for Reinhard Wilhelm. Lecture Notes in Computer Science vol. 4444 (2006), Springer
31. Nielson H.R., and Nielson F. A monotone framework for CCS. Comput. Lang. Syst. Struct. (2008) (under revision)
32. Hanne Riis Nielson, Flemming Nielson, Henrik Pilegaard. Spatial analysis of BioAmbients, in: SAS'04 11th, Lecture Notes in Computer Science, vol. 3148, 2004, pp. 69-83.
33. Henrik Pilegaard, Language based techniques for systems biology, PhD Thesis, The Technical University of Denmark, 2007.
34. Pilegaard H., Nielson F., and Nielson H.R. Static analysis of a model of the LDL degradation pathway. In: Plotkin G.D. (Ed). Computational Methods in Systems Biology (CMSB'05) (2005), University of Edinburgh
35. Henrik Pilegaard, Flemming Nielson, Hanne Riis Nielson, Context dependent analysis of bioambients, in: Francesco Ranzato (Ed.), Proceedings of the 1st International Workshop on Emerging Applications of Abstract Interpretation, 2006.
36. Priami C., and Quaglia P. Beta binders for biological interactions. Computational Methods in Systems Biology (CMSB'04). Lecture Notes in Bioinformatics (2004), Springer
37. Priami C., Regev A., Shapiro E., and Silvermann W. Applications of a stochastic name-passing calculus to representation and simulation of molecular processes. Inform. Process. Lett. 80 1 (2001) 25-31
38. Aviv Regev, Computational systems biology: a calculus for biomolecular knowledge, PhD Thesis, Tel Aviv University, 2003.
39. Regev A., Panina E.M., Silverman W., Cardelli L., and Shapiro E. BioAmbients: an abstraction for biological compartments. Theor. Comput. Sci. 325 1 (2004) 141-167
40. Aviv Regev, William Silverman, Ehud Shapiro, Representation and simulation of biochemical processes using the π-calculus process algebra, in: Proceedings of Pacific Symposium on Biocomputing (PSB 2001), 2001, pp. 459-470.
41. Shivers O. Control flow analysis in scheme. PLDI'88: Proceedings of the ACM SIGPLAN 1988 Conference on Programming Language Design and Implementation (1988), ACM Press, New York, NY, USA 164-174