Graphs for core molecular biology

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 2602, Issue , 2003, Pages 34-46

  Danos, Vincent ^a   Laneve, Cosimo ^b  

^a UNIVERSITÉ PARIS DESCARTES   (France)

^b UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMINERALIZATION; COMPUTATIONAL LINGUISTICS; MODELING LANGUAGES; MOLECULAR BIOLOGY;

AS GRAPH; DOMAIN LEVELS; INTERMEDIATE LANGUAGES; LEVEL GRAPHS; MODEL PROTEINS; OBSERVATIONAL EQUIVALENCES;

CALCULATIONS;

EID: 84958593772     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/3-540-36481-1_4     Document Type: Conference Paper

References (16)

1. [1] Gérard Berry and Gérard Boudol. The chemical abstract machine. Theoretical Computer Science, 96:217–248, 1992. 35
2. A. Bouali, S. Gnesi, and S. Larosa. JACK: Just another concurrency kit. Bulletin of the European Association for Theoretical Computer Science, 54:207–224, October 1994. Technical Contributions. 35
3. [3] Marc Chiaverini and Vincent Danos. A core modeling language for the working molecular biologist. Communication to the International Workshop on Computational Methods in Systems Biology, 2003. 34
4. [4] Vincent Danos and Cosimo Laneve. Core formal molecular biology. To appear in Proceedings of ESOP 2003 - European Symposium on Programming, Lecture Notes in Computer Science, Springer Verlag, 2003. 34, 38
5. [5] Reinhard Diestel. Graph Theory. Springer, New-York, 2000. 41
6. [6] Steven Eker, Merrill Knapp, Keith Laderoute, Patrick Lincoln, José Meseguer, and Kemal Sonmez. Pathway logic: Symbolic analysis of biological signaling. In Proceedings of the Pacific Symposium on Biocomputing, pages 400–412, January 2002. To appear. 35
7. [7] Cédric Fournet and Georges Gonthier. The reflexive chemical abstract machine and the join-calculus. In 23rd ACM Symposium on Principles of Programming Languages (POPL’96), 1996. 34, 35
8. [8] Kurt W. Kohn. Molecular interaction map of the mammalian cell cycle control and DNA repair systems. Molecular Biology of the Cell, n. 10:2703–2734, 1999. 34
9. [9] H. Lin. An interactive proof tool for process algebras. In Alain Finkel and Matthias Jantzen, editors, Proceedings of Symposion on Theoretical Aspects of Computer Science (STACS’92), volume 577 of LNCS, pages 617–618, Berlin, Germany, February 1992. Springer. 35
10. [10] Robin Milner, Joachim Parrow, and David Walker. A calculus of mobile processes I and II. Information and Computation, 100:1–41, 42–78, 1992. 34, 35
11. [11] Masao Nagasaki, Shuichi Onami, Satoru Miyano, and Hiroaki Kitano. Biocalculus: Its concept and molecular interaction. Genome Informatics, 10:133–143, 1999. 34
12. [12] Corrado Priami, Aviv Regev, Ehud Shapiro, and William Silverman. Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters, 2001. In press. 34
13. [13] Aviv Regev and Ehud Shapiro. Cells as computation. Nature, 419, September 2002. 34
14. [14] Aviv Regev, William Silverman, and Ehud Shapiro. Representation and simulation of biochemical processes using the π-calculus process algebra. In R. B. Altman, A.K. Dunker, L. Hunter, and T. E. Klein, editors, Pacific Symposium on Biocomputing, volume 6, pages 459–470, Singapore, 2001. World Scientific Press. 34
15. [15] Bjorn Victor and Faron Moller. The Mobility Workbench — a tool for the π- calculus. In David Dill, editor, CAV’94: Computer Aided Verification, volume 818 of Lecture Notes in Computer Science, pages 428–440. Springer-Verlag, 1994. 35
16. [16] Pawel T. Wojciechowski and Peter Sewell. Nomadic Pict: Language and infrastructure design for mobile agents. IEEE Concurrency, 8(2):42–52, April/June 2000. 39