The role of composition and aggregation in modeling macromolecular regulatory networks

Proceedings - Winter Simulation Conference

Volumn , Issue , 2006, Pages 1628-1635

  Shaffer, Clifford A ^a   Randhawa, Ranjit ^a   Tyson, John J ^b  

^a Virginia Polytechnic Institute and State University   (United States)

^b VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INFORMATION MANAGEMENT; LINGUISTICS; MACROMOLECULES; MINE FLOODING; MOLECULES; QUERY LANGUAGES; STRUCTURE (COMPOSITION);

AMOUNT OF INFORMATION; CELLULAR PATHWAYS; CURRENT MODELING; INDIVIDUAL (PSS 544-7); MODEL COMPOSITION; MODELING PROCESSES; MOLECULAR MACHINERY; REGULATORY NETWORKS; SYSTEMS BIOLOGY MARKUP LANGUAGE (SBML);

MARKUP LANGUAGES;

EID: 46149110545     PISSN: 08917736     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/WSC.2006.322937     Document Type: Conference Paper

References (20)

1. Bulatewicz, T., J. Cuny, and M. Warman. 2004. The potential coupling interface: Metadata for model coupling. In Proceedings of the Winter Simulation Conference, 183-190.
2. Chen, K., L. Calzone, A. Csikasz-Nagy, F. Cross, B. Novak, and J. Tyson. 2004. Integrative analysis of cell cycle control in budding yeast. Molecular Biology of the Cell 15:3841-3862.
3. DARPA 2005. DARPA BioSPICE website. 〈community.biospice.org〉.
4. Davis, P. K., and R. H. Anderson. 2004. Improving the composability of DoD models and simulations. Journal of Defense Modeling and Simulation 1 (1): 5-17.
5. DeRose, S., E. Maler, and D. Orchard. 2001. XML linking language (XLink) version 1.0 W3C recommendation. 〈www.w3.org/TR/xlink〉.
6. DOE 2005. US Department of Energy Genomes to Life website. 〈doegenomestolif e. org/〉.
7. Finney, A. 2003. Systems Biology Markup Language (SBML) level 3 proposal: Model composition features, 〈www.sbml.org/forums/index.php?t= tree&goto=171&rid=0〉.
8. Garlan, D., R. Allen, and J. Ockerbloom. 1995. Architectural mismatch or why it's hard to build systems out of existing parts. In International Conference on Software Engineering, 179-185.
9. Gilman, A. 2003. PathwayBuilder. 〈biospice.lbl.gov/PathwayBuilder/ 〉.
10. th Forum on Software Platforms for Systems Biology.
11. Ginkel, M., and M. Krasnyk. 2002. ProMoTDIVA. 〈mpi-magdeburg.mpg.de/ research/projects/1002/comp_bio/promot/distrib〉.
12. Hucka, M., A. Finney, H. Sauro, and 40 additional authors. 2003. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19 (4): 524-531.
13. Kasputis, S., and H. C. Ng. 2000. Model composability: formulating a research thrust: composable simulations. In Proceedings of the Winter Simulation Conference, 1577-1584.
14. Li, Z. 2005. Teranode Design Suite. 〈teranode.com/products/index. php〉.
15. Liang, V. C., and C. J. J. Paredis. 2003. Foundations of multi-paradigm modeling and simulation: a port ontology for automated model composition. In Proceedings of the Winter Simulation Conference, 613-622.
16. Malak, R. J., and C. J. J. Paredis. 2004. Foundations of validating reusable behavioral models in engineering design problems. In Proceedings of the Winter Simulation Conference, 420-428.
17. Marlovits, G., C. Tyson, B. Novak, and J. Tyson. 1998. Modeling M-phase control in Xenopus oocyte extracts: the surveillance mechanism for unreplicated DNA. Biophysical Chemistry 72:169-184.
18. Schroder, D., and J. Weimar. 2003. Modularization of SBML. 〈www.sbml.org/workshops/ninth/VortragSBMLForum.pdf〉.
19. Spiegel, M., P. Reynolds, and D. Brogan. 2005. A case study of model context for simulation composability and reusability. In Proceedings of the Winter Simulation Conference, 437-444.
20. Tyson, J. J., K. C. Chen, and B. Novak. 2003. Sniffers, buzzers, toggles and blinkers: Dynamics of regulatory and signaling pathways in the cell. Current Opinion in Cell Biology 15:221-231.