Abstract
Studies of biological systems are often facilitated by diagram “models” that summarize the current understanding of underlying mechanisms. The increasing complexity of our understanding of biology necessitates computational models that can extend these representations to include their dynamic behavior. We present here a new tool we call Synthesizing Biological Theories which enables biologists and modelers to construct high-level theories and models of biological systems, capturing biological hypotheses, inferred mechanisms, and experimental results within the same framework. Among the key features of the tool are convenient ways to represent several competing theories and the interactive nature of building and running the models using an intuitive, rigorous scenario-based visual language. The definition of the modeling language is geared towards enabling formal verification and analysis.
Chapter PDF
Similar content being viewed by others
References
Damm, W., Harel, D.: LSCs: Breathing life into message sequence charts. Formal Methods in System Design 19(1), 45–80 (2001)
Fisher, J., Henzinger, T.A.: Executable Cell Biology. Nature Biotechnology 25(11), 1239–1249 (2007)
Harel, D., Marelly, R.: Specifying and executing behavioral requirements: The play-in/play-out approach. In: Software and System Modeling, SoSyM (2003)
Kam, N., Kugler, H., Marelly, R., Appleby, L., Fisher, J., Pnueli, A., Harel, D., Stern, M.J., Hubbard, E.J.A.: A scenario-based approach to modeling development: A prototype model of C. elegans vulval fate specification. Developmental Biology 323(1), 1–5 (2008)
Kugler, H., Plock, C., Pnueli, A.: Controller Synthesis from LSC Requirements. In: Chechik, M., Wirsing, M. (eds.) FASE 2009. LNCS, vol. 5503, pp. 79–93. Springer, Heidelberg (2009)
Kugler, H., Segall, I.: Compositional Synthesis of Reactive Systems from Live Sequence Chart Specifications. In: Kowalewski, S., Philippou, A. (eds.) TACAS 2009. LNCS, vol. 5505, pp. 77–91. Springer, Heidelberg (2009)
Milicevic, A., Kugler, H.: Model Checking Using SMT and Theory of Lists. In: Bobaru, M., Havelund, K., Holzmann, G.J., Joshi, R. (eds.) NFM 2011. LNCS, vol. 6617, pp. 282–297. Springer, Heidelberg (2011)
Plock, C.: Synthesizing Executable Programs from Requirements. PhD thesis, New York Univ. (2008)
Microsoft Research Cambridge, Synthesizing Biological Theories (2011), http://research.microsoft.com/SBT/endthebibliography
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Kugler, H., Plock, C., Roberts, A. (2011). Synthesizing Biological Theories. In: Gopalakrishnan, G., Qadeer, S. (eds) Computer Aided Verification. CAV 2011. Lecture Notes in Computer Science, vol 6806. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-22110-1_46
Download citation
DOI: https://doi.org/10.1007/978-3-642-22110-1_46
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-22109-5
Online ISBN: 978-3-642-22110-1
eBook Packages: Computer ScienceComputer Science (R0)