Formal Methods for Biological Systems: Languages, Algorithms, and Applications Qinsi Wang CMU-CS-16-129 September 2016
Formal Methods for Biological Systems: Languages, Algorithms, and Applications Qinsi Wang CMU-CS-16-129 September 2016 School of Computer Science Computer Science Department Carnegie Mellon University Pittsburgh, PA Thesis Committee Edmund M. Clarke, Chair Stephen Brookes Marta Zofia Kwiatkowska, University of Oxford Frank Pfenning Natasa Miskov-Zivanov, University of Pittsburgh Submitted in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Copyright c 2016 Qinsi Wang This research was sponsored by the National Science Foundation under grant numbers CNS-0926181 and CNS- 1035813, the Army Research Laboratory under grant numbers FA95501210146 and FA955015C0030, the Defense Advanced Research Projects Agency under grant number FA875012C0204, the Office of Naval Research under grant number N000141310090, the Semiconductor Research Corporation under grant number 2008-TJ-1860, and the Mi- croelectronics Advanced Research Corporation (DARPA) under grant number 2009-DT-2049. The views and conclusions contained in this document are those of the author and should not be interpreted as rep- resenting the official policies, either expressed or implied, of any sponsoring institution, the U.S. government or any other entity. Keywords: Model checking, Formal specification, Formal Analysis, Boolean networks, Qual- itative networks, Rule-based modeling, Multiscale hybrid rule-based modeling, Hybrid systems, Stochastic hybrid systems, Symbolic model checking, Bounded model checking, Statistical model checking, Bounded reachability, Probabilistic bounded reachability, Parameter estimation, Sensi- tivity analysis, Statistical tests, Pancreatic cancer, Phage-based bacteria killing, Prostate cancer treatment, C. elegans For My Beloved Mom & Dad iv Abstract As biomedical research advances into more complicated systems, there is an in- creasing need to model and analyze these systems to better understand them.
[Show full text]