IEEE Transactions on Software Engineering - Special issue on formal methods in software practice
Model checking
Information Processing Letters
Giotto: A Time-Triggered Language for Embedded Programming
EMSOFT '01 Proceedings of the First International Workshop on Embedded Software
Lateral Inhibition through Delta-Notch Signaling: A Piecewise Affine Hybrid Model
HSCC '01 Proceedings of the 4th International Workshop on Hybrid Systems: Computation and Control
Hybrid Modeling and Simulation of Biomolecular Networks
HSCC '01 Proceedings of the 4th International Workshop on Hybrid Systems: Computation and Control
Formal Modeling of C. elegans Development: A Scenario-Based Approach
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
The Immune System as a Reactive System: Modeling T Cell Activation With Statecharts
HCC '01 Proceedings of the IEEE 2001 Symposia on Human Centric Computing Languages and Environments (HCC'01)
Formalization of the Protein Production by Means of Petri Nets
ICIIS '99 Proceedings of the 1999 International Conference on Information Intelligence and Systems
Probabilistic model checking of complex biological pathways
Theoretical Computer Science
Toward Verified Biological Models
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
The pathalyzer: a tool for analysis of signal transduction pathways
RECOMB'05 Proceedings of the 2005 joint annual satellite conference on Systems biology and regulatory genomics
Machine learning biochemical networks from temporal logic properties
Transactions on Computational Systems Biology VI
What Can Formal Methods Bring to Systems Biology?
FM '09 Proceedings of the 2nd World Congress on Formal Methods
Maximally Parallel Probabilistic Semantics for Multiset Rewriting
Fundamenta Informaticae - Concurrency Specification and Programming (CS&P)
Synthesis of biological models from mutation experiments
POPL '13 Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming languages
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We introduce bounded asynchrony, a notion of concurrency tailored to the modeling of biological cell-cell interactions. Bounded asynchrony is the result of a scheduler that bounds the number of steps that one process gets ahead of other processes; this allows the components of a system to move independently while keeping them coupled. Bounded asynchrony accurately reproduces the experimental observations made about certain cell-cell interactions: its constrained nondeterminism captures the variability observed in cells that, although equally potent, assume distinct fates. Real-life cells are not "scheduled", but we show that distributed real-time behavior can lead to component interactions that are observationally equivalent to bounded asynchrony; this provides a possible mechanistic explanation for the phenomena observed during cell fate specification.We use model checking to determine cell fates. The nondeterminism of bounded asynchrony causes state explosion during model checking, but partial-order methods are not directly applicable. We present a new algorithm that reduces the number of states that need to be explored: our optimization takes advantage of the bounded-asynchronous progress and the spatially local interactions of components that model cells. We compare our own communication-based reduction with partial-order reduction (on a restricted form of bounded asynchrony) and experiments illustrate that our algorithm leads to significant savings.