Statecharts: A visual formalism for complex systems
Science of Computer Programming
Communicating and mobile systems: the &pgr;-calculus
Communicating and mobile systems: the &pgr;-calculus
Model checking
LSCs: Breathing Life into Message Sequence Charts
Formal Methods in System Design
Information Processing Letters
Formal Modeling of C. elegans Development: A Scenario-Based Approach
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
LICS '96 Proceedings of the 11th Annual IEEE Symposium on Logic in Computer Science
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
Taming the complexity of biochemical models through bisimulation and collapsing: theory and practice
Theoretical Computer Science - Special issue: Computational systems biology
Modelling biochemical pathways through enhanced π-calculus
Theoretical Computer Science - Special issue: Computational systems biology
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
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
Automated symbolic reachability analysis: with application to delta-notch signaling automata
HSCC'03 Proceedings of the 6th international conference on Hybrid systems: computation and control
Hybrid modeling and simulation of genetic regulatory networks
HSCC'03 Proceedings of the 6th international conference on Hybrid systems: computation and control
Abstract machines of systems biology
Transactions on Computational Systems Biology III
Combining state-based and scenario-based approaches in modeling biological systems
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
Concurrency in Biological Modeling: Behavior, Execution and Visualization
Electronic Notes in Theoretical Computer Science (ENTCS)
Discrete Semantics for Hybrid Automata
Discrete Event Dynamic Systems
Proving stabilization of biological systems
VMCAI'11 Proceedings of the 12th international conference on Verification, model checking, and abstract interpretation
Proceedings of the International Conference on Computer-Aided Design
| Hi-index | 0.00 |
Computational modeling of biological systems is becoming increasingly common as scientists attempt to understand biological phenomena in their full complexity. Here we distinguish between two types of biological models --- mathematical and computational--- according to their different representations of biological phenomena and their diverse potential. We call the approach of constructing computational models of biological systems Executable Biology, as it focuses on the design of executable computer algorithms that mimic biological phenomena. We give an overview of the main modeling efforts in this direction, and discuss some of the new challenges that executable biology poses for computer science and biology. We argue that for executable biology to reach its full potential as a mainstream biological technique, formal and algorithmic approaches must be integrated into biological research, driving biology towards a more precise engineering discipline.