Mersenne twister: a 623-dimensionally equidistributed uniform pseudo-random number generator
ACM Transactions on Modeling and Computer Simulation (TOMACS) - Special issue on uniform random number generation
Model-checking continuous-time Markov chains
ACM Transactions on Computational Logic (TOCL)
Performance Analysis of Communication Systems with Non-Markovian Stochastic Petri Nets
Performance Analysis of Communication Systems with Non-Markovian Stochastic Petri Nets
Model Checking Continuous-Time Markov Chains by Transient Analysis
CAV '00 Proceedings of the 12th International Conference on Computer Aided Verification
Mathematical Modeling of the Influence of RKIP on the ERK Signaling Pathway
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
Logic and stochastic modeling with SMART
Performance Evaluation - Modelling techniques and tools for computer performance evaluation
Distributed disk-based algorithms for model checking very large Markov chains
Formal Methods in System Design
COPASI---a COmplex PAthway SImulator
Bioinformatics
Using probabilistic model checking in systems biology
ACM SIGMETRICS Performance Evaluation Review
The GreatSPN tool: recent enhancements
ACM SIGMETRICS Performance Evaluation Review
Performance and dependability modeling with Möbius
ACM SIGMETRICS Performance Evaluation Review
DSSZ-MC --- A Tool for Symbolic Analysis of Extended Petri Nets
PETRI NETS '09 Proceedings of the 30th International Conference on Applications and Theory of Petri Nets
Sliding Window Abstraction for Infinite Markov Chains
CAV '09 Proceedings of the 21st International Conference on Computer Aided Verification
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
CSL Model Checking of Biochemical Networks with Interval Decision Diagrams
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Computational Biology and Chemistry
Fast Adaptive Uniformization of the Chemical Master Equation
HIBI '09 Proceedings of the 2009 International Workshop on High Performance Computational Systems Biology
The Ins and Outs of the Probabilistic Model Checker MRMC
QEST '09 Proceedings of the 2009 Sixth International Conference on the Quantitative Evaluation of Systems
Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments
Transactions on Computational Systems Biology XI
A unifying framework for modelling and analysing biochemical pathways using Petri nets
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
Petri nets for systems and synthetic biology
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
How fast and fat is your probabilistic model checker? an experimental performance comparison
HVC'07 Proceedings of the 3rd international Haifa verification conference on Hardware and software: verification and testing
From petri nets to differential equations – an integrative approach for biochemical network analysis
ICATPN'06 Proceedings of the 27th international conference on Applications and Theory of Petri Nets and Other Models of Concurrency
Analysis of signalling pathways using continuous time markov chains
Transactions on Computational Systems Biology VI
PRISM: a tool for automatic verification of probabilistic systems
TACAS'06 Proceedings of the 12th international conference on Tools and Algorithms for the Construction and Analysis of Systems
How might petri nets enhance your systems biology toolkit
PETRI NETS'11 Proceedings of the 32nd international conference on Applications and theory of Petri Nets
Coloured stochastic multilevel multiset rewriting
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
MARCIE: model checking and reachability analysis done efficiently
PETRI NETS'13 Proceedings of the 34th international conference on Application and Theory of Petri Nets and Concurrency
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Stochastic models are becoming increasingly popular in Systems Biology. They are compulsory, if the stochastic noise is crucial for the behavioural properties to be investigated. Thus, substantial effort has been made to develop appropriate and efficient stochastic analysis techniques. The impressive progress of hardware power and specifically the advent of multicore computers have ameliorated the computational tractability of stochastic models. We report on a comparative study focusing on the three base case techniques of stochastic analysis: exact numerical analysis, approximative numerical analysis, and simulation. For modelling we use extended stochastic Petri nets, which allows us to take advantage of structural information and to complement the stochastic analyses by qualitative analyses, belonging to the standard body of Petri net theory.