NuSMV 2: An OpenSource Tool for Symbolic Model Checking
CAV '02 Proceedings of the 14th International Conference on Computer Aided Verification
Logic in Computer Science: Modelling and Reasoning about Systems
Logic in Computer Science: Modelling and Reasoning about Systems
Modeling and querying biomolecular interaction networks
Theoretical Computer Science - Special issue: Computational systems biology
Parameter estimation for Boolean models of biological networks
Theoretical Computer Science
Parameter inference for asynchronous logical networks using discrete time series
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
On Parameter Synthesis by Parallel Model Checking
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Parameter identification and model ranking of thomas networks
CMSB'12 Proceedings of the 10th international conference on Computational Methods in Systems Biology
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This paper is concerned with the analysis of labeled Thomas networks using discrete time series. It focuses on refining the given edge labels and on assessing the data quality. The results are aimed at being exploitable for experimental design and include the prediction of new activatory or inhibitory effects of given interactions and yet unobserved oscillations of specific components in between specific sampling intervals. On the formal side, we generalize the concept of edge labels and introduce a discrete time series interpretation. This interpretation features two original concepts: 1) Incomplete measurements are admissible, and 2) it allows qualitative assumptions about the changes in gene expression by means of monotonicity. On the computational side, we provide a Python script, erda.py, that automates the suggested workflow by model checking and constraint satisfaction. We illustrate the workflow by investigating the yeast network IRMA.