A pedagogical walkthrough of computational modeling and simulation of Wnt signaling pathway using static causal models in Matlab
A tutorial introduction to computational modeling of Wnt signaling
pathway in a human colorectal cancer dataset using static Bayesian
network models is provided. This work endeavours to expound in detail
the simulation study in Matlab along with the code while explaining the
concepts related to Bayesian networks. This is done in order to ease the
understanding of beginner students and researchers in transition to
computational signaling biology, who intend to work in the field of
modeling of signaling pathways. The case study is based on the contents
of the advance article by Sinha (2014) and takes the reader in a step by
step process of how (1) the collection and the transformation of the
available biological information from literature is done, (2) the
integration of the heterogeneous data and prior biological knowledge in
the network is achieved, (3) the simulation study is designed, (4) the
hypothesis regarding a biological phenomena is transformed into
computational framework, and (5) results and inferences drawn using
d-connectivity/separability are reported. It is hoped that the
walkthrough will aid biologists understand the design of the
computational experiments using causal models. The manuscript finally
ends with a programming assignment to help the readers get hands on
experience of a perturbation project. Matlab code with dataset is made
available under GNU GPL v3 license at
google code project on
https://code.google.com/p/static-bn-for-wnt-signaling-pathway
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