Thursday, November 6, 2014

A pedagogical walkthrough of computational modeling and simulation of Wnt signaling pathway using static causal models in Matlab

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