Academic literature on the topic 'Biopathway analysis'

Cellular processes are governed and coordinated by a multitude of biopathways. A pathway can be viewed as a complex network of biochemical reactions. The dynamics of this network largely determines the functioning of the pathway. Hence the modeling and analysis of biochemical networks dynamics is an important problem and is an active area of research. Here we review quantitative models of biochemical networks based on ordinary differential equations (ODEs). We mainly focus on the parameter estimation and sensitivity analysis problems and survey the current methods for tackling them. In this context we also highlight a recently developed probabilistic approximation technique using which these two problems can be considerably simplified.

Dynamic visualizations and expressive representations are needed in systems biology to handle multiple interactionsoccurring during the biological processes of biopathway representations. Dynamic visualizations allow users an easeof interaction with pathway models. At the same time, representations of biopathways should express how interactionstake place. In spite of the fact that diverse databases provide users with pathways, their information andrepresentation are frequently different from each other and show restricted interactions because of their staticvisualization. An adopted solution is to merge diverse representations to obtain a richer one. However, due to differentformats and the multiple links involved in the pathway representations, the merge results frequently in erroneousmodels and in a tangle web of relations very hard to be manipulated. Instead, this work introduces a concurrentdynamic visualization (CDV) of the same pathway, which is retrieved from different sites and then transformed intoPetri net representations to facilitate the understanding of their biological processes by interacting with them. Weapplied this approach to the analysis of the Notch signaling pathway, associated with cervical cancer; we obtained itfrom different sources which we compared and manipulated simultaneously by interacting with the provided CDV untilthe user generated a personalized pathway.