CellBranch : a toolset for exploring Stem Cell Differentiation and Pluripotency with Branching Process Theory

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One important biological application area is stem cell differentiation. Embryonic stem (ES) cells have the potential to produce all an animal's cell types: this is called pluripotency. In theory, stem cells could be directed to differentiate into any cell type, for therapeutic purposes. However, we cannot yet reliably direct their behaviour, and so cannot yet fully exploit this potential.To further our understanding of such biological systems, we need sophisticated tools to analyse the system's complexity and the vast amounts of data available. Computational tools provide an important route to gaining such understanding. Here we will build computational models and simulation tools based on Branching Process Theory, targeted to research questions in the domain of embryonic stem cell differentiation, as informed by high volumes of data. We will validate the tool, to ensure that it is working as desired, by application to specific existing biological datasets. Tools need to be usable and accessible to benefit the wider community. We will make the fully documented tools available to the wider research community through York's HEFCE-funded YouShare "Software as a Service" portal.