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

一个重要的生物应用领域是干细胞分化。胚胎干细胞（ES）具有产生动物所有细胞类型的潜力：这被称为多能性。理论上，干细胞可以定向分化成任何细胞类型，用于治疗目的。然而，我们还不能可靠地指导它们的行为，因此还不能充分利用这种潜力。为了进一步了解这种生物系统，我们需要先进的工具来分析系统的复杂性和大量可用的数据。计算工具为获得这种理解提供了一条重要途径。在这里，我们将建立基于分支过程理论的计算模型和模拟工具，针对胚胎干细胞分化领域的研究问题，如大量数据所示。我们将通过应用于特定的现有生物数据集来验证该工具，以确保它按预期工作。工具必须是可用的和可访问的，以使更广泛的社区受益。我们将通过约克的HEFCE资助的YouShare“软件即服务”门户网站向更广泛的研究社区提供完整的文档工具。

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.