Chaste: developing sustainable software for computational biology

全面了解复杂的生命系统对于解决21世纪世纪一些最紧迫的研究问题至关重要，从生物体的早期发育过程到衰老的影响。这种系统级行为源于生物组织许多层次上的组成过程之间的复杂相互作用。例如，从一个单细胞发展成一个功能复杂的多细胞生物体，涉及到通过短距离和长距离的生物化学和机械信号耦合起来的严格调节和协调的细胞行为，实验技术的最新进展正在产生大量高质量的数据，并详细但孤立地描述这种复杂的生物系统。为了真正理解这种复杂性，我们需要计算模型，它可以以定量，预测和实验验证的方式将观察结果与机制联系起来。该项目的目标是生产高质量的软件来支持这一点，以便研究人员可以确保他们的计算模型可靠地和可重复地生成正确的输出。我们的软件可以用来指导大学、研究机构和工业界的生物学家，帮助他们了解复杂的生物系统是如何工作的。我们已经开始朝着这个目标努力，开发了一个开源软件库Chaste，用于模拟生物组织中细胞集合的行为。这涉及到多尺度建模-即将几分之一秒内发生的事情的数学模型与需要数年时间的过程相结合，以及非常小的事情（在单个蛋白质的水平上）到整个身体的大尺度。为了充分发挥该软件的潜力，为英国生物学研究界带来益处，我们将使用该软件模拟更丰富的计算模型，使研究人员能够利用新的高质量3D实验数据。我们亦会提升我们的软件，以利用最新的计算机和硬件技术，并引入新的方法，让使用者在没有专业编程知识的情况下，也能与软件互动和互动。通过这种方式，我们将加速使用强大的，可扩展的软件来使用计算模型来帮助理解和解释复杂的生物系统。

Gaining a full understanding of complex living systems is essential to tackling some of the most pressing research questions of the 21st Century, from the processes of early development of an organism to the effects of ageing. This system-level behaviour arises from complex interactions between component processes at many levels of biological organisation. For example, the development of a complex functional multicellular organism from a single cell involves tightly regulated and coordinated cell behaviours coupled through short- and long-range biochemical and mechanical signals.Recent advances in experimental techniques are resulting in a wealth of high-quality data and detailed, but isolated, descriptions of such complex biological systems. To truly comprehend this complexity, we need computational models, which can link observations to mechanisms in a quantitative, predictive, and experimentally verifiable way. The goal of this project is to produce high-quality software to support this, so that researchers can be sure that their computational models are generating the correct outputs reliably and reproducibly. Our software can then be used to guide the work of biologists in universities, research institutes and industry who are trying to understand how complex biological systems work.We have already started working towards this goal by developing Chaste, an open-source software library for modelling the behaviour of collections of cells in biological tissues. This involves multiscale modelling - that is combining mathematical models for things that happen in fractions of a second to processes that take years, as well as things that are very small (on the level of individual proteins) to the large scale of the whole body. To fulfil this software's full potential for the benefit of the UK biology research community, we will enable a richer variety of computational models to be simulated using the software, allowing researchers to utilise new high-quality 3D experimental data. We will also upgrade our software to make use of the latest advances in computing and hardware, and introduce new ways that users can interact and interface with the software without expert programming knowledge. In this way, we will accelerate the use of robust, extensible software for using computational models to help understand and interpret complex biological systems.