Chaste: developing sustainable software for computational biology

Chaste：开发计算生物学的可持续软件

• 批准号: BB/V018647/1
• 负责人: Alexander Fletcher
• 金额: $ 43.08万
• 依托单位: University of Sheffield
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2021
• 资助国家: 英国
• 起止时间: 2021 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FV018647%2F1
• 关键词: Chaste; developing; sustainable; software; computational

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.

全面了解复杂的生命系统对于解决21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。这种系统级的行为源于生物组织的许多层次上的组成过程之间复杂的相互作用。例如，从一个单细胞发展成一个复杂功能的多细胞生物，涉及到通过短期和长期生化和机械信号耦合的严格调节和协调的细胞行为。实验技术的最新进展产生了丰富的高质量数据和对这种复杂生物系统的详细但孤立的描述。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、预测和实验可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，这样研究人员就可以确信他们的计算模型正在可靠地、可重复地产生正确的输出。然后，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的工作，他们试图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，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，即结合数学模型，从一秒钟内发生的事情到需要数年时间的过程，从很小的事情（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，使英国生物学研究界受益，我们将启用更丰富的各种计算模型来模拟使用该软件，使研究人员能够利用新的高质量的3D实验数据。我们亦会善用最新的电脑及硬件科技，升级软件，并引入新方法，让使用者无须具备专业的编程知识，也能与软件互动。通过这种方式，我们将加速使用健壮的、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。

项目成果

insideOutside: an accessible algorithm for classifying interior and exterior points, with applications in embryology.

• DOI: 10.1242/bio.060055
• 发表时间: 2023-09-15
• 期刊: Biology open
• 影响因子: 2.4