School of Life Sciences, Arizona State University, Tempe, AZ, USA
School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ, USA.
Philos Trans R Soc Lond B Biol Sci. 2018 Sep 10;373(1758):20170381. doi: 10.1098/rstb.2017.0381.
The OpenWorm Project is an international open-source collaboration to create a multi-scale model of the organism At each scale, including subcellular, cellular, network and behaviour, this project employs one or more computational models that aim to recapitulate the corresponding biological system at that scale. This requires that the simulated behaviour of each model be compared with experimental data both as the model is continuously refined and as new experimental data become available. Here we report the use of , a software framework for model validation, to attempt to achieve these goals. During project development, each model is continuously subjected to data-driven 'unit tests' that quantitatively summarize model-data agreement, identifying modelling progress and highlighting particular aspects of each model that fail to adequately reproduce known features of the biological organism and its components. This workflow is publicly visible via both GitHub and a web application and accepts community contributions to ensure that modelling goals are transparent and well-informed.This article is part of a discussion meeting issue 'Connectome to behaviour: modelling at cellular resolution'.
OpenWorm 项目是一个国际开源协作项目,旨在创建生物体的多尺度模型。在每个尺度上,包括亚细胞、细胞、网络和行为,该项目采用一个或多个计算模型,旨在在该尺度上再现相应的生物系统。这要求模拟的每个模型的行为与实验数据进行比较,包括随着模型的不断细化以及新的实验数据的出现。在这里,我们报告使用软件框架进行模型验证,以尝试实现这些目标。在项目开发过程中,每个模型都不断接受数据驱动的“单元测试”,这些测试对模型数据的一致性进行定量总结,识别建模进展,并突出每个模型的特定方面,这些方面无法充分再现生物机体及其组成部分的已知特征。该工作流程通过 GitHub 和网络应用程序公开可见,并接受社区的贡献,以确保建模目标是透明和明智的。本文是“从连接组到行为:以细胞分辨率对进行建模”讨论会议议题的一部分。