Vivarium: an interface and engine for integrative multiscale modeling in computational biology
Vivarium: an interface and engine for integrative multiscale modeling in computational biology
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DOI：
10.1093/bioinformatics/btac049
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发表时间：
2022-03-28
期刊：
影响因子：
5.8
通讯作者：
Covert, Markus W.
中科院分区：
文献类型：
--
作者：
Agmon, Eran;Spangler, Ryan K.;Covert, Markus W.
动机：本文介绍了 Vivarium 软件，其诞生的理念是计算生物学家应该尽可能轻松地定义任何可以想象的机械模型，将其与现有模型相结合，并将它们作为集成的多尺度模型一起执行。集成多尺度建模通过将异构数据集和不同的建模策略组合成统一的表示来应对生物学的复杂性。然后运行这些集成模型来模拟假设的机制作为一个整体如何运作。但构建此类模型是一个劳动密集型过程，需要许多贡献者，而且它们仍然主要是根据具体情况开发的，每个项目都重新开始。因此，简化综合建模工作并促进协作的新软件工具对于未来的计算生物学家至关重要。结果：Vivarium 是用于构建综合多尺度模型的软件工具。它提供了一个接口，将各个模型构建成模块，这些模块可以在大型复合模型中连接在一起，跨多个 CPU 并行化，并与 Vivarium 的离散事件仿真引擎一起运行。 Vivarium 的实用性通过构建结合了多种建模框架的复合模型来证明：基于代理的模型、常微分方程、随机反应系统、基于约束的模型、固体物理和空间扩散。这表明了一切可能的开始 - Vivarium 将能够支持未来集成更多类型模型和更多生物尺度的工作。可用性和实现：为本文开发的特定模型、模拟管道和笔记本都可以在 vivarium-notebooks 存储库中找到：https://github.com/vivarium-collective/vivarium-notebooks。 Vivarium-core 可在 https://github.com/vivarium-collective/vivarium-core 上找到，并已在 Python 包索引上发布。 Vivarium Collective (https://vivarium-collective.github.io) 是免费提供的 Vivarium 流程和复合材料的存储库，包括第 3 节中使用的流程。补充材料提供了广泛的方法部分，以及演示基本接口的多个代码列表。联系方式：agmon.eran@gmail.com 或 mcovert@stanford.edu 补充信息：补充数据可在生物信息学在线获取。
Motivation: This article introduces Vivarium-software born of the idea that it should be as easy as possible for computational biologists to define any imaginable mechanistic model, combine it with existing models and execute them together as an integrated multiscale model. Integrative multiscale modeling confronts the complexity of biology by combining heterogeneous datasets and diverse modeling strategies into unified representations. These integrated models are then run to simulate how the hypothesized mechanisms operate as a whole. But building such models has been a labor-intensive process that requires many contributors, and they are still primarily developed on a case-by-case basis with each project starting anew. New software tools that streamline the integrative modeling effort and facilitate collaboration are therefore essential for future computational biologists.Results: Vivarium is a software tool for building integrative multiscale models. It provides an interface that makes individual models into modules that can be wired together in large composite models, parallelized across multiple CPUs and run with Vivarium's discrete-event simulation engine. Vivarium's utility is demonstrated by building composite models that combine several modeling frameworks: agent-based models, ordinary differential equations, stochastic reaction systems, constraint-based models, solid-body physics and spatial diffusion. This demonstrates just the beginning of what is possible-Vivarium will be able to support future efforts that integrate many more types of models and at many more biological scales.Availability and implementation: The specific models, simulation pipelines and notebooks developed for this article are all available at the vivarium-notebooks repository: https://github.com/vivarium-collective/vivarium-notebooks. Vivarium-core is available at https://github.com/vivarium-collective/vivarium-core, and has been released on Python Package Index. The Vivarium Collective (https://vivarium-collective.github.io) is a repository of freely available Vivarium processes and composites, including the processes used in Section 3. Supplementary Materials provide with an extensive methodology section, with several code listings that demonstrate the basic interfaces.Contact: agmon.eran@gmail.com or mcovert@stanford.edu Supplementary information: Supplementary data are available at Bioinformatics online.