ChemChaste: Simulating spatially inhomogeneous biochemical reaction-diffusion systems for modeling cell-environment feedbacks.
ChemChaste: Simulating spatially inhomogeneous biochemical reaction-diffusion systems for modeling cell-environment feedbacks.
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ChemChaste：模拟空间非均匀生化反应扩散系统，用于模拟细胞环境反馈。
DOI：
10.1093/gigascience/giac051
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发表时间：
2022-06-17
期刊：
影响因子：
9.2
通讯作者：
中科院分区：
文献类型：
--
作者：
空间组织在许多生物系统的功能中起着重要作用，从动物发育中的细胞命运指定到微生物群落中的多步代谢转换。这种系统的研究受益于空间显式计算模型的使用，该模型将细胞的离散描述与一种或多种化学物质在周围散装介质中扩散的连续描述相结合。这些模型允许在计算机测试和细化的机制假设。然而，大多数现有的这种类型的模型不占并发批量和细胞内的生化反应和它们可能的耦合。在这里，我们描述ChemChaste，开源C++计算生物学库Chaste的扩展。ChemChaste通过扩展Chaste现有的能力，实现了多细胞和批量生物化学的空间模拟。特别是，ChemChaste能够（i）模拟任意数量的空间扩散化学品，（ii）空间异质化学扩散系数，以及（iii）包括散装和细胞内生化反应及其耦合。ChemChaste还引入了一个基于文件的界面，允许用户定义与这些功能特性相关的参数，而无需直接与Chaste的核心C++代码进行交互。我们描述了ChemChaste，并使用选择的化学和生物化学范例来展示其功能，重点是展示在建模散装化学反应及其与细胞内反应的耦合方面的能力增强。ChemChaste 1.0版是一个免费的开源C++库，可通过GitHub在https://github.com/OSS-Lab/ChemChaste上以BSD许可证获得，在zendodo doi的Zenodo存档中，以及BioTools（biotools：chemchaste）和SciCrunch（RRID：SCR022208）数据库中。
Spatial organization plays an important role in the function of many biological systems, from cell fate specification in animal development to multistep metabolic conversions in microbial communities. The study of such systems benefits from the use of spatially explicit computational models that combine a discrete description of cells with a continuum description of one or more chemicals diffusing within a surrounding bulk medium. These models allow the in silico testing and refinement of mechanistic hypotheses. However, most existing models of this type do not account for concurrent bulk and intracellular biochemical reactions and their possible coupling. Here, we describe ChemChaste, an extension for the open-source C++ computational biology library Chaste. ChemChaste enables the spatial simulation of both multicellular and bulk biochemistry by expanding on Chaste’s existing capabilities. In particular, ChemChaste enables (i) simulation of an arbitrary number of spatially diffusing chemicals, (ii) spatially heterogeneous chemical diffusion coefficients, and (iii) inclusion of both bulk and intracellular biochemical reactions and their coupling. ChemChaste also introduces a file-based interface that allows users to define the parameters relating to these functional features without the need to interact directly with Chaste’s core C++ code. We describe ChemChaste and demonstrate its functionality using a selection of chemical and biochemical exemplars, with a focus on demonstrating increased ability in modeling bulk chemical reactions and their coupling with intracellular reactions. ChemChaste version 1.0 is a free, open-source C++ library, available via GitHub at https://github.com/OSS-Lab/ChemChaste under the BSD license, on the Zenodo archive at zendodo doi, as well as on BioTools (biotools:chemchaste) and SciCrunch (RRID:SCR022208) databases.
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从微生物学基因到生态系统：建模方法和个性的重要性
影响因子：
5.2
作者：
Kreft JU;Plugge CM;Prats C;Leveau JHJ;Zhang W;Hellweger FL
通讯作者：
Hellweger FL
DOI：
10.1073/pnas.1706920115
发表时间：
2018-04-17
影响因子：
11.1
作者：
Bocci, Federico;Suzuki, Yoko;Onuchic, Jose N.
通讯作者：
Onuchic, Jose N.
影响因子：
4.4
作者：
Figueredo, Grazziela P.;Joshi, Tanvi V.;Owen, Markus R.
通讯作者：
Owen, Markus R.
影响因子：
3.5
作者：
An, G.;Fitzpatrick, B. G.;Christley, S.;Federico, P.;Kanarek, A.;Neilan, R. Miller;Oremland, M.;Salinas, R.;Laubenbacher, R.;Lenhart, S.
通讯作者：
Lenhart, S.
DOI：
10.1111/j.1469-1809.1937.tb02153.x
发表时间：
1937-06-01
期刊：
ANNALS OF EUGENICS
影响因子：
--
作者：
Fisher, RA
通讯作者：
Fisher, RA