Tellurium: An extensible python-based modeling environment for systems and synthetic biology.
Tellurium: An extensible python-based modeling environment for systems and synthetic biology.
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DOI：
10.1016/j.biosystems.2018.07.006
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发表时间：
2018-09
期刊：
影响因子：
--
通讯作者：
Sauro HM
中科院分区：
文献类型：
--
作者：
Choi K;Medley JK;König M;Stocking K;Smith L;Gu S;Sauro HM
在这里，我们介绍了Tellurium，一个基于Python的环境，用于模型构建，模拟和分析，促进了系统和合成生物学中模型的再现性。Tellurium是一个模块化、跨平台和开源的仿真环境，由多个库、插件和专用模块和方法组成。Tellurium是一个自包含的建模平台，它带有一个完全配置的Python发行版。提供了两个界面，一个基于Spyder IDE，它具有类似于MATLAB的可访问用户界面，另一个基于Spyter Notebook，它是一种包含实时代码，方程，可视化和叙述性文本的格式。Tellurium使用libRoadRunner作为默认的SBML仿真引擎，它支持确定性仿真、随机仿真和稳态分析。Tellurium还包括Antimony，这是一种人类可读的模型定义语言，可以与SBML相互转换。其他标准的Python科学库，如NumPy，SciPy和matplotlib，默认情况下也包含在内。此外，我们还包括几个用户友好的插件和高级模块，适用于各种应用，从复杂的分叉分析算法到多维参数扫描。通过将多个库、插件和模块组合到一个包中，Tellurium为新手和专家提供了一个统一但可扩展的生物建模和分析解决方案。可用性：tellurium.analogmachine.org
Here we present Tellurium, a Python-based environment for model building, simulation, and analysis that facilitates reproducibility of models in systems and synthetic biology. Tellurium is a modular, cross-platform, and open-source simulation environment composed of multiple libraries, plugins, and specialized modules and methods. Tellurium is a self-contained modeling platform which comes with a fully configured Python distribution. Two interfaces are provided, one based on the Spyder IDE which has an accessible user interface akin to MATLAB and a second based on the Jupyter Notebook, which is a format that contains live code, equations, visualizations, and narrative text. Tellurium uses libRoadRunner as the default SBML simulation engine which supports deterministic simulations, stochastic simulations, and steady-state analyses. Tellurium also includes Antimony, a human-readable model definition language which can be converted to and from SBML. Other standard Python scientific libraries such as NumPy, SciPy, and matplotlib are included by default. Additionally, we include several user-friendly plugins and advanced modules for a wide-variety of applications, ranging from complex algorithms for bifurcation analysis to multidimensional parameter scanning. By combining multiple libraries, plugins, and modules into a single package, Tellurium provides a unified but extensible solution for biological modeling and analysis for both novices and experts. Availability: tellurium.analogmachine.org
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