Python as a federation tool for GENESIS 3.0.
Python as a federation tool for GENESIS 3.0.
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DOI：
10.1371/journal.pone.0029018
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Bower JM
中科院分区：
文献类型：
--
作者：
Cornelis H;Rodriguez AL;Coop AD;Bower JM
Genesis模拟平台是计算生物学中第一批大规模建模系统之一，旨在鼓励建模者开发和共享模型特征和组件。在大型开发人员社区的支持下，它参与了诸如基准测试、并行化和声明性模型规范等创新的模拟器技术，并且是第一个为Python脚本语言定义绑定的神经模拟器。最新版本的Genesis的一个重要功能是，它按照计算生物学倡议的联合软件架构将其分解为自包含的软件组件。该体系结构允许为模拟器的不同必要组件(例如，数学解算器和图形用户界面)定义单独的脚本绑定。Python是一种脚本语言，它提供了丰富的免费开放源码库集。通过干净的动态面向对象设计，它们可以生成高度可读的代码，并广泛应用于软件组件集成的专门领域。我们使用简化的包装器和接口生成器来检查应用程序编程接口，并使其可用于给定的脚本语言。这使得独立的软件组件可以“粘合”在一起，并从用户定义的Python或Perl脚本连接到外部库和应用程序。我们用三个Python脚本编写示例来说明我们的方法。(1)生成并运行连接到独立数学求解器的简单单室模型神经元。(2)将数学解算器与Genesis 3.0接口，以从交互式命令行或图形用户界面探索神经元形态。(3)应用脚本绑定将Genesis 3.0模拟器连接到外部图形库和开源三维内容创建套件，该套件支持基于电子显微镜的模型可视化及其到计算模型的转换。以这种方式使用，Genesis 3.0模拟器的独立软件组件为计算神经科学中的渐进式联邦软件开发提供了一个框架。
The GENESIS simulation platform was one of the first broad-scale modeling systems in computational biology to encourage modelers to develop and share model features and components. Supported by a large developer community, it participated in innovative simulator technologies such as benchmarking, parallelization, and declarative model specification and was the first neural simulator to define bindings for the Python scripting language. An important feature of the latest version of GENESIS is that it decomposes into self-contained software components complying with the Computational Biology Initiative federated software architecture. This architecture allows separate scripting bindings to be defined for different necessary components of the simulator, e.g., the mathematical solvers and graphical user interface. Python is a scripting language that provides rich sets of freely available open source libraries. With clean dynamic object-oriented designs, they produce highly readable code and are widely employed in specialized areas of software component integration. We employ a simplified wrapper and interface generator to examine an application programming interface and make it available to a given scripting language. This allows independent software components to be ‘glued’ together and connected to external libraries and applications from user-defined Python or Perl scripts. We illustrate our approach with three examples of Python scripting. (1) Generate and run a simple single-compartment model neuron connected to a stand-alone mathematical solver. (2) Interface a mathematical solver with GENESIS 3.0 to explore a neuron morphology from either an interactive command-line or graphical user interface. (3) Apply scripting bindings to connect the GENESIS 3.0 simulator to external graphical libraries and an open source three dimensional content creation suite that supports visualization of models based on electron microscopy and their conversion to computational models. Employed in this way, the stand-alone software components of the GENESIS 3.0 simulator provide a framework for progressive federated software development in computational neuroscience.
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影响因子：
16.2
作者：
Gleeson P;Steuber V;Silver RA
通讯作者：
Silver RA
影响因子：
3
作者：
Djurfeldt, Mikael;Hjorth, Johannes;Ekeberg, Orjan
通讯作者：
Ekeberg, Orjan
影响因子：
6
作者：
Cornelis, H;De Schutter, E
通讯作者：
De Schutter, E
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DOI：
10.1523/jneurosci.4198-07.2008
发表时间：
2008-07-23
期刊：
The Journal of neuroscience : the official journal of the Society for Neuroscience
影响因子：
--
作者：
Günay C;Edgerton JR;Jaeger D
通讯作者：
Jaeger D
影响因子：
2.5
作者：
DESCHUTTER, E;BOWER, JM
通讯作者：
BOWER, JM