Cornelis H. Research Imaging Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America.
PLoS One. 2012;7(1):e29018. doi: 10.1371/journal.pone.0029018. Epub 2012 Jan 20.
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.
GENESIS 模拟平台是计算生物学中最早的大规模建模系统之一，鼓励建模者开发和共享模型功能和组件。在庞大的开发人员社区的支持下，它参与了创新的模拟器技术，如基准测试、并行化和声明式模型规范，并且是第一个为 Python 脚本语言定义绑定的神经模拟器。GENESIS 最新版本的一个重要特点是，它分解为符合计算生物学倡议联邦软件架构的自包含软件组件。这种架构允许为模拟器的不同必要组件定义单独的脚本绑定，例如数学求解器和图形用户界面。Python 是一种脚本语言，提供了丰富的自由可用的开源库。凭借简洁的动态面向对象设计，它们生成高度可读的代码，并广泛应用于软件组件集成的专业领域。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。这允许独立的软件组件“粘合”在一起，并连接到外部库和应用程序，来自用户定义的 Python 或 Perl 脚本。我们通过三个 Python 脚本的示例来说明我们的方法。（1）生成并运行一个简单的单室模型神经元，连接到独立的数学求解器。（2）将数学求解器与 GENESIS 3.0 接口，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一个开源的三维内容创建套件，该套件支持基于电子显微镜的模型的可视化及其转换为计算模型。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渐进式联邦软件开发提供了一个框架。
