Garny Alan, Hunter Peter J
Auckland Bioengineering Institute, The University of Auckland Auckland, New Zealand.
Front Physiol. 2015 Feb 6;6:26. doi: 10.3389/fphys.2015.00026. eCollection 2015.
Computational biologists have been developing standards and formats for nearly two decades, with the aim of easing the description and exchange of experimental data, mathematical models, simulation experiments, etc. One of those efforts is CellML (cellml.org), an XML-based markup language for the encoding of mathematical models. Early CellML-based environments include COR and OpenCell. However, both of those tools have limitations and were eventually replaced with OpenCOR (opencor.ws). OpenCOR is an open source modeling environment that is supported on Windows, Linux and OS X. It relies on a modular approach, which means that all of its features come in the form of plugins. Those plugins can be used to organize, edit, simulate and analyze models encoded in the CellML format. We start with an introduction to CellML and two of its early adopters, which limitations eventually led to the development of OpenCOR. We then go onto describing the general philosophy behind OpenCOR, as well as describing its openness and its development process. Next, we illustrate various aspects of OpenCOR, such as its user interface and some of the plugins that come bundled with it (e.g., its editing and simulation plugins). Finally, we discuss some of the advantages and limitations of OpenCOR before drawing some concluding remarks.
近二十年来，计算生物学家一直在制定标准和格式，目的是便于描述和交换实验数据、数学模型、模拟实验等。其中一项成果就是CellML（cellml.org），一种用于编码数学模型的基于XML的标记语言。早期基于CellML的环境包括COR和OpenCell。然而，这两种工具都有局限性，最终被OpenCOR（opencor.ws）所取代。OpenCOR是一个开源建模环境，支持Windows、Linux和OS X系统。它采用模块化方法，这意味着其所有功能都以插件的形式呈现。这些插件可用于组织、编辑、模拟和分析以CellML格式编码的模型。我们首先介绍CellML及其早期的两个采用者，其局限性最终促使了OpenCOR的开发。然后我们继续描述OpenCOR背后的一般理念，以及它的开放性和开发过程。接下来，我们展示OpenCOR的各个方面，例如其用户界面以及随附的一些插件（例如其编辑和模拟插件）。最后，在得出一些结论之前，我们讨论OpenCOR的一些优点和局限性。
