Alves Rui, Antunes Fernando, Salvador Armindo
Departament Ciencies Mediques Basiques, Universidad de Lleida, Montserrat Roig, 4; 25008 Lleida, Spain.
Nat Biotechnol. 2006 Jun;24(6):667-72. doi: 10.1038/nbt0606-667.
The number of software packages for kinetic modeling of biochemical networks continues to grow. Although most packages share a common core of functionality, the specific capabilities and user interfaces of different packages mean that choosing the best package for a given task is not trivial. We compare 12 software packages with respect to their functionality, reliability, efficiency, user-friendliness and compatibility. Although most programs performed reliably in all numerical tasks tested, SBML compatibility and the set-up of multicompartmentalization are problematic in many packages. For simple models, GEPASI seems the best choice for non-expert users. For large-scale models, environments such as Jarnac/JDesigner are preferable, because they allow modular implementation of models. Virtual Cell is the most versatile program and provides the simplest and clearest functionality for setting up multicompartmentalization.
用于生化网络动力学建模的软件包数量持续增加。尽管大多数软件包都有共同的核心功能，但不同软件包的具体功能和用户界面意味着为特定任务选择最佳软件包并非易事。我们从功能、可靠性、效率、用户友好性和兼容性方面对12个软件包进行了比较。尽管大多数程序在所有测试的数值任务中都能可靠运行，但许多软件包在SBML兼容性和多隔室设置方面存在问题。对于简单模型，GEPASI似乎是非专业用户的最佳选择。对于大规模模型，Jarnac/JDesigner等环境更可取，因为它们允许模型的模块化实现。Virtual Cell是功能最丰富的程序，在设置多隔室方面提供了最简单、最清晰的功能。
