论文标题
Odebase：用于系统生物学的ODE系统的存储库
ODEbase: A Repository of ODE Systems for Systems Biology
论文作者
论文摘要
最近，符号计算和计算机代数系统已成功地应用于系统生物学，尤其是在化学反应网络理论中。符号计算的优点之一是它对生物学问题的定性答案的潜力。定性方法将动态输入系统分析为形式对象，与仅研究状态空间的一部分相比，与数值模拟一样。但是，符号计算工具和库对其输入数据的要求集与其数值对应物不同。 SBML是生物过程数学建模中使用的常见格式。我们说明，在符号计算中使用SBML数据需要重大的预处理，并结合了外部生物学和数学专业知识。 Odebase提供了从已建立的现有生物模型得出的高质量符号计算输入数据，尤其涵盖了生物模型数据库。
Recently, symbolic computation and computer algebra systems have been successfully applied in systems biology, especially in chemical reaction network theory. One advantage of symbolic computation is its potential for qualitative answers to biological questions. Qualitative methods analyze dynamical input systems as formal objects, in contrast to investigating only part of the state space, as is the case with numerical simulation. However, symbolic computation tools and libraries have a different set of requirements for their input data than their numerical counterparts. A common format used in mathematical modeling of biological processes is SBML. We illustrate that the use of SBML data in symbolic computation requires significant pre-processing, incorporating external biological and mathematical expertise. ODEbase provides high quality symbolic computation input data derived from established existing biomodels, covering in particular the BioModels database.
