Suzuki Yasuyuki, Asai Yoshiyuki, Oka Hideki, Heien Eric, Urai Takahito, Okamoto Tatsuhide, Yumikura Yosuke, Tominaga Keisuke, Kido Yoshiyuki, Nakanishi Masao, Hagihara Kenichi, Kurachi Yoshihisa, Nomura Taishin
Graduate School of Engineering Science at Osaka University, Toyonaka, Osaka 560-8531, Japan.
Annu Int Conf IEEE Eng Med Biol Soc. 2009;2009:2803-6. doi: 10.1109/IEMBS.2009.5333775.
Physiome and systems biology have been recognized as emerging and important research areas that can integrate quantitatively growing knowledge about biological structure and physiological functions at multiple scales of time and space. For the integration, it is important to build physiologically plausible and sharable mathematical models that can be used for dynamic simulations of functions at multi-scale and multi-level. Here we describe new features of our open platform insilicoML (ISML) and insilicoIDE (ISIDE) that have been presented previously. The platform can support reuse existing mathematical models of physiological functions in the model databases, to construct brand new models, and to simulate models. The major new features of the platform include improvement of the capabilities to incorporate experimentally obtained data such as time-series and morphological data with dynamic simulation of models that may be driven by the data, and extension of variety of model types that can be described by ISML and simulated on ISIDE, such as multi agent systems and models described by partial differential equations that are solved by the finite element method.
生理组学和系统生物学已被公认为新兴且重要的研究领域，它们能够整合在多个时空尺度上关于生物结构和生理功能的数量不断增长的知识。对于这种整合而言，构建生理上合理且可共享的数学模型非常重要，这些模型可用于多尺度和多层次功能的动态模拟。在此，我们描述我们之前介绍过的开放平台insilicoML（ISML）和insilicoIDE（ISIDE）的新特性。该平台能够支持在模型数据库中重用现有的生理功能数学模型、构建全新模型以及模拟模型。该平台的主要新特性包括提高将实验获得的数据（如时间序列和形态数据）与可能由数据驱动的模型动态模拟相结合的能力，以及扩展ISML能够描述并在ISIDE上模拟的模型类型的种类，例如多智能体系统和通过有限元法求解的偏微分方程描述的模型。
