| 系统生物模型转换研究--从SBML到 Stochastic Pi Calculus |
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| 引用本文： | 董驻鹏,董笑菊,倪佳华.系统生物模型转换研究--从SBML到 Stochastic Pi Calculus[J].上海交通大学学报,2005,39(8):1280-1283. |
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| 作者姓名： | 董驻鹏 董笑菊 倪佳华 |
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| 作者单位： | 上海交通大学,计算机科学与工程系,上海,200030 |
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| 基金项目： | 国家杰出青年科学基金资助项目(60225012);上海科委交叉领域创新团队专项课题(03DZ14025) |
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| 摘 要： | 分析了系统生物标记语言（SBML）模型和用随机Pi演算对生物建模（BioSPI）的不同特点，给出了两种模型之间转换的一系列处理规则；在规则的指导下将具体的SBML模型转换为BioSPI表示的程序语言，并借助分析工具来模拟该SBML模型运动变化过程，提出了自动实现转换的方法以及将转换扩展到其他进程演算形式的构想。
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| 关 键 词： | 系统生物 系统生物标记语言 随机Pi演算对生物建模 形式化方法 DNA计算机 |
| 文章编号： | 1006-2467(2005)08-1280-04 |
| 修稿时间： | 2004年8月7日 |
Researches on Systems Biology Models Conversion--From SBML to Stochastic Pi Calculus |
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| DONG Zhu-peng,DONG Xiao-Ju,NI Jia-hua.Researches on Systems Biology Models Conversion--From SBML to Stochastic Pi Calculus[J].Journal of Shanghai Jiaotong University,2005,39(8):1280-1283. |
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| Authors: | DONG Zhu-peng DONG Xiao-Ju NI Jia-hua |
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| Abstract: | Using BioSPI(Modeling Biology with Stochastic Pi Calculus) to do plenty SBML (Systems Biology Markup Language) is a common,text-based model for storage and exchange systems biology information;but BioSPI model is mainly for simulating and analyzing biology's change and movement.Based on the study on these two models' characteristic,a series rules were given for the conversion from SBML to BioSPI.Guided by these rules,a real SBML model was converted to formal language of BioSPI and was analyzed using tools. A method for automation conversion tool design and a thought for conversion extending to other calculus were brought out. |
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| Keywords: | systems biology systems biology markup language (SBML) modeling biology with stochastic Pi calculus (BioSPI) formal method DNA computer |
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