Similarities and dissimilarities between biomolecular networks cannot be intuitively recognized even after the development of several comparison algorithms because of the lack of visualization tools. In this paper, an...Similarities and dissimilarities between biomolecular networks cannot be intuitively recognized even after the development of several comparison algorithms because of the lack of visualization tools. In this paper, an integrated tool kit named Biomolecular Network Match（BNMatch） is designed and developed based on Cytoscape—a popular and open-source tool for analyzing and visualizing networks. BNMatch integrates the comparison of the outputs of algorithms used for processing biomolecular networks and expresses the matching data between them by defining similar vertices and links with similar attributes. Moreover, in order to maintain consistency, their counterparts in other networks change when the nodes and edges in one of the compared networks are changed. It becomes easy for users to analyze similar networks by invoking comparison algorithms and visualizing the matching data between the networks using BNMatch.展开更多
Cytoscape is one of the most popular platforms for biomolecular networks research. However Cytoscape cannot display biomolecular names according to their accession identifiers in different databases. A plugin named Ai...Cytoscape is one of the most popular platforms for biomolecular networks research. However Cytoscape cannot display biomolecular names according to their accession identifiers in different databases. A plugin named Ai2NU is designed and implemented in this paper. It can make biomolecular names displayed automatically in biomolecular networks graphs in Cytoscape by constructing a local dictionary. It is convenient for researchers to recognize biomolecules and enhance the research efficiency.展开更多
This paper presents a solution methodology for H<sub>∞</sub>-feedback control design problem of Heparin controlled blood clotting network under the presence of stochastic noise. The formulaic solution pro...This paper presents a solution methodology for H<sub>∞</sub>-feedback control design problem of Heparin controlled blood clotting network under the presence of stochastic noise. The formulaic solution procedure to solve nonlinear partial differential equation, the Hamilton-Jacobi-Isaacs equation with Successive Galrkin’s Approximation is sketched and validity is proved. According to Lyapunov’s theory, with solutions of the nonlinear PDEs, robust feedback control is designed. To confirm the performance and robustness of the designed controller, numerical and Monte-Carlo simulation results by Simulink software on MATLAB are provided.展开更多
This paper presents a design method of H<sub>2</sub> and H<sub>∞</sub>-feedback control loop for nonlinear smooth gene networks that are in control affine form. Formulaic solution methodology ...This paper presents a design method of H<sub>2</sub> and H<sub>∞</sub>-feedback control loop for nonlinear smooth gene networks that are in control affine form. Formulaic solution methodology for solving the nonlinear partial differential equations, namely the Hamilton-Jacobi-Bellman and Hamilton-Jacobi-Isaacs equations through successive Galerkin’s approximation is implemented and the results are compared. Throughout the implementation, there were several caveats that need to be further resolved for practical applications in general cases. Such issues and the clarification of causes are mathematically established and reviewed.展开更多
该研究运用生物分子网络分析方法,预测注射用丹参多酚酸盐与阿司匹林联合用药治疗稳定型心绞痛的作用机制。从Genecards,STITCH,Dis Ge NET数据库获取注射用丹参多酚酸盐、阿司匹林及稳定型心绞痛(stable angina pectoris,SAP)的相关基...该研究运用生物分子网络分析方法,预测注射用丹参多酚酸盐与阿司匹林联合用药治疗稳定型心绞痛的作用机制。从Genecards,STITCH,Dis Ge NET数据库获取注射用丹参多酚酸盐、阿司匹林及稳定型心绞痛(stable angina pectoris,SAP)的相关基因;采用Agilent Literature Search文献搜索软件构建生物分子网络;经AP,MCODE和MCL 3种方法对生物网络进行模块识别;通过DAVID软件进行相关KEGG通路识别。结果表明注射用丹参多酚酸盐和阿司匹林对SAP分子网络的覆盖率分别为45.92%,62.56%,联合用药的覆盖率为71.64%。注射用丹参多酚酸盐、阿司匹林与SAP前10个重要节点中,MAPK14,MAPK8,IL-6,IL-8为2个药物共同重叠的SAP重要节点,AKT1和IFNG为注射用丹参多酚酸盐单独重叠的SAP重要节点,EPHB2和TP53为阿司匹林单独重叠的SAP重要节点。2个药物共同参与的SAP相关信号通路包括JAK-STAT信号通路和MAPK信号通路等;注射用丹参多酚酸盐单独参与的SAP相关信号通路包括VEGF信号通路和1型糖尿病信号通路;阿司匹林单独参与的SAP相关信号通路包括AA代谢、亚油酸代谢信号通路等。该研究表明联合用药一方面在抗炎症反应和抑制动脉粥样硬化发展方面有疗效增强作用;另一方面注射用丹参多酚酸盐在阿司匹林抗血小板聚集的基础上能够保护血管内细胞和调节糖代谢,起到疗效相加作用。展开更多
基金supported by Key Project of Science and Technology Commission of Shanghai Municipality (No.11510500300)Ph.D.Programs Fund of Ministry of Education of China (No.20113108120022)
文摘Similarities and dissimilarities between biomolecular networks cannot be intuitively recognized even after the development of several comparison algorithms because of the lack of visualization tools. In this paper, an integrated tool kit named Biomolecular Network Match（BNMatch） is designed and developed based on Cytoscape—a popular and open-source tool for analyzing and visualizing networks. BNMatch integrates the comparison of the outputs of algorithms used for processing biomolecular networks and expresses the matching data between them by defining similar vertices and links with similar attributes. Moreover, in order to maintain consistency, their counterparts in other networks change when the nodes and edges in one of the compared networks are changed. It becomes easy for users to analyze similar networks by invoking comparison algorithms and visualizing the matching data between the networks using BNMatch.
基金Project supported by the Shanghai Leading Academic Discipline Project(Grnat No.J50103)the Ph D Programs Foundation of Ministry of Education of China(Grant No.20080280007)+1 种基金the Innovation Program of Municipal Education Commission of Shanghai Municipality(Grant No.11Y203)the Innovation Foundation of Shanghai University
文摘Cytoscape is one of the most popular platforms for biomolecular networks research. However Cytoscape cannot display biomolecular names according to their accession identifiers in different databases. A plugin named Ai2NU is designed and implemented in this paper. It can make biomolecular names displayed automatically in biomolecular networks graphs in Cytoscape by constructing a local dictionary. It is convenient for researchers to recognize biomolecules and enhance the research efficiency.
文摘This paper presents a solution methodology for H<sub>∞</sub>-feedback control design problem of Heparin controlled blood clotting network under the presence of stochastic noise. The formulaic solution procedure to solve nonlinear partial differential equation, the Hamilton-Jacobi-Isaacs equation with Successive Galrkin’s Approximation is sketched and validity is proved. According to Lyapunov’s theory, with solutions of the nonlinear PDEs, robust feedback control is designed. To confirm the performance and robustness of the designed controller, numerical and Monte-Carlo simulation results by Simulink software on MATLAB are provided.
文摘This paper presents a design method of H<sub>2</sub> and H<sub>∞</sub>-feedback control loop for nonlinear smooth gene networks that are in control affine form. Formulaic solution methodology for solving the nonlinear partial differential equations, namely the Hamilton-Jacobi-Bellman and Hamilton-Jacobi-Isaacs equations through successive Galerkin’s approximation is implemented and the results are compared. Throughout the implementation, there were several caveats that need to be further resolved for practical applications in general cases. Such issues and the clarification of causes are mathematically established and reviewed.
文摘该研究运用生物分子网络分析方法,预测注射用丹参多酚酸盐与阿司匹林联合用药治疗稳定型心绞痛的作用机制。从Genecards,STITCH,Dis Ge NET数据库获取注射用丹参多酚酸盐、阿司匹林及稳定型心绞痛(stable angina pectoris,SAP)的相关基因;采用Agilent Literature Search文献搜索软件构建生物分子网络;经AP,MCODE和MCL 3种方法对生物网络进行模块识别;通过DAVID软件进行相关KEGG通路识别。结果表明注射用丹参多酚酸盐和阿司匹林对SAP分子网络的覆盖率分别为45.92%,62.56%,联合用药的覆盖率为71.64%。注射用丹参多酚酸盐、阿司匹林与SAP前10个重要节点中,MAPK14,MAPK8,IL-6,IL-8为2个药物共同重叠的SAP重要节点,AKT1和IFNG为注射用丹参多酚酸盐单独重叠的SAP重要节点,EPHB2和TP53为阿司匹林单独重叠的SAP重要节点。2个药物共同参与的SAP相关信号通路包括JAK-STAT信号通路和MAPK信号通路等;注射用丹参多酚酸盐单独参与的SAP相关信号通路包括VEGF信号通路和1型糖尿病信号通路;阿司匹林单独参与的SAP相关信号通路包括AA代谢、亚油酸代谢信号通路等。该研究表明联合用药一方面在抗炎症反应和抑制动脉粥样硬化发展方面有疗效增强作用;另一方面注射用丹参多酚酸盐在阿司匹林抗血小板聚集的基础上能够保护血管内细胞和调节糖代谢,起到疗效相加作用。
