Network modeling in systems biology

...........................................................................................................iv CHAPTER 1. INTRODUCTION ................................................................................... 1 1.1 Background ......................................................................................................... 1 1.2 Network Diagram................................................................................................ 1 1.3 Two major methodologies to model biological systems in network .................. 3 1.3.1 Static large-scale biological network modeling ........................................... 3 1.3.2 Dynamic Quantitative modeling .................................................................. 6 1.4 Proposed methods and contributions of this work .............................................. 7 1.5 Organization ........................................................................................................ 8 CHAPTER 2. OMICSVIZ AND OMICSANALYZER FOR INTEGRATING AND ANALYZING OMICS DATA IN NETWORK CONTEXT .......................................... 10 2.1 Network provides graceful and concrete modeling platform to integrate complex large-scale biological datasets. ...................................................................... 10 2.2 Introduction to Cytoscape ................................................................................. 12 2.3 OmicsViz: Cytoscape plug-in for visualizing omics data across species ......... 14 2.3.1 Omics data import and mapping ................................................................ 14 2.3.2 Data Visualization ..................................................................................... 16 2.3.3 Usage example ........................................................................................... 17 2.4 OmicsAnalyzer: a Cytoscape plug-in suite for modeling omics data ............... 17 2.4.1 Architecture of OmicsAnalyzer ................................................................. 18 2.4.2 Data collection and pre-processing ............................................................ 19 2.4.3 OmicsAnalyzer Statistical Analysis .......................................................... 20 2.4.4 OmicsAnalyzer Visualization .................................................................... 22 CHAPTER 3. CYTOMODELER, A TOOL FOR BRIDGING LARGE SCALE NETWORK ANALYSIS AND DYNAMIC QUANTITATIVE MODELING ............. 25 3.1 Introduction ....................................................................................................... 25 3.1.1 Architecture of CytoModeler ..................................................................... 28 3.1.2 CytoModeler Model Editor ....................................................................... 30 3.1.3 CytoModeler SBML Exchanger ................................................................ 33 3.1.4 CytoModeler Simulation Interface ............................................................ 34 3.1.5 CytoModeler Visualizer ............................................................................ 38 3.2 An Usage Example: Build SM-SNARE Model Using CytoModeler ............... 43