網路生物學實作及應用
Implementation and Application of Network Biology
| 節 | 週三 |
|---|---|
2 09:00–09:50 | 網路生物學實作及應用 BI305（博愛） 3 節連堂 |
3 10:10–11:00 | |
4 11:10–12:00 |
* 根據陽明交大上課時間表所列
This course covers the practical tutorials for the construction of biological networks, the implementation of statistical/functional analysis, and the data integration as follows. (1) Introduction of databases or web servers for biological networks. (2) Basic and advanced tutorials for using Cytoscape, an open-source software platform for visualizing complex networks and integrating these with any type of attribute data. (3) Tutorials for processing raw data from gene regulation, protein-protein interactions, and protein complexes/modules as well as for network establishment, clustering, and enrichment analysis. (4) Practical tutorials of how to use genomic/proteomic data for biological network reconstruction, integration, and analysis. (5) Practical tutorials of how to use biological networks for exploring disease mechanisms and identifying biomarkers.
Basic knowledge in molecular biology, systems biology, and network biology
無備註
Class Participation (課堂參與) 20%,Oral Presentation and Written Report (期末口頭與書面報告) 40%
Homework (課後作業) 40%
Tool tutorials
Tutorial of Cytoscape, a tool for network data integration, analysis, and visualization
- 講授：
- 1
- 示範：
- 2
- 實作：
- 3
Data collection and processing
1. Gene expression, gene co-expression, and mutually exclusivity/ co-occurrence of genetic alterations 2. Protein-protein interactions, protein complexes/modules, and module-module interactions
- 講授：
- 2
- 示範：
- 1
- 實作：
- 3
Construction and analysis of biological networks
1. Gene regulatory network 2. Protein-protein interaction network 3. Protein/module interaction network 4. Functional enrichment 5. Network clustering
- 講授：
- 3
- 示範：
- 3
- 實作：
- 6
Integration of networks and biodata
1. Integration of biological networks/pathways with genomic/proteomic data 2. Identification of cancer biomarkers by using biological networks/pathways and genomic/proteomic data
- 講授：
- 2
- 示範：
- 2
- 實作：
- 5
Evaluation
1. Homework 2. Final oral presentation
- 實作：
- 6
Introduction
Introduction of databases or web servers for biological networks
- 講授：
- 3
- 示範：
- 3
- 實作：
- 3
| 週次 | 主題 |
|---|---|
| 第 1 週 | Class information (課程說明) 2/24 |
| 第 2 週 | Introduction of databases or web servers for biological networks I (常見生物網路資料庫及網站服務介紹 I) 3/3 |
| 第 3 週 | Introduction of databases or web servers for biological networks II (常見生物網路資料庫及網站服務介紹 II) 3/10 |
| 第 4 週 | The tutorial I of Cytoscape: construction of biological networks (Cytoscape 工具介紹 I: 生物網路建置) 3/17 |
| 第 5 週 | The tutorial II of Cytoscape: network data integration, analysis, and visualization (Cytoscape 工具介紹 II: 生物網路數據集成、分析及可視化) 3/24 |
| 第 6 週 | Data collection and processing for gene expression, gene co-expression, and mutually exclusivity/co-occurrence of genetic alterations (基因表現、基因共表現及遺傳改變中互斥及共存之數據收集和處理) 3/31 |
| 第 7 週 | Anniversary of the founding of a school (校際活動週) 4/7 |
| 第 8 週 | The practices of constructing gene regulatory networks and network topological/statistical analysis I (實作基因調控網絡及網路拓撲/統計分析 I) 4/14 |
| 第 9 週 | The practices of constructing gene regulatory networks and network topological/statistical analysis II (實作基因調控網絡及網路拓撲/統計分析 II) 4/21 |
| 第 10 週 | Data collection and processing for protein-protein interactions, protein complexes/modules, and module-module interactions (蛋白質-蛋白質交互作用及蛋白質複合物/模塊的數據收集和處理) 4/28 |
| 第 11 週 | The practices for constructing protein/module interaction networks and network clustering and functional enrichment analysis I (實作蛋白質/模組交互作用網絡、網絡聚類及富集分析 I) 5/5 |
| 第 12 週 | The practices for constructing protein/module interaction networks and network clustering and functional enrichment analysis II (實作蛋白質/模組交互作用網絡、網絡聚類和富集分析 II) 5/12 |
| 第 13 週 | The practice of integrating biological networks/pathways with genomic/proteomic data I (整合基因體/蛋白質體資料與生物網路/途徑之實作 I) 5/19 |
| 第 14 週 | The practice of integrating biological networks/pathways with genomic/proteomic data II (整合基因體/蛋白質體資料與生物網路/途徑之實作 II) 5/26 |
| 第 15 週 | Network medicine: identification of cancer biomarkers by using biological networks/pathways and genomic/proteomic data I (網路醫學:透過生物網路/途徑及基因組/蛋白質組資料辨識癌症生物標記 I) 6/2 |
| 第 16 週 | Oral presentation of the final project (期末作業報告) 6/9 |
| 第 17 週 | Network medicine: identification of cancer biomarkers by using biological networks/pathways and genomic/proteomic data II (網路醫學:透過生物網路/途徑及基因組/蛋白質組資料辨識癌症生物標記 II) 6/16 |
1. Albert-László Barabási, Network Science, Cambridge University Press, ISBN: 9781107076266, 2016 http://networksciencebook.com/ 2. Cytoscape tutorials https://github.com/cytoscape/cytoscape-tutorials/wiki
- 地點
- 賢齊館413室 (Room 413, Jan Qi Biomedical Engineering Building)
- 時間
- 14:00-16:00 pm, Thursday
- 聯絡方式
- Email: chunyulin@nctu.edu.tw ext.: 59735