系統生物學 Systems Biology


教學網頁http://syslab.nchu.edu.tw/

授課老師:劉俊吉老師 陳盈璁老師

上課時間:週三 5, 6 節 (1:10pm ~ 3:00pm)

上課教室:703 (劉俊吉老師 研究室)

10/12 上課教室: 防檢疫大樓6樓 電腦教室 615 (COPASI 教學)

 

Textbook:


An Introduction to Systems Biology: Design Principles of Biological Circuits 

Author: Uri Alon

Publisher: Chapman and Hall/CRC

http://www.weizmann.ac.il/mcb/UriAlon/


References:



Syllabus:

  1. Transcription networks (ppt)
  2. Autoregulation (ppt) 
  3. The Feed-Forward Loop Network Motif (ppt) 
  4. Temporal Programs and the Global Structure (ppt) 
  5. Network Motifs (ppt) 
  6. Discovering regulatory and signaling circuits in molecular interaction (ppt)  
  7. Discovery of multi-dimensional modules (ppt)  
  8. Bayesian Probabilistic model (ppt)  
  9. Label propagation algorithm (ppt)
  10. A human phenome-interactome network of protein complexes (ppt)
  11. Hidden Markov Models (ppt)
  12. Baum-Welch Algorithm
  13. Bayesian Network 

 


Homework 1 (Due: Oct 19)



Homework 2 (Due: Nov 2)

1. Design a network motif. 
2. Write the equations with production and removal rates. 
3. Run COPASI to generate the simulated data. 
4. Explain your simulated data.



Homework 3  (Due: Nov 23)
  1. Select a time-course dataset from NCBI GEO ( >10 time points) http://www.ncbi.nlm.nih.gov/geo/
  2. For example, 
  3. Use Win-RAR to unzip data (http://www.winrar.com/)
  4. Write a program to search temporal programs.  
  5. You can refer to the R program (txt).
  6. Output a temporal program. 

Comments