Department information

 

Course: Metabolic Modelling, Spring 07 (4 cr, 2 cu)

General information

Lectures:  Juho Rousu, Ari Rantanen
Exercises: Ari Rantanen


The course will cover some main topics of computational modelling of metabolism (see the schedule below)

Passing the course

• The course has been graded. The results can be seen on the 2. floor bulletin board. Feedback session on the exam is on May 11, 2007 from 15.15-16. Alternatively, visit Juho during his office hours
• Course exam (2.5. from 9 to 12):  maximum 40 points
• Exercises: maximum 20 points

30 points required for passing the course (grade 1/5), 50 points give maximum grade 5/5.

Course exam

• Wednesday 2.5.2007 9am-12pm, in B123
• Examined contents: lecture slides and exercises
• Not included: Lecture 26.3.07, slides 9-11 (SVD), Lecture 2.4.07, Slides 27-36
• Equations for kinetic rate laws will be given in the question paper, if required
• Probable composition of the exam: 5 questions, each worth 8 points, one question on term definitions, probably one essay

News

• Next exercises will be held on Thursday, 19.4. 14.15 - 16.00 in C222.
  
• There was a typo in the assingment 5 of exercises 3:  The last reaction to be removed from the netowrk should be C -> D, not A -> C.
  
• Intensive course on Proteomics and Bioinformatics, 7-11.5.2007.
• Lecture on tuesday, 3.4., will start at 15.15.
• no exercises on 6.4., no lectures on 9. -10. 4. (eastern break)
  

Time and place

• Lectures: 12.03.-24.04. Monday, Tuesday  14-16 B222
• Exercises: 12.03.-27.04. Friday 10-12 C221 
  

Exercises

• 16.3. MATLAB exercises (Jarmo Hurri's MATLAB slides, MATLAB on-line help)
• Solutions to assignments 1 -5, a solution to assignment 6.
• 23.3. Exercises, Sequences for assignments 3 and 4
  
• KEGG BLAST
• PROSITE
• ExPASy RandSeq
• 30.3. Exercises
• A solution to assignment 2, a solution to assignment 3
• We'll revisit assignment 1 on the next lecture
• 13.4. Exercises
• Solutions, MATLAB function for assingment 5.
  
• 19.4. Exercises
• Solutions,
  
• Augmented stoichiometric matrix for Assignment 2,
  
• Matrix A and vector b for Assignment 6 (A * v = b)
  
• 27.4. Exercises
  • Correction to assignment 2: the rate law should read Vmax S / (Km (1 + I /K_I) + S)
  • Article for assignment 5
  • Solutions for assignments 1-4

Tentative Schedule

• 12.3.  Introduction (slides), recap of linear algebra (slides)
  
• 13.3.  Metabolic reconstruction (slides)
  
• 19.3.  Structural analysis of metabolic networks (slides)
  
• 20.3.  Stoichiometric analysis of metabolic networks (slides)
  
• 26.3.  Biologically meaningful pathways in metabolic networks (slides)
  
• 27.3.  Introduction to linear programming (slides), Flux balance analysis (slides) (See also a solution to Assingment 1 of Exercises 3!)
  
• 2.4.   13C metabolic flux analysis (slides)
  
• 3.4.    NMR and metabolic flux ratio analysis
  
• 16.4.  Enzyme kinetics (slides)
• 17.4.  Metabolic control analysis(slides)
• 23.4.  Metabolic control analysis(slides)
• 24.4.  Recap
  

Background literature

• E. Klipp, R. Herlig, A. Kowald, C. Wierling, H. Lehrach: Systems Biology in Practice. Wiley-VCH, 2005.
• B. Palsson: Systems Biology: Properties of Reconstructed Networks. Cambridge University Press, 2006.