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FRTF01 Physiological Models and Computation FRTF01 Fysiologiska modeller och Beräkningar

FRTF01 Syllabus

This course is scheduled for the second quarter of the fall (Lp2) with a course syllabus.




News

 

Welcome to Carolina's office (M:2427b) on Thursday January 19, 12.15-12.45, for a display of the exams. 

8/12: No exercise session next week (week 50). You will be given feedback on your project by December 20.

29/11: Updated example code for exercise 5.4 given next to the exercise below.  

21/11: Extra exercise session on December 5 in M:E 13-15. The "Repetition" lecture is rescheduled to December 12. 

15/11: Supervisors have been assigned. See link under Project Groups and assigned supervisors

4/11: Suggestions for projects are now up. See link under Projects. Link to form for signing up for a project is found under Projects as well.

31/10: Handins and exercises are uploaded. See links under Exercises and Home-Work assignments, respectively.

The course starts Tuesday Nov 1.

Personnel & Instructors

The lectures are given by Rolf Johansson (Rolf.Johansson@control.lth.se, tel. 046-222 87 91, office M:5145; Office hour M16.00-17.00).

Problem solving sessions are given by:

Carolina Lidström (tel. 046-222 1570, Carolina.Lidstrom@control.lth.se, Office hour Mon 11-12, M:2427b)

Course Literature

C. Cobelli & E. Carson, Introduction to Modeling in Physiology and Medicine, Academic Press, Amsterdam, 2008.

Course Plan

Lectures

Lectures will be held in M:E, M:B and M:2112B as indicated below:

Week

Date

Nr

Contents

44

1/11

1

Introduction. Physiological Complexity. (M:B)

 

3/11

2

Modeling in Physiology.

 45

8/11

3

Control in Physiological Systems.

 

10/11

4

Physiological Feedback, Adaptation, Learning.

 46

15/11

5

Pharmacokinetics & Tracers.

 

17/11

6

Metabolism, Glucose & Insulin Dynamics.  (M:2112B)

 47

22/11

7

Biomechanics: Muscle Models, Postural Control, Gait.

 

24/11

8

Electrophysiology. The Hodgkin-Huxley Model. 

 48

28/11

9

Blood Flow Control, Temperature Control, Acid-Base Control.

 

29/11

10

System Identification. Measurements & Data-based modeling.

49

6/12

11

Project Presentation Seminar

 50 12/12 12 Repetition

 

Exercises

Problem solving sessions are given on alternating days each week in M:Ina3-4. The exercises can be found here

Week

Date

Time

Nr

Contents

44

1/11

15-17

E0

Matlab & Simulink Introduction.

 

3/11

13-15

E1

Biochemical Reactions.

 45

8/11

15-17

E2

Modeling in Physiology.

      

10/11

13-15

E3

Control in Physiological Systems.

 46

15/11

15-17

E4

Control in Physiological Systems.

 

17/11

13-15

E5

Pharmacokinetics & Tracers. Example code exercise 5.4

 47

22/11

15-17

E6

Glucose & Insulin Dynamics and solutions. insulin_data.mat

 

25/11

13-15

E7

Biomechanics.

 48

29/11

13-15

E8

The Hodgkin-Huxley Model.

 

1/12

15-17

E9

Blood Flow Control, Temperature Control, Concentration & pH Control.

 49

5/12

13-15 (M:E)

15-17 (Ina3:4)

Extra

E10

Compensation for cancelled exercise. 

System Identification. Metanol_data.mat

 

6/12

15-17

Extra

Repetiton


Home-Work Assignments

There are four compulsory home-work assignments throughout the course. You may undertake the assigments in groups of two. Your solutions should be:

  • clearly written using a word processor (Microsoft Word, Open Office, Latex, etc). Save and send in the assignment as a .pdf-file.
  • each page should have your name(s) at the top of the page, one assignment report per 2 students if possible.
  • if you include figures, make sure they are of good quality and that you state the source. If you include plots, make sure that the axes are labeled. Below each figure or plot you should add a description.
  • handed in according to the deadlines by e-mail to FRTF01@control.lth.se.

 

Solutions not fulfilling these requirements will not be considered. The assigments are due according to the following:

Week

Date

Nr

Contents

47

16/11

HW1

EnzymeKinetics. Files: HW1

48

23/11

HW2

PupilReflexDynamics. Files: HW2

49

30/11

HW3

Glucose & InsulinDynamics. Files: HW3

50

7/12

HW4

The Hodgkin-HuxleyModel. Files: HW4

 

Projects

Choose a model of a physiological system from the project list (see link below) or from the literature according to your interest. Perform mathematical analysis of the model and evaluate its properties with a comparison of published experimental data, if possible. Otherwise you should make a qualitative assasment of the properties of your model. Draw conclusions on the relationships among structure and function. Perform a critical analysis of the model quality and the accuracy.

For topics and information about the projects, CLICK HERE

The FRTF01 course project can be done individually or in groups of two students. To make sure that two groups are not doing identical projects, you will have to register your project by filling in thisform (click). Also check here(click) that your intended project is not already registered by another group and contact the TAs if you are unsure about if your project is unique enough.  

Make a short project proposal with a work plan and send it to FRTF01@control.lth.se for approval by November 14. You will be assigned a supervisor. Make sure you set an appointment with him/her to initiate your project. A brief project report on scientific format should be written and sent to FRTF01@control.lth.se no later than December 12. A short presentation (5 min) should be given on the project seminar December 6  in M:E. We expect the project to take less than one week of work.

The examination of the FRTF01 projects will result in grades passed or passed with distinction. If your project grade is passed with distinction, the final grade of the course will be raised by one unit. If your exam grade is 3, then your final grade will be 4. If your exam grade is 4, then your final grade will be 5. The qualification for the grade with distinction is a well done project with some contribution beyond the minimum-effort project. Discuss such options with your advisor.

Deadlines: 

To decide upon project and group: 14/11

Project seminar: 6/12

To hand in final report: 12/12

Project Groups and assigned supervisors

Click HERE for the list of project groups with assigned supervisors. Please contact your supervisor as soon as possible to initiate the project. Contact information is given under Personnel and Instructors above.

 

Examination

The examination will be of a problem solving type. It is to be held on Wednesday, Jan 11, 14.00–19.00 in MA:9E, MA:9F. You may use the lecture slides, any books (without relevant exercises with solutions), standard mathematical tables, “Formelsamling i reglerteknik” and calculator at the examination.

Exam 2017-01-11

Exam, 2016-01-13

Exam, 2015-01-12

Other

Some material that helps you prepare for the course.

A Matlab tutorial - Control Toolbox

Modeling basics in Simulink

Download Matlab as LTH-student

Collection of common results and formulae in control (formelsamling i reglerteknik)