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KTH / CSC / Courses / DD2435 / biomod08

Mathematical modeling of biological systems, biomod08

Information for biomod08


Course administrator is Erik Fransén, erikf @ Office hours: according to personal agreement.
Teacher: Erik Fransén (EF)
Lab assistant: Sten Andersson (SA)


The re-exam (omtenta) will be January 5, 10.00-15.00 at Roslagstullsbacken 35. Send an email to erikf @ if you want to participate.

The course is finished. If you want to do a lab review, mail Erik at erikf(at) and suggest 3 different times. I will be out on a conference Nov 10-21.

The exam is corrected. You can pick up the exam in the student office at Osquars backe 2. The exam and suggesion of answer is found in the "Old Exams" file folder of the course. Grades are set according to the following: F:0-8.5 , E:9-10.5 , D:11-12.5 , C:13-14.5 , B:15-16.5 , A:17-20. If you wish to file a complaint, do not take the exam out of the student office. Instead, supply a letter to me with the exam.

Course evaluationThe course is soon finished and we would appreciate your feed-back and comments.

The exersizes and example problems given during lectures are now available in the folder for lecture notes as LectureExamples. The reading quality is not always great, and some notes are in Swedish, sorry about that.

Old exams in english. There were already 3 exams in english: 071025 (we will not have the format like Part I - but of course the content is still in the course), 051025 (ignore problem 1), 040819 (ignore problems 5, 6, 8). I have translated 061019 (look at 061019eng and 061019answ).

To check out the articles for the project, see PROJ2 towards the end of this page. There is a link to all articles. Then, you can also reserve an article by klicking the button.

Information about the exam, see questions and answers about the exam.

To get lab help, use the lab reservation system and book a time. In the field, indicate you need help. If you need additional help, book one more time, but book only when you have questions and not just in case.

Schedule / times for lab reviews. Please note that some hours for the lab reviews have been moved. See the reservation page for dates and times.

Background material tips. For a background in chemistry and specifically stochiometry, see chemical kinetics and stochiometry


Background material tips. In the folder with lecture notes, please see "CellularNeuroBG" for a background of the cell, see "Book of Genesis chapter 10 The network within" for biochemical signaling pathways in the cell, see lecture F8 Gibson and Mjolsness" for a background on genes and transcription.

The webpage and its content is now in english.

The first lecture is Sept 3 at 15-17 in room Q11.

Preliminary course plan

The course consists of three parts LAB1 1.5p (3 labs: L1, L2, L4 (L4 can be replaced by L3)), PROJ2 3p (lab L5 and one lab project), TEN2 4.5p (exam). See preliminary course plan.

Comments on the course

Comments on the course are very welcome. The earlier we get your commments, the sooner we are able to take action. A written web-based survey will be undertaken towards the end of the course. You can also contact the course administrator directly.

Course registration

If you want to attend the course, you should contact your student office (kansli/studievägledning) of your study programme. There is no maximum of participants, but note the course prerequisits listed in the study handbook.
As soon as the course has started you have to sign up for the labs. This is done by logging on to any of the unix-computers of the school. Please do the following commands:
res checkin biomod08

Course catalog

The course has a catalog (folder, map) on the Unix-computers: /info/biomod08. On this catalog there are text files, lab files etc for the course.

Reading material

The reading material is exptected to be read during the course. Lectures and labs only cover a part of the course content. During the course, additional material is handed out.


There will be a set of printed articles and book chapters sold by the school. This contains reading material covering the course. In addition to this we reccomend the following books:

Daniel Johnston and Samuel Miao-Sin Wu: Fundamentals of Cellular Neurophysiology, The MIT Press, ISBN 0-262-10053-3. Can be bought/ordered at larger book stores or the Internet.
C.P. Fall, E.S Marland, J.M. Wagner, J.J. Tyson (ed): Computational cell biology, Springer-Verlag, ISBN 0-387-95369-8.

You may also read the book by Gerstner and Kistler
Spiking Neuron Models. Single Neurons, Populations, Plasticity
Cambridge University Press, 2002
which can be found at the web

Additional course material

* Reading material (the pile of printed notes, kursbunt) can be found here.
* Reading directions (läsanvisningar) can be found here.
* Reading directions for Johnston and Wu are here.
* Lecture notes, see list here.
* Old exams. Entering the Bologna system, new forms for exams are used. Please find old exams here, but note that the format for this year might be different. Old exams

Labs (LAB1)

The course consists of three labs, to be done in groups of preferably two students. Each lab is to be worked out by the lab group and then shown/reviewed to the lab assistant (labredovisning). Note that labs take a considerable portion of the time you alot for the course. Three out of four labs are to be done according to the following: L1, L2, L4 (alternatively to L4 the lab L3 can be done instead). Those who already took DD2401/HL1009/7E1201 Neuroscience/Neurovetenskap should not do lab 4.The labs are shown (redovisade) at booked times, for reservation, see below. If all labs are not completed within one year from the start of the course, the course administrator may demand that all labs are redone.

You can find files for lab3b here. Files for lab4 and lab5 are found at CSCs unix computers at /info/biomod08/lab4/ and /info/biomod08/lab5/.

Lab review (labredovisning) Lab review of each lab is done according to the following: lab review format. To prepare for a lab review is this a part of the lab work. This preparation takes a considerable amount of time.

To get access to some programs, you should add the biomod08 unix module to your account: course join biomod08 (after this, log out and then log in again ). Files for the labs can be found at /info/biomod08/lab#

* Lab 1 notes "Computational biochemistry" (.pdf)
* Lab 2 notes "Membrane potential and stochastic voltage dependent ion channels" (.pdf)
* Lab 3a notes "Pattern formation in reaction-diffusion systems" (.pdf)
* Lab 3b notes "Reverse engineering" (.pdf)
* Lab 4a notes "Neural models: the axon" (.pdf)
* Lab 4b notes "Neuron and synapse models" (.pdf)
* Lab 5 notes "Biological neural networks" (.pdf)

CSCs computer halls

Your access card gives you access to the CSC computer halls 24 hours, but computer halls may be reserved during day time for other courses. Go here to find out if they are reserved.

There are rules of conduct for the computer halls. These prescribe how you should or should not behave in the computer halls.

General computer assistants are available in the computer halls on the 4th floor some hours each working day.

Code of honor, Hederskodex

The basic rule of course work is that the work you do (labs, assignments etc) you shold do yourself (except that labs may be done in groups of two). During lab review, all participants of the lab group must be able to present all the material, even material that may have been worked out by the lab partner.

Sometimes, when doing lab work or programming, it may be necessary to ask someone (another student, a lab assistant or teacher) for help or advice. This is allowed as long as the following is considered:

* If you have recieved help with more than a single line of code/text, you should give a written comment in the code/document stating who helped out, and with what.
* You have to understand the complete solution, including the parts you have recieved help with.

Any other form of collaboration or useage of other persons solutions or texts will be treated as breaking the rules of conduct, and can lead to loss of course credits or that a complaint is filed in.
This is a translated and changed version of the honorary codex used in the course "Introduction to computer science" at Stanford University. It is used in a multitude of the courses offered by CSC.

Doing labs at home

If you have a computer and access to internet at home, you may log in to the computers at CSC.

Project (PROJ2)

The first part of the project is lab L5. The second part is a project conducted in a group of 1-3 students. You can select between a reading project analyzing a scientific article about modeling, or you can do a small modeling project. If you choose your own project, it must be accepted by a teacher at the course. The project is presented as a verbal presentation for the class at the last lecture of the course. The schedule of the presentations will be found at the headline "News". Articles for the projects can be found here.

Book your project at the latest just after lecture F10 (please ignore the time information in the booking system).

The formant of the project presentation is as follows: The group has 5 minutes per person in the group. All members of a group must be present during the whole lecture (if presentations are split into two separate lectures, you only have to attend the lecture of your presentation). For a 3 person group, you have 15 minutes where one student presents the core problem adressed in the article as well as key results, the second student addresses strengths and what was most interesting of the study, and the third student addresses weaknesses of the study including suggestions of how it could have been done differently. In a group of 2 students, you have 10 minutes where one student addresses the core problem including key results and the second addresses strengths and weaknesses. On one person groups, you have 5 minutes to present core problems and key results. It is adviced to use a small number (about 2 per person) of OH or computer presentation slides to illustrate your points. It is important to not exceed the time allocated, this is part of your preparation.

Exam (TEN2)

Time and place of the exam is 21/10 at 14-19 in D41-D42.

The result of the exam is ready at the latest 3 weeks after the exam, and may be found at "My pages". Corrected exams can be requested at the student office (studentexpeditionen) at Osquars backe 2, floor 2 (ground floor). Complaints on the correction should be filed in in written form to the course administrator within 3 weeks from the time results were announted.

Sign-up for the exam

There is no separate sign-up for the exam.

Copyright © Sidansvarig: Erik Fransén <>
Uppdaterad 2008-12-21