Modeling of processes in cell biology, cellmod10

Information for cellmod10

Staff

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

News

The course evaluation (kursanalys) can now be found by selecting "Kursanalys" in the menue to the left.

Information about room for lectures:
The lectures will be in room 4523, D-building, Lindstedsvägen 5, floor 5. There will be signs in the stairway on floor 5 to guide you to the room. (Exceptions to this location is on Sept 23 and Oct 7 when we will be in room 1537.)
Note, there is a schedule change: F3 on Sept 7 is moved to Sept 11 at 13-15 (in 4523).

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

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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.

Reading material (in kursbunten) has been updated. The chapters from the material "Petersen, Basic Biophysics and cellular modeling, class notes" has been updated to the version from 2006. Please use this material instead of the material in the kursbunt.

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.

Preliminary course plan

The course consists of two parts LAB1 1.5p (3 labs: L1, L2, L3), 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 cellmod10

Course catalog

The course has a catalog (folder, map) on the Unix-computers: /info/cellmod10. 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.

Book

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:

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
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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, L3. 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.

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 biomod10 unix module to your account: course join cellmod10 (after this, log out and then log in again ). Files for the labs can be found at /info/cellmod10/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.

Exam (TEN2)

Time and place of the exam is 23/10 at 14-19 in L41, L42, L43.

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.