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DD2398 Quantitative Systems Biology 7.5 credits

Kvantitativ systembiologi

The purpose of the course is to present molecular
biology from a mechanistic perspective, and on
topical problems and methods in Systems Biology.
The focus of the course is describing gene regulation
and regulatory networks.

  • Educational level

    Second cycle

  • Academic level (A-D)

    D

  • Subject area

    Computer Science and Engineering

  • Grade scale

    A, B, C, D, E, FX, F

Course offerings

Spring 13 TBSBM for programme students

Spring 14 sysbio14 for programme students

Learning outcomes

After the course the student should be able to

* formulate mathematical models of gene regulatory networks on the level of kinetic equations

* simulate such systems and compare to experimental
  data

* discuss network properties in genomic data

* compute simple graph theoretical properties of such data

so that they will be able to

* independently construct computer programs that
  model melecular mechanisms of gene regulation

* in professional life identify biological problems
  that a sufficiently well describe that mathematical
  modeling and simulation could be of added value

Course main content

The basic circuitry in transcription regulation,
and other biological networks, including examples.
The principle of robustness in biological systems
of control.Kinetic proofreading and other
error-correcting mechanisms in biological
information-processing. Principles of kinetic
equations in gene regulatory modelling. Motifs
in biological and other networks.

Eligibility

Single course students: 90 university credits including 45 university credits in Mathematics or Information Technology. English B, or equivalent.

Prerequisites

The courses in the basic block on mathematics, computer science and numerical analysis on the D-, E- or F-programme.
The course SK2530 Introduction to Biomedicine
or equivalent.

Literature

Uri Alon, 2007
An Introduction to Systems Biology: Design Principles of Biological Circuits
Chapman & Hall/CRC Mathematical and Computational Biology Series
ISBN-10: 1-58488-642-0
ISBN-13: 978-158488-642-6

Examination

  • LAB1 - Laboratory Work, 2.5 credits, grade scale: P, F
  • TEN1 - Examination, 5.0 credits, grade scale: A, B, C, D, E, FX, F

Students will have one opportunity to correct every iuncorrectly executed homework assignment until the individual examination on the course start, no longer however than until three weeks after the last lecture in the course. Other possibilities and modalities to be examined on the course to be discussed with the examiner in each case.

In this course all the regulations of the code of honor at the School of Computer science and Communication apply, see: http://www.kth.se/csc/student/hederskodex/1.17237?l=en_UK.

Requirements for final grade

Four homework assignments give one grade point per
correctly executed assignments. For the highest grade, four correctly executed assignments and an individual examination are required.

The individual examination is conducted by the examiner with one assistant under at least 30 minutes and at most 60 minutes per student.

Offered by

CSC/Computer Science

Contact

Erik Aurell, tel: 5537 8813, e-post: eaurell@kth.se

Examiner

Erik Aurell <eaurell@kth.se>

Add-on studies

Courses in KTHs International Master's Program in
Computational and Systems Biology, in particular
Omic data systems biology (Jens Lagergren examiner,
course code missing), 2D1450 Algorithmic Bioinformatics,  SK2520 Experimental Methods in Molecular Biophysics, HL1008 Cellular and Molecular Biology, and DD2447 Statistical Methods in Applied Computer Science.

Version

Course plan valid from: Autumn 09.
Examination information valid from: Spring 09.