Mathematical Biology:
Metabolic Network Analysis - 2017
The course discusses the mathematical modelling of large
biochemical
networks, metabolic networks in particular, and the subsequent
contrained-based analysis of their dynamic properties. Focus will be on
the mathematical underpinning and algorithms involved. We introduce the
fundamental concepts of the stoichiometric matrix and flux vector and
show what information can already deduced from the first, e.g.
concerning possible steady state flux vectors for the system: extreme
pathways, elementary modes and the relationships among the two. Several
algorithms will be explained for computing them together with software
packages that implement these (e.g. FluxAnalyzer). The concepts are
applied to the problem of optimal metabolite production for a model
organism. If time permits, parametric sensitivity is discussed.
The course targeted at students in the Life Sciences,
Mathematics
and Bioinformatics. The topics will be dicsussed in a well-balanced
mixture of biology, biochemistry, mathematics and computer science.
Examination will be by means of assignments that students need to make
individually, and final team assignments in which in a small
interdisciplinary team specially selected research papers on
applications of metabolic network analysis are studied. The results are
presented to the other students. The team presentation and a written
report of the study are evaluated. The results of individual
assignments, team presentation and team reports are combined to obtain
the final grade.
Literature (facultative):
Systems Biology: properties of reconstructed networks,
Bernhard
O. Palsson, Cambridge University Press, 2006 (ISBN-13 978-0-521-85903-5)
Relevant papers from the scientific literature will be mentioned during
the lectures.
Announcements:
- There is NO LECTURE on Monday 6th March, to ease attendence of the Quantum Computing course.
- Instead there is a lecture on Monday 13th March, contrary to the mathematics course schedule.
- There is NO LECTURE on Monday 3rd April, due to an exam and the 'Nederlands Wiskunde Symposium'in Leiden.
- There is a lecture on Monday 10th April, contrary to the Computer Science schedule
- The LECTURE on Monday 10th April is CANCELLED, because of personal circumstances of the lecturer. (Posted: 06-04-2017, 10:18h).
- The first assignment has been handed out during the lecture of Monday, 24th April. A pdf-fiole is availble below. Deadline is May 8th, 2017, 23.59h.
- The LECTURE on Monday 1st May is CANCELLED, because of continuing personal circumstances of the lecturer. (Posted: 24-04-2017, 14:26h).
- The last lecture will take place on Monday 22nd May. On Monday 29th May the final presentation will take place in room Sn 402 in the morning (between 9.00-13.00h). A detailed time schedule will be made available. (Posted: 16-05-2017, 10:14h).
Course material
Slides of lectures:
- Lecture 1: Course introduction [pdf]
(0.4 MB)
- Lecture 1: Modelling biochemical reaction networks [pdf]
(1.4 MB)
- Lecture 2: Modelling biochemical reaction networks II [pdf]
(1.7 MB)
- Lecture 8: Computing ECs and EFMs [pdf]
(707 kB)
Lecture Notes (subject to updates):
An updated version of the Lecture Notes becomes available section-wise
during the course.
- Front matter (title page and table of contents) [pdf] (71 kB, vs. of 17 Feb 2017)
- Chapters 1-4 (mostly covered already by slides - see above)[pdf] (81 kB, vs. of 17 Feb 2017)
- Chapter 5: Mathematical modelling of metabolic network dynamics [pdf] (131 kB, vs. of 18 Feb 2017)
- Chapter 6: Extreme Currents, Elementary Flux Modes and Extreme Pathways [pdf] (142 kB, updated: vs. of 7 May 2017)
- Chapter 7: Algorithms for computing EC and EFMs [pdf] (273 kB, vs. of 26 Mar 2017)
- Appendices: A) Linear Algebra and B) Fundamental properties of convex cones [pdf] (164 kB, vs. of 17 Feb 2017)
- Bibliography [pdf] (31 kB, updated vs. of 7 May 2017)
- Handwritten notes on the Input-Output Feasability Array (IOFA)[pdf] (216 kB, vs. of 24 Apr 2017)
Examination
Assignments:
Assignments are sent to the students by email and become available