|
Code of course |
Name of course |
Responsible |
ECTS. |
Period |
|
|
Portal course part 1 |
Krab |
5 |
06-09-2004
/ 01-10-2004 |
|
|
Molecular
microbiology |
Oudega |
6 |
04-10-2004
/ 29-10-2004 |
|
|
Integrative
Bioinformatics |
Heringa |
5 |
01-11-2004 / 24-12-2004 |
|
|
Portal
course part 2 |
Krab |
4 |
01-11-2004 / 24-12-2004 |
|
|
Ethics, history of
science |
General course |
5 |
03-01-2005 / 28-01-2005 |
|
|
Interacting molecules |
Lill |
6 |
07-02-2005 / 04-03-2005 |
|
|
Proteins: structures,
folding and dynamics |
Vermeulen/Va der Vies |
5 |
07-03-2005 / 01-04-2005 |
|
|
Intracellular networks |
Westerhoff |
5 |
04-04-2005 / 29-04-2005 |
|
|
Self-organization and
emergence of function |
Westerhoff |
3 |
02-05-2005 / 13-05-2005 |
|
|
Scientific writing in
English |
General course |
3 |
|
|
|
International research
project |
Westerhoff |
65 |
June 2005, September
2005-June 2006 |
|
|
Comprehensive exam |
Westerhoff |
4 |
June 2006 |
|
name |
Portal course (parts 1 and 2) |
|
code |
|
|
coördinator |
Dr K. Krab and Prof.
Dr. H.V. Westerhoff |
|
lecturers |
Prof.
Dr H.V. Westerhoff, Dr K. Krab, Drs. F. Bruggeman, Dr. F.C. Boogerd, and guests |
|
ECTS |
9 |
|
Time
period |
September 2004,
November-December 2004 (half-time) |
|
aim |
An intensive course
for introduction of students with a Biology bachelor or Medical Biology
bachelor (or equivalent) to concepts and methods of physics, chemistry and
mathematics as necessary for the rest of the curriculum Systems
Biology/Biomolecular Integration. An intensive course
for introduction of students with a Physics, Chemistry of Mathematics
oriented bachelor to concepts and methods of Biology and Medical Biology as
necessary for the rest of the curriculum Systems Biology/Biomolecular
Integration. Goals: ·
Obtain sufficient
insight and knowledge across the range from medical biology to mathematics to
be able to follow the rest of the topmaster Systems Biology/Biomolecular
Integration ·
Appreciation and
understanding of the importance and motives of the ‘other’ disciplines ·
Ability of the
student to engage in thorough scientific discussions with students of the
‘other’ blood group |
|
contents |
Theor.
Introduction to: ·
Cell
Biology ·
Biophysics ·
Biochemistry ·
Chemistry ·
Mathematics ·
Molecular
genetics ·
Physics ·
Pathophysiology Practical: ·
short
course in experimentation (pipeting, centrifugation, spectrophotometer,
mathematical modeling) ·
socialization
weekend/midweek of the group |
|
methodology |
·
Lectures ·
Tutorials/discussions
of book material, lecture notes ·
Web-courses
·
Computer practicals ·
Lab- work:
Experiments |
|
literature |
·
Reader (10 euro) ·
Molecular Biology
of the Cell (‘Alberts’) |
|
teaching |
Active participation |
|
test |
Written exam |
|
target
group |
Students with
Bachelor Physics, Chemistry, Mathematics, Biology, Medical Biology with a
strong interest in the interface between these disciplines |
|
remarks |
The course is taught
in the English language, and involves much direct contact with the professors
and associate professors.
|
|
Required
knowledge |
Bachelor Physics,
Chemistry, Mathematics, Biology, Medical Biology or equivalent (see www.systembiology.net/topmaster
) |
|
name |
Molecular Microbiology |
|
code |
|
|
coördinator |
Prof. dr. B. Oudega |
|
lecturers |
Prof. Dr B. Oudega,
and the guest-lecturers dr. Luirink, dr. Otto, dr. Harms, Prof. dr. Lill,
Prof. dr. Westerhoff, dr. Van Spanning |
|
ECTS |
6 |
|
Time
period |
October 2004 |
|
aim |
Goals:
At the end, the
students should be able to understand and know:
|
|
contents |
Theory: ·
Lectures on:
functional aspects of the bacterial cell envelope, structure and function of
membrane components, chaperones and protein folding processes,
stress-response, biogenesis of membrane proteins, protein secretion routes,
biogenesis and function of fimbriae, iron uptake mechanisms, virulence
factors, regulation of gene expresion and DNA structure Practical: ·
for some students
laboratory work with several different molecular genetic and molecular
microbiology techniques and methods ·
for other students,
when appropriate, literature stuy and essay-writing |
|
methodology |
·
Lectures ·
Tutorials/discussions
of book material, lecture notes ·
Laboratory work:
students work in small groups (2-3 persons) ·
Literature study,
writing essay ·
Presentations |
|
literature |
Reader (ca 10 €) |
|
teaching |
Active participation
(October 2004). |
|
test |
Written exam |
|
target
group |
Students with
Bachelor Physics, Chemistry, Mathematics, Biology, Medical Biology with a
strong interest in the interface between these disciplines |
|
remarks |
The course is taught
in the English language, and involves much direct contact with the professors
and associate professors. |
|
required
knowledge |
Bachelor Physics,
Chemistry, Mathematics, Biology, Medical Biology plus topmaster portal
course, or equivalent |
|
name |
Sequence Analysis |
|
code |
|
|
coördinator |
Prof. Dr J. Heringa |
|
lecturers |
Prof. Dr J. Heringa,
Dr. J. Kleinjung, and other lecturers |
|
ECTS |
5 |
|
Time
period |
November/December
2004 |
|
aim |
·
A
theoretical and practical bioinformatics course about biological sequence
analysis. The course provides an introduction to the algorithmic and
biological principles of sequence analysis, as well as practical
implications. Goals:
|
|
contents |
Theory: ·
Dynamic
programming, database searching, pairwise and multiple alignment,
probabilistic methods, pattern matching, evolutionary models, and phylogeny. Practical: ·
Assignment
programming own alignment software based on dynamic programming ·
Assignment homology
searching and pattern recognition using biological and disease examples ·
Assignment multiple
alignment of biological sequences |
|
methodology |
·
13
Lectures (2 two-hour lectures per week) ·
Assignment
introductions ·
Computer practicals ·
Hands-on support |
|
literature |
·
E-course
material: http://ibivu.cs.vu.nl ·
Books: Arthur M. Lesk (2002) Introduction to
Bioinformatics, Oxford University Press, pp. 289, ISBN (Pbk) 0 19 925196 7. |
|
teaching |
Active participation
(November/December 2004). |
|
test |
Assignment results
and oral or written exam (depending on number of course students) |
|
target
group |
Students with Bachelor
Physics, Chemistry, Mathematics, Computer Science, Biology, or Medical
Natural Sciences, with a strong interest in Bioinformatics |
|
remarks |
The course is taught
in English. |
|
required
knowledge |
Bachelor Physics,
Chemistry, Mathematics, Computer Science, Biology, Medical Natural Sciences.
Some experience in programming is required. |
|
name |
Biological Fluorescence – Interactions of Biomolecules |
|
code |
|
|
coördinator |
Dr Y. Bollen |
|
lecturers |
Prof. Dr H. Lill,
Prof. Dr T. Visser, Dr. Y. Bollen, and guests |
|
ECTS |
6 |
|
Time
period |
February 2005 |
|
aim |
Goals: To introduce students into the
application of various fluorescent methods to tackle biochemical problems. Students should be
able to ·
plan and conduct
experiments utilizing fluorescent techniques to tackle own questions ·
evaluate
results on the basis of recent
literature Students should know ·
theoretical
principles and application of different fluorescence methods |
|
contents |
Theory: Theoretical
fundaments and practical applications of (time-resolved) fluorescence will be
covered. Practical: ·
laboratory
work with several different fluorescent methods, including a unique one
(PEFFLS) which has been developed within the department of Structural Biology ·
Interpretation
and evaluation of results will be carried out on site by course participants, assisted by lab personnel |
|
methodology |
·
Lectures ·
Tutorials/discussions
of book material, lecture notes ·
Laboratory
work: students work in small groups (2-3 persons) within the department’s
labs |
|
literature |
Reader (ca 5 €) |
|
teaching |
Active participation
(February 2005) |
|
test |
Written report |
|
target
group |
Students with
Bachelor Physics, Chemistry, Mathematics, Biology, Medical Biology with a
strong interest in the interface between these disciplines |
|
remarks |
The course is taught
in the English language, and involves much direct contact with the professors
and associate professors. |
|
Required
knowledge |
Bachelor Physics,
Chemistry, Mathematics, Biology, Medical Biology plus topmaster portal
course, or equivalent |
|
name |
Proteins: structures,
folding and dynamics |
|
code |
|
|
coördinator |
Prof. Dr. S. van der
Vies, Prof. Dr. N. Vermeulen |
|
lecturers |
Guest lecturers |
|
ECTS |
5 |
|
Time
period |
March 2005 |
|
aim |
An intensive course
to acquaint the students with the most modern and effective concepts and
methods for the study of proteins in action Goals: · To obtain knowledge and insights in the structure and the molecular mechanisms of action of proteins, in order to understand their basic and special biological functions. Special emphasis is will be given to the folding and the dynamics of proteins. |
|
contents |
Theory ·
The molecular
properties of the basic structural elements of DNA, lipids and proteins, such
as helices, sheets, strands, barrals etc will be discussed as well as the
forces and interactions responsible for the structure, the functions and the
flexibility of proteins. Special attention will be given to the complexity of
the protein folding process. The basic concepts and typical applications of
experimental techniques to solve macromolecular structures and to study their
dynamical behaviour will be reviewed, as well as computational techniques
that can be used to generate protein structures and to simulate their own
dynamics and the dynamics of their ligands. A number of more specific proteins
or complex protein systems will be discussed with the aim to understand, in
an intergrative way, the complexity of protein-protein and protein-ligand
interactions and the way the protein (complex) functions, if possible while
in action. Practical: ·
In silico
visualisation of selected proteins and protein-ligand interactions ·
In silico
construction and engineering of proteins ·
In silico control
analysis on the basis of earlier experimental results |
|
methodology |
·
Tutorials/discussions
of book material, lecture notes ·
Web-courses ·
Computer practical
classes ·
Lab-inspection
work: Students follow and assist an experienced postdoc/Ph D student
performing a key experiment. Data evaluation and interpretation on site. |
|
literature |
·
Introduction to
Protein Structure, Carl Branden en John Tooze, 1999, Garland Publishing Inc. ·
E-course material ·
Recent articles
from Nature Structural and Molecular Biology |
|
teaching |
Active participation
(March 2005) |
|
test |
Written exam |
|
target
group |
Students with
Bachelor Physics, Chemistry, Mathematics, Biology, Medical Biology with a
strong interest in the interface between these disciplines |
|
remarks |
The course is taught
in the English language, and involves much direct contact with (associate)
professors.
|
|
Required
knowledge |
Bachelor Physics,
Chemistry, Mathematics, Biology, Medical Biology plus topmaster portal
course, or equivalent |
|
name |
Intracellular networks |
|
code |
|
|
coördinator |
prof. Dr H.V.
Westerhoff |
|
lecturers |
Prof.
Dr H.V. Westerhoff, Dr B.M. Bakker, Prof. Dr J. L. Snoep, and guests |
|
ECTS |
5 |
|
Time
period |
February 2005 |
|
aim |
An intensive course
for introduction to cell biological networks. Goals: ·
The
course gives an introduction into the behavior of intracellular networks,
including metabolic pathways, signal transduction chains, gene expression
pathways and their hierarchical organization. Metabolic and Hierarchical Control Analysis, Biological Non
Equilibrium Thermodynamics, Biological (Self-), Genetic Network Analysis,
Elementary Mode Analysis, Flux (Balance Analysis) will be explained and
practiced. The levels of genomics
(genome, transcriptome, proteome, metabolome and function) and their
interrelationships will be clarified, both theoretically and experimentally. |
|
contents |
Theory: ·
The
course gives an introduction into the behavior of intracellular networks,
including metabolic pathways, signal transduction chains, gene expression
pathways and their hierarchical organization. ·
Metabolic
and Hierarchical Control Analysis, Biological Non Equilibrium Thermodynamics,
Biological (Self-), Genetic Network Analysis, Elementary Mode Analysis, Flux
(Balance Analysis) will be explained and practiced. ·
The
levels of genomics (genome, transcriptome, proteome, metabolome and function)
and their interrelationships will be clarified, both theoretically and
experimentally. Practical: ·
inspection
experiments performing flux and metabolite measurements and subsequent
regulation analysis ·
inspection
experiments deigning network targeted inhibitors of parasites flux analysis
on the basis of a set of computer data ·
control
analysis on the basis of earlier experimental results |
|
methodology |
·
Lectures ·
Tutorials/discussions
of book material, lecture notes ·
Web-courses
(www.siliconcell.net ) ·
Computer practicals ·
Lab-inspection
work: Students follow and assist an experienced postdoc/Ph D student
performing a key experiment. Data evaluation and interpretation on site. |
|
literature |
·
Reader (10 euro) ·
E-course
material: http://www.bio.vu.nl/hwconf/teaching/Mathbiochemie/;
www.siliconcell.net
·
Books: Chapters from:Understanding the Control of
Metabolism (Fell, D) Portland Press; Metabolic Engineering in the Postgenomic
Era (Kohlodenko & Westerhoff, Editors), Horizon Bioscience;
Thermodynamics and Control of Biological Free-energy transduction (Westerhoff
and Van Dam), Elsevier |
|
teaching |
Actieve participation
(January 2005) |
|
test |
Written exam |
|
target
group |
Students with
Bachelor Physics, Chemistry, Mathematics, Biology, Medical Biology with a
strong interest in the interface between these disciplines |
|
remarks |
The course is taught
in the English language, and involves much direct contact with the professors
and associate professors.
|
|
Required
knowledge |
Bachelor Physics,
Chemistry, Mathematics, Biology, Medical Biology plus topmaster portal
course, or equivalent |
|
name |
Self-organization and emergence of function |
|
code |
Self-organisation,
emergence, function and complexity |
|
coördinator |
prof. dr H.V.
Westerhoff |
|
lecturers |
Prof.
Dr H.V. Westerhoff, Dr Ir. B. Kooi, Dr F.C. Boogerd, and guests |
|
ECTS |
3 |
|
Time
period |
May 2005 |
|
aim |
An intensive course
for introduction to biological self-organization Goals: ·
Appreciation and
understanding of the phenomenon that nonlinearly interacting processes can
lead to the generation of new properties.
|
|
contents |
Theory: ·
Stability
analysis ·
Far-from-equilibrium
thermodynamics ·
Biology
of pattern formation in ealry development ·
Fourier
and Metabolic Control Analysis of oscillatory systems ·
Biochemistry
of glycolytic oscillations and their synchronization ·
Biology
of adaptation, induction, robustness and selection ·
Dynamic
energy budget theory Practical: ·
inspection
experiments with synchronizing yeast glycolytic oscillaitons ·
computer
modelling of early development ·
use
of mathematica and maple for stability analysis |
|
methodology |
·
Lectures ·
Tutorials/discussions
of book material, lecture notes ·
Web-courses
·
Computer practicals ·
Lab- work:
Experiments ·
Data evaluation and
interpretation on site. |
|
literature |
·
Reader (10 euro) |
|
teaching |
Active participation
(May 2005) |
|
test |
Written exam |
|
target
group |
Students with
Bachelor Physics, Chemistry, Mathematics, Biology, Medical Biology with a
strong interest in the interface between these disciplines |
|
remarks |
The course is taught
in the English language, and involves much direct contact with the professors
and associate professors.
|
|
Required
knowledge |
Bachelor Physics,
Chemistry, Mathematics, Biology, Medical Biology plus topmaster portal
course, or equivalent |