COMPUTATIONAL BIOLOGY
AN INTENSIVE TRAINING COURSE IN A RAPIDLY EVOLVING FIELD
Offered by the BioSymTM and SIMOLIFETM Teams of the
Universities of Zürich
and Winterthur and the ETH Zürich
Sponsored by Swiss Virtual Campus
| Time: |
August 5 to August 11, 2007 |
| Participants: |
Students and researchers at the graduate, postgraduate and professional
level |
| Location: |
Alpine Lyceum Disentis, GR, Switzerland |
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| Application online: |
Deadline May, 25 |
| Student application forms: |
Application Process |
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Applicant's Statements |
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Financial Information |
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Submission Check |
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| Evaluation forms (for evaluators only) |
Evaluation |
COURSE OBJECTIVES
The purpose of the course is to provide an overview of the many
facets of the exciting field of computational biology by bringing together
various aspects of a number of biological and mathematical sciences. It
is primarily a skills course. Participants will develop mathematical models
to solve biological questions.
Since a major goal of the course is to initiate contacts between workers
in scientific fields which are not usually combined, it encourages
a rapprochement between various areas of biology, biochemistry, biophysics
and mathematics and treats them with an interdisciplinary outlook.
COURSE DESCRIPTION
Over a period of six days the participants
will be exposed to an in-depth treatment of how biological processes
can be described in mathematical terms and how biological concepts can be
translated into mathematical models. We will employ Matlab-Simulink and
other software tools.
This year’s course will focus on seven main themes which are most
central to the discipline of computational biology:
- Growth: Regulation of microbial growth, metabolism
and propagation in communities
- Biofilm formation: Development of single and multispecies
biofilms in 1, 2 and 3 dimensions
- Epidemics: Benefits from livestock vaccination to contain
infectious diseases in developing countries, e.g. Brucellosis
- Virulence and pathogenicity: Within-host HIV dynamics - estimation
of parameters
- Ecology and evolution: Definition of microbial diversity;
environmental regulation of selection and adaptation; phylogeny
- Human physiological processes: Glucose-Insulin regulation
in the human body
- Pharmacokinetics: Physiologically based predictions
of human pharmacokinetics
- Antibiotic resistance: Dynamics of resistant infections
and influence of control measures within patients, hospitals and communities
We will emphasize these topics but not exclude other biological systems
which are of interest to course students.
A core team of biologists, physicists and mathematicians will introduce
the topics, and a number of modelers will lead the course research
teams. The course will include daily lectures, exercises on pre-designed
models and the design of models for ones own research application. Participants
will get hands-on experience on designing models for solving current
questions relevant to the field, and they will exchange the results of their
modelling research via the BioSym platform.
The course will take place at the boarding school associated with the
Benedictine monestary in the beautiful mountain town
of Disentis. The atmosphere
lends itself well to the concentration needed for success in the course.
COURSE STRUCTURE
The course comprises short introductory lectures and exercises in
the morning and project work in the afternoon and the evening.
An important component are literature evaluations and discussions about
systems biological concepts. These will be offered during the course
as requested by the participants.
Literature evaluations will introduce the participants
to the motivation and processes which often underly model constructions.
The first day will be primarily devoted to the introduction of the
software tools and to biomathematical basics.
The project work is investigative, i.e. we will carry
out virtual experiments with the models, and thus discovering the role
of model parameters for an entire system. Course research themes will
be designed to educate students in current modeling techniques and
to encourage independent investigations.
The location offers an atmosphere for intensive studies
with full student participation in all aspects of the program for the
duration of the course. Proficiency in the English
language and basic mathematical
skills are essential. Course work begins early
in the morning and may typically run late into the evening. Although there
will be little time for activities other than course work, past experience
has shown that the very intensity of the work encourages long lasting friendships
and collaborations among the participants.
COURSE RESEARCH PROJECTS OFFERED
On the application form students will be asked to select themes
out of a number of course research topics.
The course directors will make the final assignments to research projects
from the most frequently chosen priorities and optimize the course
contents to student needs.
PARTICIPANTS
The contents and the academic level are directed towards advanced students
enroled in PhD and Special Masters programs as well as professionals
who would like to become acquainted with biological modelling.
A maximum of 25 participants will be accepted, a minimum of 15 are
needed to run the course.
WHAT WILL BE EXPECTED FROM THE PARTICIPANTS
During the course students are expected to
- actively participate in the lectures and discussions by bringing up
topics relating to course themes
- formulate systems biological problems and search for solutions
- carefully plan, carry out, document and interpret virtual experiments
- familiarize themselves with using the software and the pre-designed
models for their research topic
- search for and get acquainted with the relevant literature
- read recommended papers and translate them into models if appropriate
- write an electronic summary about their project theme, present the model
at the final minisymposium and make it available on the BioSymTM platform.
| LOCATION AND TIME |
| Lodging |
School dormitories of the Benedictine monestary at Disentis. All meals
at the school Cafeteria |
| Classes |
Daily at 08.00 in the assigned group rooms of the Disentis Lyceum. |
| Computer work |
Exercises and project work in the group rooms. All rooms
are equiped with Internet connections and WLAN for your own notebook.
Matlab and Simulink licenses are accessible via the terminal server at
the Faculty for Mathematics and Natural Sciences (MNF) of the University
of Zürich. |
| Lectures & colloquia |
Course lecture room or computer laboratories of the Disentis Lyceum. |
| Field trip |
Wednesday afternoon will be reserved for a field trip to the meromictic
Lago Cadagno in the Piora valley if the weather allows. Special schedule. |
| Minisymposium: |
Presentation of project work results Friday and Saturday morning in the lecture room.
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| COURSE ORGANIZERS |
| The course is organized by the BioSymTM project
group of the University of Zürich. Course instructors and teaching
staff are drawn from the BioSymTM team and from other systems biology research
groups as well as from applied fields. |
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| Advisory committee |
Barbour, Andrew D. |
Mathematical Biology, Institute of Mathematics,
University of Zürich |
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Bonhoeffer, Sebastian |
Theoretical Biology, ETH, Zürich |
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| Coordinator |
Kurt Hanselmann |
University of Zürich |
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| Teaching team |
Christoph Fuchs |
e-Learning coordinator MNF, University of Zürich |
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Kurt Hanselmann |
Microbiology, Institute of Plant Biology / Microbiology, University
of Zürich |
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Dominik Heinzmann |
Mathematics, Parasitology, University of Zürich |
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Barbara Hellriegel |
Theoretical
Biology, Anthropological Institute and Museum, University
of Zurich
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Roman Kälin |
Mathematics, Institute of Mathematics, University
of Zürich |
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Hansueli Schwarzenbach |
Physics, Center for Computational Physics, University of Applied
Sciences, Winterthur |
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Jakob Zinsstag
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Veterinary Medicine, Dept. of Epidemiology and Public Health, Swiss
Tropical Institute, Basel |
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Others |
TBA |
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| Web scripts, Matlab and Simulink models |
Stefan Schafroth |
Physics, ErSt Electronic GmbH and Physics Institute, University
of Zürich |
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| APPLICATION DETAILS |
| Admission |
The
admission process for the course is competitive. A maximum of 25
participants are admitted on the basis of their academic or teaching
records, demonstrated research and/or teaching interests and abilities,
originality, recommendations and career goals as they are related
to the course objectives. All applications will be reviewed by
the course education committee. If necessary, selection between
equally qualified participants will be made according to the time
of arrival of the application. Notification of acceptance and further
information will be sent to all applicants by the beginning of
June. |
| How to apply |
Complete the application included with this
announcement and submit it via the internet before May 25, 2007
to the Admission Office of the Computational Biology Course (BioSymTM
Computational Biology Course Coordinator, University of Zürich, Institute
of Mathematics, Winterthurerstr. 190, 8057 Zürich, Switzerland)
Students
who would like to apply for financial assistance should supply the appropriate
information on the application form. |
| Selection |
Please
respond to the details asked on the application forms. Your application
must contain two names of people,
other than a faculty member of the course, who would be able to
evaluate your professional experience, your committment to the
field of the course, your scientific abilities (creativity, imagination,
curiosity, initiative, skills) and your overall potential for success
in applying the course contents in your professional career. |
| Tuition |
1600 € for
the entire 6 day course. Included are lectures, course assistance, Internet
connections, modelling software and other course materials, room (single
occupancy, toilet and shower) and full board (breakfast, lunches and dinner).
Travel to Disentis and back is the responsibility of the participant.
Funds to cover the course costs should come from three sources: employer
support; personal investment; course stipend. |
| Stipends |
The
course is supported by a grant from the Swiss Virtual Campus, and
a number of stipends are thus available for students who would
not otherwise be able to pay the course fee. The awards will partially
cover tuition, room and board, but not travel. If you are a student
applying for financial aid, please submit the Scholarship application
form ("Financial Information"). Course students who are not Swiss-residents
may apply for the stipends as well. |
| Prerequisites |
Participants
should be relatively experienced in their scientific field. Basic
knowledge of biology, chemistry and mathematics are prerequisites
for successful participation. We recommend that participants review
basics in mathematics before the course. We encourage the use of
a personal notebook. It must contain a WLAN card. Students who
do not have a notebook or Powerbook MAC can apply for a rental
computer for the duration of the course. The organizers will arrange
for the rental computer. |
| Language |
The course will be taught in English. Proficiency in the English language
is an essential prerequisite for participation. |
| Student credit |
3 credits (ECTS) are given for the course (workload: 60 hrs during
and 30 hrs before the course). Upon request, the organizers will certify
the successful completion of the course, offer an opinion as to the credit
value of the program, and suggest an appropriate grade if requested to
do so. It is the student`s responsibility to validate these credits at
his or her home institution. Students may copy and distribute their certificates
as necessary; institutions desiring authentication may contact the organizers. |
| Insurance |
Accident and health insurance are the responsibility of the participant.
All participants will have to sign a “health insurance memo of understanding” which
shows prove of appropriate insurance coverage. The organizers undertake
no liability. Course fees do not include insurance coverage. |
| Visa requirements |
If you are an accepted foreign applicant who will require a visa
for participation in this training program in Switzerland, we will
mail the Internet link where you can find the necessary forms and
send you a formal invitation letter needed for the visa application. You
will then have to apply for the visa through the Swiss embassy in your
country. |
| Information |
Kurt Hanselmann, swiss | i-research and training, P.O. Box 1206, CH-8032 Zürich, Switzerland,
tel:
+41-44-63 48284, fax: +41-44-63 48204, Kurt Hanselmann |
Addresses
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before
and after the course: BioSymTM Computational Biology Course Coordinator,
University of Zürich, Institute of Mathematics, Winterthurerstr.
190, 8057 Zürich, Switzerland)
during the course, August 5 to August
11, 2007: BioSymTM Computational Biology Course, Klosterschule
Disentis, Postfach 74, CH-7180 Disentis/ Mustér / Switzerland
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| Conditions |
Your application will be confirmed by e-mail.
The
course costs are to be paid within 10 days after receiving notification of acceptance.
If
you withdraw your application before July 1, we will reimburse the paid fee minus
30 € administrative fee. No fees are reimbursed after July 1 unless your
reserved place in the course can be filled by someone else. You will then be
charged an administrative fee of € 100. |
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| Draft Program BioSymTM Computational Biology
Summer Course 2007 |
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Sunday |
Monday |
Tuesday |
Wednesday |
Thursday |
Friday |
Saturday |
| August 2007 |
5. |
6. |
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8. |
9. |
10. |
11. |
| 7-8 |
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Breakfast |
Breakfast |
Breakfast |
Breakfast |
Breakfast |
Breakfast |
| 8-9 |
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Minisymposium
Project presentations |
Minisymposium
Project presentations
continued |
| 9-10 |
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| 10-11 |
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| 11-12 |
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| 12-13 |
Travel to Disentis |
Lunch |
Lunch |
Lunch |
Lunch |
Lunch |
Lunch |
| 13-14 |
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End of course |
| 14-15 |
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Return from Disentis |
| 15-16 |
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| 17-18 |
Check-in,
Welcome |
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| 18-19 |
Reception and Dinner |
Dinner |
Dinner |
Dinner |
Dinner |
Dinner |
| 19-20 |
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| 20-21 |
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Pre-course preparation
30 hrs |
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Theory
10 hrs |
Exercises
10 hrs |
Project work 15 hrs |
Open discussions 10 hrs |
Presentations 10 hrs |
Report
5hrs |
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