[Coral-List] 2 PhD Student Positions in Simulation of developmental regulatory networks in sponges and corals

Jaap Kaandorp jaapk at science.uva.nl
Tue Jan 27 05:51:59 EST 2004





Two Ph.D. students Scientific Computing (position 1) / Numerical Mathematics & Scientific 
Computing (position 2)



Project: ``Simulation of developmental regulatory networks in sponges and sceleractinian
corals''

The project is financed by the Netherlands Organisation for Scientific 
Research, NWO, research program Computational Life Sciences  and consists 
of 2 Ph.D. positions, one (position 1) at the Section Computational Science 
of the Universiteit van Amsterdam (http://www.science.uva.nl/research/scs/) 
and one (position 2) at the Center for Mathematics and Computer Science (CWI) 
in Amsterdam (http://www.cwi.nl/~gollum/RegNet).

In this project we will develop a model for simulating regulatory networks
that is capable of quantitatively reproducing spatial and temporal
expression patterns in developmental processes.  The model will be coupled
with a biomechanical model of cell aggregates and used to study the
formation of spatial and temporal expression patterns of gene products
during development in cellular systems.  A major issue are correct
estimations of the parameter settings in the network model. Therefore the
model will be used in combination with optimization algorithms (simulated
annealing) to explore large parameter spaces of regulatory networks and to
infer parameters from actual spatial and temporal gene expression
patterns. As a case study we are planning to use the body plan formation
in relatively simple multi-cellular organisms (sponges and sceleractinian
corals).  Here we will closely collaborate with Prof W.E.G. Mueller
(Institut fuer Physiologische Chemie Johannes Gutenberg-Universitaet
Mainz, Germany) and Prof D.J. Miller (Biochemistry and Molecular Biology,
James Cook University, Australia).  The PhD student Scientific Computing 
within the Section Computational Science will in particular work on 
optimization methods and modelling cellular aggregates, while the PhD student 
at the Center for Mathematics and Computer Science will focus on the numerical 
methods for modelling the regulatory networks.


Details position 1 at the Section Computational Science of the Universiteit van Amsterdam
_____________________________________________________________________________________

It is a full-time position for a period of 4 years.
Candidates should have a master's degree (or equivalent) in scientific
computing or computational science, (computational) physics, chemistry, biology  or a
comparable expertise.  Candidates are also expected to have an active interest in
life science applications.  For information on appointment (salary, vacation pay, etc.) 
please read the full description on www.uva.nl/vacatures or www.english.uva.nl, choose 
'Vacancies'.  Applications quoting job reference number and marked ``strictly confidential'' 
(in the upper left hand corner of the envelope) should include a letter of motivation, a 
curriculum vitae, if available copies of research papers, MSc thesis and the names of three 
persons from who references may be obtained.  Students who are about to finish their 
M.Sc thesis are also encouraged to apply.  The UvA offers an international working 
environment, flexible working conditions and is willing to help with housing for foreigners.  
Applications should be sent to the Universiteit van Amsterdam, Faculty of Science / Personnel 
Department, to the attention of Mrs. A. A. Crajé, personnel advisor, Kruislaan 404, 1098 SM 
Amsterdam, The Netherlands.  Applications by E-mail will also be accepted: 
anny at science.uva.nl.  The application period will remain open until the position 
is filled; however, review of applications will commence on March 15, 2004, with the intent 
of filling the position as quickly as possible.

More information can be found at http://www.science.uva.nl/research/scs/ or contact
Dr. Jaap A. Kaandorp, E-mail jaapk at science.uva.nl, telephone +31 20 525 7539.


Details position 2 at the Center for Mathematics and Computer Science (CWI) in Amsterdam
________________________________________________________________________________________

It is a full-time position for a period of 4 years.  Applications are invited from candidates 
with with a good knowledge of the numerical analysis of ODEs/PDEs and an MSc in mathematics, 
scientific computing or computational science, (computational) physics, chemistry, biology, 
computational fluid dynamics, or a comparable expertise.  Candidates are also expected to 
have an active interest in life science applications.  The salary with related employment 
conditions is according to regulations for OIOs (Onderzoekers in Opleiding) in the 
"CAO-onderzoekinstellingen" (collective employment agreement Dutch research institutes). 
Moreover CWI offers attractive working conditions, including flexibility, child care, and 
help with housing for foreigners.  Applications should be sent to Joke Blom, CWI/MAS, 
P.O. Box 94079, 1090 GB Amsterdam, the Netherlands.  E-mail: gollum at cwi.nl, with mentioning 
of "PhD Vacancy MAS1 - RegNet".  The application period will remain open until the position 
is filled; however, review of applications will commence on February 1, 2004, with the intent 
of filling the position as quickly as possible.  Your application should provide a concise 
description of your mathematical education, your CV, examination marks and if possible a copy 
of your M.Sc thesis. Students who are about to finish their M.Sc thesis are also encouraged to 
apply.

More information can be found at http://www.cwi.nl/~gollum/RegNet or contact Joke Blom, 
E-mail: gollum at cwi.nl, telephone +31 20 592 4263



-- 
Dr. Jaap A. Kaandorp
Section Computational Science
Faculty of Science
University of Amsterdam
Kruislaan 403
1098 SJ Amsterdam
The Netherlands
Phone: +31 20 5257539 / +31 20 5257463
email: jaapk at science.uva.nl
fax: +31 20 5257490
URL: http://www.science.uva.nl/~jaapk/

See for the 1st International Symposium on Networks in Bioinformatics
March 22 - 23, 2004 in Amsterdam
http://www.science.uva.nl/research/scs/AMGC2004/




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