[Coral-List] PhD Computational biology of sponges and corals

[Jaap Kaandorp]

PhD Student for the project ``A Visual Exploration environment for 
Analyzing gene Regulation in Developmental processes (VEARD)''


The Section computational Science (University of Amsterdam) has a vacancy 
for a PhD Student for the project ``A Visual Exploration environment for 
Analyzing gene Regulation in Developmental processes (VEARD)'' Full-time 
(38 hours per week)

The project is financed by the Netherlands Organisation for Scientific 
Research, NWO, research program Visual Interactive Effective Worlds (VIEW). 
The project is a collaboration with the research group from Prof. R. van 
Liere of the Center for Mathematics and Computer Science (CWI) in Amsterdam.  
In this project we propose to develop visualization techniques for 
quantitative research on complex shaped and variable biological and 
simulated objects and techniques for the visualization of abstract 
n-dimensional parameter spaces in models of gene regulatory networks. 
The project aims to develop methods and tools to extract and present 
geometrical information from spatial measurements and simulation, to develop 
visualization methods to compare simulation models and measured data, and 
techniques for the navigation of morphometric parameter spaces (morphospaces) 
and model parameter spaces. We will focus on a prototypical case study: gene 
regulation of development in metazoans with a relatively simple body plan 
(sponges and scleractinian 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).  


Tasks
The PhD student Scientific Computing  and visualization will work on a visual 
exploration system suitable for analyzing bio-mechanical  models of growth 
and form,  models of the genetic regulatory network controlling the 
developmental process and methods for quantifying morphologies. The visual 
exploration system will used to explore virtual morphospaces.


Requirements
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.  Ability to operate in an 
international research team.  Fluency in oral and written English.


More information
Further information can be obtained from : Dr Jaap A. Kaandorp, Section 
Computational Science, University of Amsterdam, e-mail: jaapk at science.uva.nl. 
More information (application procedure, deadlines etc.) is available on 
the website http://www.uva.nl/vacatures

-- 
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 5257462
email: jaapk at science.uva.nl
fax: +31 20 5257490
URL: http://www.science.uva.nl/~jaapk/