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Doctoral candidate position (PhD student) Systems Biology/Database and Information Systems open

Doctoral candidate position (PhD student)
Systems Biology/Database and Information Systems

Job offer opened: 26th of March, 2012

The junior research group „Simulation Experiment Management System" (SEMS) is looking for a PhD student. The offered contract is for a 40h/week, 3yrs, full time position (TVL-E13), starting from June 2012.

Area: Systems Biology, Database and Information Systems

Project objectives:
"Tools and concepts for Simulation Experiment Management in Systems Biology: Improving the production of simulation experiments through standard formats and management support" (SEMS)

Standardization efforts and the exchange of protocols to generate data in the life sciences have become a necessity for large scale projects and multinational collaborations. The data under consideration are highly context dependent and if the processes by which the data were generated are not sufficiently well documented, it becomes difficult to reproduce these results and to share and integrate results across projects. The same arguments apply to the generation of scientific results that are based on mathematical models and computer simulations. Systems biology is a scientific approach characterized by an iterative cycle of data-driven modelling and model-driven experimentation. The present project is to provide support for this iterative cycle through techniques and tools that improve and ease the working with simulation setups, in particular through better model version control.

Further information: www.sbi.uni-rostock.de/sems


Specific objectives for the PhD position:

The successful applicant for a PhD position will investigate methods and techniques for model version control. Models are here regarded as XML encodings of computational models of biological systems. Today, version changes on these models are not sufficiently stored, maintained, curated, classified and presented to the users of model databases. This project will enable model version control to ensure improved reusability of models in the computational biology field.

Main tasks
- Evaluation of existing version control techniques (XML and non-XML)
- Development of methods and concepts tailored to model version control in computational systems biology
- Development of an ontology of model changes
- Design and implementation of a database for the management of XML-encoded simulation descriptions & their integration with existing model data
- Data import, creation of sample XML files, prototype search interface

What we expect
- Experience with database systems and version control
- Experience with XML-data
- An interest in biological questions
- Good programming experience (preferred: Java)
- Good command of English
- Dedication & enthusiasm
- Master's degree or equivalent

What we offer
- International interdisciplinary training
- International working environment 
- Participation at presentations & scientific group events
- An excellent preparation for a scientific career
- Equal opportunity employer

Applications should include standard documents (cover letter, curriculum vitae, diploma certificate, etc.) and be addressed to (postal or e-mail):

Dr. Dagmar Waltemath
Department of Systems Biology and Bioinformatics
Institute for Computer Science
Ulmenstrasse 69 (building 3, 3rd floor)
18057 Rostock, Germany
dagmar.waltemath(at)uni-rostock.de

posted 2012.03.29