Postdoctoral researcher: BioExpert for
the definition of biological systems in systems biology
Note: this is a position at the Science Faculty (BioSystems Data
Analysis Group) of the University of Amsterdam and not at the AMC.
Function
title: Postdoctoral
Researcher
FTE:
1,0 fte (38
hours per week) / 4 years
Available per:
A.s.a.p.
About the
position:
BioExpert for
the definition of biological systems in systems biology
Project
Systems
biology is rapidly developing as the scientific approach to understand
complex biological systems consisting of a large number of components
and their interactions. Experimental information about the components
of the system and their interplay is used to develop and test
mathematical models. The experimental work, biological knowledge and
experimental data and computational models are cornerstones in an
iterative cycle of data-driven modelling and model-driven
experimentation in the Netherlands Consortium for Systems Biology
(NCSB; www.sysbio.nl).
A
systems bioinformatics project is defined as part of the NCSB
programme. In this project five bioinformatics centers collaborate to
provide bioinformatics support to NCSB systems biology projects through
the development of methods for data and knowledge management and
through development, exchange, and computation of models. This
bioinformatics project in turn entails collaboration with several
experimental projects in the consortium. This project is also part of
the BioAssist programme of the Netherlands Bioinformatics Centre (NBIC;
www.nbic.nl).
As
part of the systems bioinformatics project the postdoc will work on the
BioExpert (bioexpert.nl) project. The overall aim of the BioExpert
project is to develop a framework to represent, integrate and present
(curated) knowledge of specific biological systems and to use this
information in subsequent modelling applications. The overall framework
is based on state-of-the-art approaches for Information Management
(e.g., RDF/OWL) and novel approaches for information (re)presentation
(i.e., concept map network). The BioExpert knowledge base stores
conceptual models that provide a comprehensive, accurate, and
up-to-date description of selected biological
systems to serve as input for
mathematical modeling.
Tasks
Your
main tasks are (a) acquisition of domain knowledge (biological, models
and parameters, etc) for selected biological systems, (b)
representation of this information in the current RDF/OWL framework,
(c) construction of concept maps to (re)present this information (d)
integration with systems biology markup languages (e.g., SBML, CellML,
KiSAO, Teddy, SBO) and modeling environments, (e) further development
of the BioExpert application (user interface, navigation/querying,
web-services to access data, visualization, etc) to enhance its use in
systems biology.
Requirements
We
are looking for an enthusiastic candidate with a background in
(bio)informatics and or biology with a strong interest in information
management research. The candidate is willing to combine research with
substantial tasks in knowledge acquisition and software development in
order to develop BioExpert into a functional systems biology tool.
The
candidate should meet the following requirements:
·
A PhD in a
relevant scientific discipline (e.g., (bio)informatics);
·
Experience with
information management research;
· Excellent
software developer (Java, Java frameworks (J2E, JENA , AJAX ),
web-applications/services).
·
Knowledge of RDF
and OWL;
·
Experience with
systems biology markup languages (e.g., SBML)
·
Sufficient
social skills to perform optimally in a dynamic scientific team and
willingness to collaborate with colleagues from other NCSB groups.
About the
employer:
The
University
of
Amsterdam
(UvA) is a
university with an internationally acclaimed profile, located at the
heart of the Dutch capital. As well as a world centre for business and
research, Amsterdam
is a hub of
cultural and media activities. The University
of
Amsterdam
is a member of
the League of European Research Universities.
The
Faculty of Science of the University
of
Amsterdam
(UvA) is one of Europe 's foremost
institutions for higher education and research in its chosen fields of
specialization. It plays an active role in international science
networks and collaborates with universities and industry. The Faculty
has approximately 2,000 students and 1,500 staff members spread over
four departments and ten research institutes. Each institute has its
own research programme, a substantial part of which is externally
financed by the Netherlands Organization for Scientific Research (NWO),
the Dutch government, the EU and various private enterprises.
In
2010, the Faculty will relocate to Science Park Amsterdam. Ambitious
building projects are paving the way for this relocation. The move will
make the Park one of the largest centres of academic research in the Netherlands
.
The
Swammerdam Institute for Life Sciences (SILS) is one of the Faculty's
largest institutes. Within it, approximately 250 scientists and staff
members perform excellent research centred on four themes: 1) The
Living Cell, 2) Plants and Health, 3) Inside and Beyond the Brain, and
4) Life Science Technologies. Institute members give advanced lectures
and courses, while the SILS itself stimulates scientific cooperation
between participating groups and colleagues all over the world.
Additional
information:
Employment
basis: Temporary for specified period
Duration
of the contract: 3 years
Maximum
hours per week: 38
Additional
conditions of employment:
The
appointment will be on temporary basis for a maximum period of three
years. Based on a full-time appointment (38 hours per week), the gross
monthly salary depends on the postdoc's expertise and experience. The
collective employment agreement of Dutch universities is applicable.
Additional
information about the vacancy can be obtained from:
Prof. A.H.C. van Kampen
BioSystems
Data Analysis (Medical Bioinformatics)
Telephone
number: +31 (0) 20 566 7096
E-mail
address: a.h.vankampen@amc.uva.nl
www.bioinformaticslaboratory.nl
www.bdagroup.nl
Contact:
Applications
should include a detailed curriculum vitae and a letter of motivation,
and send by email to a.h.vankampen@amc.uva.nl
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