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<strong>Postdoctoral researcher: <span
style="font-size: 10pt; font-family: 'Trebuchet MS';">BioExpert for
the definition of biological systems in systems biology<br>
<br>
</span></strong><br>
<em>Note: this is a position at the Science Faculty (BioSystems Data
Analysis Group) of the University of Amsterdam and not at the AMC.<br>
</em><br>
<b><span style="font-size: 10pt; font-family: 'Trebuchet MS';">Function
title:<span> </span></span></b><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">Postdoctoral
Researcher<b><br>
</b></span><STOCKTICKER><b><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">FTE</span></b></STOCKTICKER><b><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">:<span>
</span></span></b><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">1,0 fte (38
hours per week) / 4 years<b><br>
</b></span><b><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">Available per:<span>
</span></span></b><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">A.s.a.p.<br>
</span><b><span style="font-size: 10pt; font-family: 'Trebuchet MS';"><br>
</span></b><b><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">About the
position: <br>
</span></b><b><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">BioExpert for
the definition of biological systems in systems biology<br>
</span></b><span style="font-size: 10pt; font-family: 'Trebuchet MS';"><br>
</span><b><span style="font-size: 10pt; font-family: 'Trebuchet MS';"
lang="EN-GB">Project<br>
</span></b><span style="font-size: 11pt;" lang="EN-GB"><font
face="Times New Roman">S</font></span><span
style="font-size: 10pt; font-family: 'Trebuchet MS';" lang="EN-GB">ystems
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; <a class="moz-txt-link-abbreviated" href="http://www.sysbio.nl">www.sysbio.nl</a>). <br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';">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;
<a class="moz-txt-link-abbreviated" href="http://www.nbic.nl">www.nbic.nl</a>). <br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';">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<span style="color: blue;">
</span>systems<span style="color: blue;"> </span>to serve as input for
mathematical modeling.<br>
</span><span style="font-size: 11pt;">
<p><font face="Times New Roman"> </font> </p>
</span><span
style="font-size: 10pt; color: red; font-family: 'Trebuchet MS';"><br>
</span><b><span style="font-size: 10pt; font-family: 'Trebuchet MS';">Tasks<br>
</span></b><span style="font-size: 10pt; font-family: 'Trebuchet MS';">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.<br>
</span><span
style="font-size: 10pt; color: red; font-family: 'Trebuchet MS';"><br>
</span><span
style="font-size: 10pt; color: red; font-family: 'Trebuchet MS';"><br>
</span><b><span style="font-size: 10pt; font-family: 'Trebuchet MS';"
lang="EN-GB">Requirements <br>
</span></b><span style="font-size: 10pt; font-family: 'Trebuchet MS';">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.<br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';"><br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';">The
candidate should meet the following requirements:<br>
</span><span style="font-size: 10pt; font-family: Symbol;"><span>·<span
style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span></span><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">A PhD in a
relevant scientific discipline (e.g., (bio)informatics);<br>
</span><span style="font-size: 10pt; font-family: Symbol;"><span>·<span
style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span></span><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">Experience with
information management research;<br>
</span><span style="font-size: 10pt; font-family: Symbol;"><span>·<span
style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"> </span></span></span><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">Excellent
software developer (Java, Java frameworks (J2E, </span><CITY><PLACE><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">JENA</span> </PLACE></CITY><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">, </span><CITY><PLACE><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">AJAX</span> </PLACE></CITY><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">),
web-applications/services).<br>
</span><span style="font-size: 10pt; font-family: Symbol;"><span>·<span
style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span></span><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">Knowledge of RDF
and OWL;<br>
</span><span style="font-size: 10pt; font-family: Symbol;"><span>·<span
style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span></span><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">Experience with
systems biology markup languages (e.g., SBML)<br>
</span><span style="font-size: 10pt; font-family: Symbol;"><span>·<span
style="font-family: 'Times New Roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span></span><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">Sufficient
social skills to perform optimally in a dynamic scientific team and
willingness to collaborate with colleagues from other NCSB groups.<br>
</span><b><span style="font-size: 10pt; font-family: 'Trebuchet MS';"><br>
</span></b><b><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">About the
employer:<br>
</span></b><span style="font-size: 10pt; font-family: 'Trebuchet MS';">The
</span><PLACE><PLACETYPE><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">University</span>
</PLACETYPE><span style="font-size: 10pt; font-family: 'Trebuchet MS';">of
</span><PLACENAME><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">Amsterdam</span>
</PLACENAME></PLACE><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">(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, </span><CITY><PLACE><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">Amsterdam</span>
</PLACE></CITY><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">is a hub of
cultural and media activities. The </span><PLACE><PLACETYPE><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">University</span>
</PLACETYPE><span style="font-size: 10pt; font-family: 'Trebuchet MS';">of
</span><PLACENAME><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">Amsterdam</span>
</PLACENAME></PLACE><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">is a member of
the League of European Research Universities.<br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';"><br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';">The
Faculty of Science of the </span><PLACE><PLACETYPE><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">University</span>
</PLACETYPE><span style="font-size: 10pt; font-family: 'Trebuchet MS';">of
</span><PLACENAME><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">Amsterdam</span>
</PLACENAME></PLACE><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">(UvA) is one of </span><PLACE><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">Europe</span> </PLACE><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">'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.<br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';"><br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';">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 </span><COUNTRY-REGION><PLACE><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">Netherlands</span>
</PLACE></COUNTRY-REGION><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">.<br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';"><br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';">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.<br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';"><br>
</span><b><span style="font-size: 10pt; font-family: 'Trebuchet MS';"><br>
</span></b><b><span
style="font-size: 10pt; font-family: 'Trebuchet MS';">Additional
information:<br>
</span></b><span style="font-size: 10pt; font-family: 'Trebuchet MS';">Employment
basis: Temporary for specified period<br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';">Duration
of the contract: 3 years<br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';">Maximum
hours per week: 38<br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';"><br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';">Additional
conditions of employment:<br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';">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.<br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';"><br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';">Additional
information about the vacancy can be obtained from:<br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';"
lang="NL"><br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';"
lang="NL">Prof. A.H.C. van Kampen<br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';">BioSystems
Data Analysis (Medical Bioinformatics)<br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';">Telephone
number: +31 (0) 20 566 7096<br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';">E-mail
address: <a class="moz-txt-link-abbreviated" href="mailto:a.h.vankampen@amc.uva.nl">a.h.vankampen@amc.uva.nl</a><br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';"><a class="moz-txt-link-abbreviated" href="http://www.bioinformaticslaboratory.nl">www.bioinformaticslaboratory.nl</a><br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';"><a class="moz-txt-link-abbreviated" href="http://www.bdagroup.nl">www.bdagroup.nl</a><br>
</span><span style="font-size: 10pt; font-family: 'Trebuchet MS';"><br>
</span><b><span style="font-size: 10pt; font-family: 'Trebuchet MS';">Contact:<br>
</span></b><span style="font-size: 10pt; font-family: 'Trebuchet MS';">Applications
should include a detailed curriculum vitae and a letter of motivation,
and send by email to <a class="moz-txt-link-abbreviated" href="mailto:a.h.vankampen@amc.uva.nl">a.h.vankampen@amc.uva.nl</a><br>
</span>
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