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Dear all,<br>
<br>
We currently have a position for Scientific Programmer (see
attachment). <br>
<br>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify; line-height: normal;"><b><span
style="font-size: 10pt; font-family: "Trebuchet MS","sans-serif";">Scientific
programmer: <o:p></o:p></span></b></p>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify; line-height: normal;"><b><span
style="font-family: "Trebuchet MS","sans-serif";" lang="EN-US">BioExpert
for the definition
of biological systems in systems biology<br>
<br style="">
<!--[if !supportLineBreakNewLine]--><br style="">
<!--[endif]--><o:p></o:p></span></b></p>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify; line-height: normal;"><b><span
style="font-size: 10pt; font-family: "Trebuchet MS","sans-serif";">Function
title:
</span></b><span
style="font-size: 10pt; font-family: "Trebuchet MS","sans-serif";">Scientific
programmer<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify; line-height: normal;"><b><span
style="font-size: 10pt; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">FTE:
</span></b><span
style="font-size: 10pt; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">1,0 fte (38 hours per week) /
4 years<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify; line-height: normal;"><b><span
style="font-size: 10pt; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">Available
per:
</span></b><span
style="font-size: 10pt; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">A.s.a.p.<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify; line-height: normal;"><span
style="font-size: 10pt; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US"><br>
<b><br>
</b></span><b><span
style="font-size: 10pt; font-family: "Trebuchet MS","sans-serif";">About
the position: <o:p></o:p></span></b></p>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify; line-height: normal;"><b><span
style="font-size: 10pt; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US"><br>
</span></b><span
style="font-size: 10pt; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US"><br>
</span><b><span
style="font-size: 10pt; font-family: "Trebuchet MS","sans-serif";"
lang="EN-GB">Project<br>
</span></b><span style="font-family: "Times New Roman","serif";"
lang="EN-GB">S</span><span
style="font-size: 10pt; font-family: "Trebuchet MS","sans-serif";"
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","sans-serif";"
lang="EN-US">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>
As part of the systems bioinformatics project the scientific programmer
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.</span><span
style="font-family: "Verdana","sans-serif";" lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify;"><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif"; color: red;"
lang="EN-US"><br>
</span><b><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">Tasks<br>
</span></b><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">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 style="color: red;"><br>
<br>
</span></span><b><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-GB">Requirements <br>
</span></b><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">We are looking for an enthusiastic candidate with a
background in
(bio)informatics and or biology with a strong interest in information
management. The candidate is willing to take on substantial tasks in
knowledge
acquisition and software development in order to develop BioExpert into
a
functional systems biology tool.<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: justify;"><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">The candidate should ideally meet
the following requirements:<o:p></o:p></span></p>
<p class="MsoListParagraphCxSpFirst"
style="text-align: justify; text-indent: -18pt;"><!--[if !supportLists]--><span
style="font-size: 10pt; line-height: 115%; font-family: Symbol;"
lang="EN-US"><span style="">·<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><!--[endif]--><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">Background in a relevant scientific discipline
(e.g., (bio)informatics);<o:p></o:p></span></p>
<p class="MsoListParagraphCxSpMiddle"
style="margin-bottom: 0.0001pt; text-align: justify; text-indent: -18pt; line-height: normal;"><!--[if !supportLists]--><span
style="font-size: 10pt; font-family: Symbol;" lang="EN-US"><span
style="">·<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><!--[endif]--><span
style="font-size: 10pt; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">Experience with information management;<o:p></o:p></span></p>
<p class="MsoListParagraphCxSpMiddle"
style="margin-bottom: 0.0001pt; text-align: justify; text-indent: -18pt; line-height: normal;"><!--[if !supportLists]--><span
style="font-size: 10pt; font-family: Symbol;" lang="EN-US"><span
style="">·<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><!--[endif]--><span
style="font-size: 10pt; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">Excellent software developer (Java, Java frameworks (J2E,
JENA, AJAX),
web-applications/services).<o:p></o:p></span></p>
<p class="MsoListParagraphCxSpMiddle"
style="margin-bottom: 0.0001pt; text-align: justify; text-indent: -18pt; line-height: normal;"><!--[if !supportLists]--><span
style="font-size: 10pt; font-family: Symbol;" lang="EN-US"><span
style="">·<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><!--[endif]--><span
style="font-size: 10pt; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">Knowledge of RDF and OWL;<o:p></o:p></span></p>
<p class="MsoListParagraphCxSpLast"
style="margin-bottom: 0.0001pt; text-align: justify; text-indent: -18pt; line-height: normal;"><!--[if !supportLists]--><span
style="font-size: 10pt; font-family: Symbol;" lang="EN-US"><span
style="">·<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><!--[endif]--><span
style="font-size: 10pt; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">Experience with systems biology markup languages (e.g.,
SBML)<br>
Sufficient social skills to perform optimally in a dynamic scientific
team and
willingness to collaborate with colleagues from other NCSB groups.<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify;"><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US"><br>
<b><br>
About the employer:<o:p></o:p></b></span></p>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify;"><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">The University</span><span
style="font-size: 10pt; line-height: 115%; font-family: "Verdana","sans-serif";"
lang="EN-US"> </span><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">of Amsterdam</span><span
style="font-size: 10pt; line-height: 115%; font-family: "Verdana","sans-serif";"
lang="EN-US"> </span><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">(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</span><span
style="font-size: 10pt; line-height: 115%; font-family: "Verdana","sans-serif";"
lang="EN-US"> </span><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">is a hub of cultural and media activities. The University</span><span
style="font-size: 10pt; line-height: 115%; font-family: "Verdana","sans-serif";"
lang="EN-US"> </span><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">of Amsterdam</span><span
style="font-size: 10pt; line-height: 115%; font-family: "Verdana","sans-serif";"
lang="EN-US"> </span><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">is a member of the League of
European Research Universities.<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify;"><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US"><br>
The Faculty of Science of the University</span><span
style="font-size: 10pt; line-height: 115%; font-family: "Verdana","sans-serif";"
lang="EN-US"> </span><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">of Amsterdam</span><span
style="font-size: 10pt; line-height: 115%; font-family: "Verdana","sans-serif";"
lang="EN-US"> </span><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">(UvA) is one of Europe</span><span
style="font-size: 10pt; line-height: 115%; font-family: "Verdana","sans-serif";"
lang="EN-US"> </span><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">'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.<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify;"><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US"><br>
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</span><span
style="font-size: 10pt; line-height: 115%; font-family: "Verdana","sans-serif";"
lang="EN-US"> </span><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">.<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify;"><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US"><br>
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 centered 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>
<br>
<b>Additional information:<o:p></o:p></b></span></p>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify;"><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">Employment basis: Temporary for specified period<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify;"><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">Duration of the contract: 3 years<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify;"><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">Maximum hours per week: 38<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify;"><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">Additional conditions of employment:<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify;"><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US"><br>
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 expertise and experience. The collective employment
agreement
of Dutch universities is applicable.<br>
<br>
Additional information about the vacancy can be obtained from:<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify;"><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify;"><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";">Prof.
A.H.C. van Kampen<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify;"><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">BioSystems Data Analysis (Medical Bioinformatics)<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify;"><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">Telephone number: +31 (0) 20 566 7096<o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify;"><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US">E-mail address: <a class="moz-txt-link-abbreviated" href="mailto:a.h.vankampen@amc.uva.nl">a.h.vankampen@amc.uva.nl</a><o:p></o:p></span></p>
<p class="MsoNormal"
style="margin-bottom: 0.0001pt; text-align: justify;"><span
style="font-size: 10pt; line-height: 115%; font-family: "Trebuchet MS","sans-serif";"
lang="EN-US"><a class="moz-txt-link-abbreviated" href="http://www.bioinformaticslaboratory.nl">www.bioinformaticslaboratory.nl</a><br>
<a class="moz-txt-link-abbreviated" href="http://www.bdagroup.nl">www.bdagroup.nl</a><br>
<br>
<b>Contact:<br>
</b>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><o:p></o:p></span></p>
<br>
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<pre class="moz-signature" cols="72"><font color="#000099"
face="Times New Roman, Times, serif"><b>Prof dr Antoine H.C. van Kampe</b></font><font
face="Times New Roman, Times, serif"><font color="#000099"><b>n</b></font>
</font><font><font face="Times New Roman, Times, serif">
</font></font><font face="Times New Roman, Times, serif"><b>Netherlands Bioinformatics Centre (</b></font><i><font><font
face="Times New Roman, Times, serif"><a
class="moz-txt-link-abbreviated" href="http://www.nbic.nl">www.nbic.nl</a></font></font></i><font
face="Times New Roman, Times, serif"><b>)</b>
Scientific Director
<b>Bioinformatics Laboratory (Monday, Tuesday, Thursday)
</b> Clinical Epidemiology, Biostatistics and Bioinformatics (KEBB)
Academic Medical Center (AMC)
Visiting address: Meibergdreef 9, J1B-217-1 (J-building, floor 1B)
Postal address: PO Box 22700, 1100 DE Amsterdam, the Netherlands
</font><small><b><big><font face="Times New Roman, Times, serif"> </font></big></b><big><font
face="Times New Roman, Times, serif"> <font color="#000099"><i><a
class="moz-txt-link-abbreviated"
href="http://www.bioinformaticslaboratory.nl">www.bioinformaticslaboratory.nl</a></i></font></font></big><b><big><font
face="Times New Roman, Times, serif">
Biosystems Data Analysis (Wednesday, Friday)</font></big></b></small>
<big><font face="Times New Roman, Times, serif"><small> Swammerdam Institute for Life Sciences (SILS)</small></font></big>
<font face="Times New Roman, Times, serif"> University of Amsterdam</font>
<big><font face="Times New Roman, Times, serif"><small> Visiting address: Nieuwe Achtergracht 166, C-710
1018 WV Amsterdam, The Netherlands
<font color="#000099"><i><a class="moz-txt-link-abbreviated"
href="http://www.bdagroup.nl">www.bdagroup.nl</a></i></font>
</small></font></big><font><font><font><font
face="Times New Roman, Times, serif">Phone: ++31-20-5667096 (AMC) / ++31-20-5256547 (SILS)
Mobile: 06-41768067 (not switched on in the AMC)
Email: <a class="moz-txt-link-abbreviated"
href="mailto:a.h.vankampen@amc.uva.nl">a.h.vankampen@amc.uva.nl</a>
<a class="moz-txt-link-freetext" href="Skype:antoine.van.kampen">Skype:antoine.van.kampen</a>
Secretaresse: 020-5664626</font></font></font></font></pre>
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