[BBC] Research pogrammer position
Lodewyk Wessels
l.wessels at nki.nl
Thu Dec 20 15:59:15 CET 2007
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High-throughput, high-content support platform: research programmer
position.
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About the position:
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The recent developments in functional genomic technologies have made it
possible to unravel the role of large numbers of genes in important cellular
processes. A powerful new technology is based on RNA interference (RNAi) by
which the expression of individual genes can be silenced through small
interfering RNAs (siRNAs). The combination of RNAi with cell-based assays in
high- throughput screening (HTS) will yield valuable new insights for the
detection and treatment of disease. Several platforms have been developed to
systematically examine the consequence of inactivation of individual genes
in cell-based assays. In order to study more complex cellular phenotypes,
High-Content Screening (HCS) was introduced. HCS defines the role of targets
in cellular processes by combining fluorescence-based reagents, automated
fluorescence microscopy and image analysis to automatically extract temporal
and spatial information about multiple parameters within single cells. By
combining HCS and HTS, it is now possible to study the consequence of
inactivation of large numbers of individual genes, in large numbers of
individual cells, measured by multiple cellular parameters.
The implementation of HCS in HTS generates a wealth of data that will
require a dedicated support platform. The challenges involved in this
project include 1) efficient handling of the sheer volume of data (a
relatively small screen already produces 150 000 images, each 1.4 Mb in
size) and to do this across different locations; 2) processing of the images
to extract the relevant parameters; 3) the integration of these parameters
with other high-throughput data sources to extract new biological knowledge
and 4) providing capabilities to enable users to effectively visualize and
browse the database. It is essential that the platform include a flexible
database or data warehouse infrastructure. The platform will provide web
services, support for software development, and set software standards. The
support platform will be developed based on the GRID and VL-e infrastructure
as established by the Netherlands Bioinformatics Centre.
To help build this support platform we are looking for a scientific
programmer, who will participate in the design and implementation of the
platform and the required software tools.
About the candidate - Requirements:
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1. HBO, Bachelor or Masters degree in either informatics or biology with a
clear programming component;
2. Experience with dfatabases, webservices and workflow management systems,
programming (C, Java, Python, Perl and/or Shell programming, Unix) and/or
experience with bioinformatics / biostatistics software (R, Matlab) is
preferred;
3. Good communication and interpersonal skills to facilitate collaboration
with clinicians and biologists with very diverse scientific and statistical
background.
4. Good command of English.
About the employer:
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The position is embedded within the groups of Dr Roderick Beijersbergen who
is head of the NKI Robotics and Screening Center (NRSC)
(http://www.screeninc.nl) and the Bioinformatics and statistics group lead
by Dr Lodewyk Wessels (http://bioinformatics.nki.nl). These groups closely
collaborate with the Central Microarray facility at the NKI-AvL, which has
ample experience in constructing databases for expression data.
Research in the Netherlands Cancer Institute covers all major areas of
cancer research, with special emphasis on mouse models, mouse (reverse)
genetics, cell biology, immunology, translational research requiring close
collaboration between clinical and basic scientists and epidemiology and
psychosocial cancer research.
Employment conditions:
=================
The employment conditions follow general employment rules as laid down in
the CAO for hospitals. The salary will be determined depending on education
and experience.
Want to find out more?
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For further information about the position please contact Dr. Lodewyk
Wessels, tel. +31 20 512 7987 or e-mail: l.wessels at nki.nl
How to apply:
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Applications for this position should include a Curriculum Vitae with the
names and contact information of two professional references that can be
contacted for further information.
Send applications to:
The Personnel Department
The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital
Plesmanlaan 121
1066 CX Amsterdam
The Netherlands, or via email to work at nki.nl.
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