[BBC] Research pogrammer position

[Lodewyk Wessels]

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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:
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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.