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Generic infrastructure

Microarray technology

Micro-array

In life-science experimentation microarray technology has become an important tool in genome and gene-expression studies. However, nearly all array experiments are unique due to differences in experiment design, experimental procedure, level of completeness of the data and cellular responses. Also methods with which array studies are analyzed are topic of much bioinformatics research. Therefore state-of-the-art array analysis is subject to change and must be highly flexible.

Since a command line interface offers maximum flexibility, many bioinformaticians favor such an environment. On the other hand, the life sciences is an interdisciplinary science in which it is important to share methods and results. This is a dilemma because a command line interface in itself does not have facilities to share and manage experiment pipelines. Another aspect to array analysis is that at some points much computing power is needed. Since computational requirements are far from constant over time some kind of sharing of computational resources is needed.

e-BioGrid is open to take microarray dedicated projects on board. Contact us if you are involved in micro-array technology and you need support in software or hardware infrastructure.


Projects in this technology area

Development of PSEs for micro-array-based experiments. *
description:Nearly all micro-array experiments are unique due to differences in experiment design, experimental procedure, level of completeness of the data and cellular responses. Also methods with which array studies are analyzed are topic of much bioinformatics research. Therefore state-of-the-art array analysis is subject to change and must be highly flexible. Another aspect to array analysis is that at some points much computing power is needed. Here we propose to set up an architecture that implements Problem Solving Environments for six problem areas from array design to downstream expression analysis. We will do this by setting up web services and by the configuration of dedicated Virtual Laboratory Machine Images that can be instantiated in a High Performance Compute Cloud. These Machine Images can be shared and dynamically scaled to a large virtual computer cluster. The content of these Machine Images will be documented and stored in a public Document Management Server. The resources used, input data and experimental results can be stored in a private Result Representation Server.
applicant:Timo Breit, University of Amsterdam
results: Progenius is a new tool for micro-array design that was not yet available to the public
status:ongoing
team:Linda Bakker, Wim de Leeuw
type:This is a main project.
e-science tool for identifying common haplotypes
description:From SNP data common haplotypes are identified by using a tools prepared by the NBIC BRS team. The tool is running in Galaxy and will be made available on the BiG Grid computing infrastructure
applicant:Cisca Wijmenga, University of Groningen
results:
status:ongoing
team:Leon Mei, Marcel Kempenaar, Marc van Driel, Gerard te Meerman, Andre de Vries
type:This is a dedicated project.


* This is the main project in this technology area

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