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Förslaget inkom 2010-10-11

Distributed software for large-scale gene expression analysis

OBS! ANSÖKNINGSTIDEN FÖR DETTA EXJOBB HAR LÖPT UT.
Genome-wide gene expression data acquired by microarrays is the most common high-throughput data type in biology and biomedicine today. We have recently developed a fast, scalable method for exploratory analysis of a large repository of such data, comprising approx. 100,000 microarrays and billions of data points. This master’s thesis work consists of further development of an existing in-house data analysis engine implemented in C/C++. In particular, this work involves implementation of (i) client/server communication, possibly via the Windows Remote Procedure Call (RPC) protocol, to enable data retrieval from client applications such as MatLab or Mathematica sessions, and (ii) a concurrent execution model, to take advantage of multiple CPU cores and/or multiple servers. A front end/user interface for this software will be developed separately. The software engine will be evaluated in pilot studies by biologists at Karolinska Institute and Harvard Medical School. This work is part of a larger project aiming to establish a major resource for gene expression analysis in collaboration with leading research groups in Sweden and abroad.

Prerequisites: strong computer science background, strong programming skills in C/C++, interprocess communication, computer networks, concurrent programming. Prior experience in bioinformatics and keen interest in biology and biomedicine is considered advantageous.



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