GECKO: a complete large-scale gene expression analysis platform
Speaker: Joachim Theilhaber , Cambridge Genomics Center
Date: February 13 2006
Time: 11:30AM to 1:00PM
Location: TOC lab 32-G575
Host: P Clote/ BC & B Berger/ MIT
Contact: Kathleen Dickey, 617 253 3037, kvdickey@mit.edu
Relevant URL: http://www-math.mit.edu/compbiosem/
Gecko (Gene Expression: Computation and Knowledge Organization) is a
complete, high-capacity centralized gene expression analysis system,
developed in response to the needs of a distributed user community.
Based on a client-server architecture, with a centralized repository
of typically many tens of thousands of Affymetrix scans, Gecko
includes automatic processing pipelines for uploading data from remote
sites, a data base, a computational engine implementing ~50 different
analysis tools, and a client application. Among available analysis
tools are clustering methods, principal component analysis, supervised
classification including feature selection and cross-validation,
multi-factorial ANOVA, statistical contrast calculations, and various
post-processing tools for extracting data at given error rates or
significance levels. A unique feature of the Gecko architecture is
the concept of the Analysis Tree (actually, a directed acyclic graph),
in which all successive results in ongoing analyses are saved. This
approach has proven invaluable in allowing a large (~100 users) and
distributed community to share results, and to repeatedly return over
a span of years to older and potentially very complex analyses of gene
expression data.
The Gecko system is publicly available as free software
(http://geckoe.sourceforge.net). In totality or in parts, the
Gecko framework should prove useful to users and system developers
with a broad range of analysis needs.
MIT
Department of Mathematics
& The Theory of
Computation Group
At CSAIL
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