The Stanford Microarray Database: implementation of new analysis tools and open source release of software.
The Stanford Microarray Database (SMD; http://smd.stanford.edu/) is a research tool and archive that allows hundreds of researchers worldwide to store, annotate, analyze and share data generated by microarray technology. SMD supports most major microarray platforms, and is MIAME-supportive and can export or import MAGE-ML. The primary mission of SMD is to be a research tool that supports researchers from the point of data generation to data publication and dissemination, but it also provides unrestricted access to analysis tools and public data from 300 publications. In addition to supporting ongoing research, SMD makes its source code fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD. In this article, we describe several data analysis tools implemented in SMD and we discuss features of our software release.
Demeter
Janos
J
Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
Beauheim
Catherine
C
Gollub
Jeremy
J
Hernandez-Boussard
Tina
T
Jin
Heng
H
Maier
Donald
D
Matese
John C
JC
Nitzberg
Michael
M
Wymore
Farrell
F
Zachariah
Zachariah K
ZK
Brown
Patrick O
PO
Sherlock
Gavin
G
Ball
Catherine A
CA
D000818:Animals; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D006801:Humans; D020407:Internet; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software; D014584:User-Computer Interface