Topics
PUMAdb is a project within the Lewis-Sigler Institute for
Integrative Genomics of Princeton University. PUMAdb is
based on the Stanford Microarray
Database (SMD) software package.
If you want to refer to PUMAdb within a publication, please use:
http://puma.princeton.edu
The PUMAdb project is a collaboration with SMD, as mentioned above.
Most of the tools and software can referenced in the following SMD
publications:
Ball CA, Awad IA, Demeter J, Gollub J, Hebert JM,
Hernandez-Boussard T, Jin H, Matese JC, Nitzberg M, Wymore F,
Zachariah ZK, Brown PO, Sherlock G
The Stanford Microarray Database accommodates additional microarray
platforms and data formats. Nucleic Acids Res 2005 Jan
1;33(1):D580-2
Full text | PubMed
Gollub J, Ball CA, Binkley G, Demeter J, Finkelstein DB, Hebert JM,
Hernandez-Boussard T, Jin H, Kaloper M, Matese JC, Schroeder M, Brown
PO, Botstein D, Sherlock G. The Stanford Microarray Database: data
access and quality assessment tools. Nucleic Acids Res 2003
Jan 1;31(1):94-6.
Full
text | PubMed
Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese
JC, Dwight SS, Kaloper M, Weng S, Jin H, Ball CA, Eisen MB, Spellman
PT, Brown PO, Botstein D, Cherry JM. The Stanford Microarray
Database. Nucleic Acids Res 2001 Jan 1;29(1):152-5.
Full
text | PubMed
Various database statistics are available here
The external sources of biological annotation used in the database are
listed here.
For comparison (and other suggestions), see SMD's
system
- Hardware
The PUMAdb system currently operates on a Dell PowerEdge R820 with 4
Xeon ARK Processors (6 cores each) at 2.4 GHz, with 256 GB RAM.
Storage systems include a PowerVault MD3220 storage array (9 TB), 6
TB local disk and Network Appliance clustered storage.
- Database Management System (DBMS)
Currently using Oracle Database 11g Enterprise Edition Release
11.2.0.4.0 - 64bit Production, with partitioning option.
Also, see our database statistics).
- System Software and Web Server
The server is Linux [Red Hat Enterprise Linux Server release 6.6] and Apache 2.2.15
- Other software:
- Netpbm package 10.19 available from http://netpbm.sourceforge.net/
Some of the utilities from netpbm are used to create a proxy image
(.png) file on the fly from the two tiffs that are produced from
scanning of the array.
- perl, v5.8.4 built for sun4-solaris-64
Perl Modules (with version) :
- CGI : 4.51
- DBI : 1.643
- DBD::Oracle : 1.90
- LWP : 6.53
- GD : 2.73
- Storable : 3.21
C libraries :
Many other university microarray projects were initialized with the
Stanford package, and so could be considered part of the larger
collaboration:
