About the Stanford Microarray Database (SMD)

Topics

• Citing SMD
• SMD Fees
• SMD Statistics
• External references in SMD
• The SMD system
  • Database Management System
  • System Software
  • Other Software

• Citing SMD
  
  Please cite :
  
  Demeter J, Beauheim C, Gollub J, Hernandez-Boussard T, Jin H, Maier D, Matese JC, Nitzberg M, Wymore F, Zachariah ZK, Brown PO, Sherlock G, Ball CA. The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res 2007 Jan 1;35(Database Issue):D766-770
  Full text  |  PubMed
  
  Our previous SMD publications are:
  
  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 pdf  |  PubMed
  
  If you want to refer to a URL for SMD, please use:
  
  http://smd.stanford.edu/
  
  
• SMD Usage Charges
  
  
  
  There may be charges associated with using SMD. The charges depend on the number of uploaded arrays within a year and they are slightly different depending on whether the lab loading them is at Stanford or at a different institution. This payment will cover access to SMD services for the period 01/01/2008 through 12/31/2008. We ask that you provide Ruth Graves with the source of the funds you will use, an administrative contact's name, phone number and e-mail address. Ruth Graves can be reached by e-mail at rgraves@stanford.edu or phone at 650-723-6163.
  

  SMD charges are detailed below. The actual charge includes an additional 56% surcharge, that covers standard Stanford overhead fees.

Labs at Stanford:



Number of arrays (#/year)	Charge (US$)
> 200	15,000.00
100 - 199	9,000.00
50 - 99	4,500.00
25 - 50	2,250.00
< 25	FREE


Labs outside Stanford:



Number of arrays (#/year)	Charge (US$)
> 200	15,000.00
100 - 199	9,000.00
50 - 99	4,500.00
< 50	2,250.00

• SMD statistics
  
  Various SMD statistics are available here
  
  
• External references in SMD
  
  The external sources of biological annotation used in SMD are listed here.
  
  
• The SMD system
  
  SMD's database server is currently an eight-processor Sun V880, which has 32GB of RAM installed. Our webserver is an eight-processor Sun E4500, with 8GB of RAM installed. We use the following software:
  
  
  • Database Management System (DBMS)
    
    SMD uses Oracle Server Enterprise Edition version 9i (9.2.0.1.0). In addition we have also purchased Oracle software for partitioning tables, as our table of results is several hundreds of millions of rows (see our SMD statistics).
    
    While it would be technically possible for SMD to run another DBMS, much of our code has Oracle specific features, in terms of some of the functions that SELECT statements may use, or in querying the database dictionary.
    
    
  • System software.
    
    The machine on which SMD resides currently uses SunOS 5.9 (aka Solaris 9).
    
    Again, there's no specific reason that a Solaris environment needs to be used, but our experience is that Oracle version upgrades and patches are more timely on the Solaris platform.
    
    
  • Other software:
    
    Perl 5.004_04 or later. We use 5.6.1
    
    Perl Modules :
    
    
    • CGI 2.78 (3.05 is available, but we haven't tried it)
    • DBI 1.42 (1.46 is available)
    • DBD::Oracle 1.15 (1.16 is available)
    • GD 1.19 (2.19 is available, and supports GIFs again, but we haven't yet upgraded)
    • LWP 5.53 (5.803 is available)
    • Storable 2.12 (2.13 is available)
    
    Web Server
    
    
    • Apache Web Server 1.3.20 (2.0.44 is available)
    
    C libraries :
    
    
    • GD 2.0.28 (2.0.33 is available)
    • Net pbm package 9.10 (10.26 is available - we haven't tested it) available from http://download.sourceforge.net/netpbm/ Some of the utilities from netpbm are used to create a gif file on the fly from the two tifs that are produced from scanning of the array.

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  Please send comments or questions to: array@genome.stanford.edu

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