Chip Scanner  
(GeneChip Scanner 30007G) Raw Hybridization Data-->----+
                                                       |
                                                       |
                                                       |
                                                       v

Affymetrix Workstation Computer                        |
(Windows XP)                                           |
                                          Affymetrix program
                                                   |
        Disk Storage                               |         
                           +-----<------------- Raw Data     
                           |                       |         
                           +-<--Processed Data     |         
                           |             |         |         
                           |             ^         |
                           |             |         |
                           |             +-<- Analysis programs (e.g., RMA)
                           |
                           v
                           |
                   Explorer file manager
                           | (mapped drive, e.g., h:)
                           |
                           v

• Before a GeneChip scan can be performed, an investigator (PI/technician) must complete a Project Folder and cRNA target record. This is done using a Web browser. This client interaction is depicted in the lowest level of this diagram.
• The core facility technician performs GeneChip hybridizations and scanning. The resulting raw data is transferred to the server. If secondary analyses are performed on the raw data, then the results can be transferred to the server.

Intranet                   |
(Fast ethernet)            | 
                          |||
                           |
                           v

• This is typically a 100 megabit ethernet connection that can transfer data at approximately 8 megabytes per second.

Server                     |
(Linux)                    v 
                      Samba share
                           |
   Disk Storage            |                                      
                           |                                      
        Raw Data-----Processed Data      Meta Data               
             |(.DAT)       |(.EXP,.RPT)     |(Project/cRNA info) 
             |             |                | (w/data links)     
             |             |                |                    
             |             |                |
             |       Mining Tools         mySQL 
             |             |                ^
   µArrayDB  |             |                |                          
    LIMS     v             v                v                          
             |             |                |    PHP4 glue code        
             |             |                |                          
             |             |                |                          
             |             |                |
             |             |                |    Apache Web server   
             +- - - > - - -+ - - - - > - - -|                        
                                            |
                                            ^
                                            |
                                            |
                                            |
                                            v

• Samba allows Windows PCs to map Linux disk drive space.
• Data is transferred to a server directory that is structured as follows: PI name / Project name / Experiment Group Name
• 'Meta data' is a term that refers to the descriptive information contained in the Project and cRNA target records.
• Each cRNA target record has a directory path link that points to the raw data.
• Mining tools are usually combinations of system utility functions with PHP control code.
• LIMS is an acronym for 'Laboratory Information Management System'.
• The PHP programming language is run as a module of the Apache Web Server.
• The Apache web server restricts browsing of microarrray data mapped into web space.

Internet                                    ^
                                            |  
                                           |X|
                                          |XXX|
                                           |X|
                                            |
                                            v

• This connection type varies. Common types are DSL and Cable modems which can transfer data at 1.5 megabits per second to yield approximately 100-150 kilobytes per second.

Client PC                                   |
(Browser                Registered Access   |       Password Access
 w/HTML/Javascript)                         |
                                          +-+-+
                                 Miner    |   |    PI      Administrator 
                           +-----------<--+   +-<->-+----------+
                           |                        |          |
                        Download                  Create     Manage
                           |                      - - - - - - - - -
                           v                         Meta data
                           |
   Disk Storage            |            
                        Raw Data        
                        Meta Data       
                      Processed Data    

• Client types are as follows: Principle Investigators (data contributors), Database Administrators and Data Miners.
• Miners must register to gain access to the database although a database preview feature is available without registration. A registered miner can only view data that has been released into the public domain at the discretion of the contributor. A registered miner can also download publicly available data, but can never modify data in the repository.
• Principal Investigators must create Project and cRNA target records via the web/browser interface prior to submitting their samples for quality control, GeneChip hybridization and scanning. These records can be modified as needed by the PI or the administrator.
• Administrators can access all data and modify it as required.