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System requirements for deploying the TMA data management system
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Chih Long Liu

System Requirements

This is a quick summary of the items you will need to set up your data management system for your TMAs. You will be needing the following:

  • Excel-format raw scoring workbooks representing data in the layout of your TMA. More on the format of these workbooks.

  • A lookup file, in text tabulated table format, containing your case descriptor information. More on the format of these workbooks.

  • The TreeView program. You will use this to rapidly visualize the scoring results of large sections of your TMA data. This program can be used in conjunction with Stainfinder. You can obtain TreeView at http://rana.lbl.gov/EisenSoftware.htm.

  • The Cluster program. You will use this to perform hierarchical clustering analysis on your data, if desired. The files output by this program are designed to work with TreeView. You can obtain Cluster at http://rana.lbl.gov/EisenSoftware.htm.

  • An on-line database of stored images. In the present configuration, the TMA-Deconvoluter and Stainfinder have been configured to work with image filenames defined by the nomenclature of the Bliss microscope system (Bacus Laboratories Inc.). Your database can run on the platform of your choice.

  • A web server that is capable of running CGI programs written in PERL. The Stainfinder walkthrough will include instructions on setting up a web server. Note: it is highly recommended that a system administrator or some other person experienced in networking and internet technologies set up the web server, since an improperly configured server can be vulnerable to attack by malicious users.

  • A Windows PC running Microsoft Excel 97 or later. This is necessary to run the TMA-Deconvoluter program. Note: the Mac OS is NOT supported, because the TMA-Deconvoluter makes the use of Active X controls, which are not available in Macintosh versions of Microsoft Office. See the FAQ for details.

When you have fulfilled all of these requirements, you may proceed to the walkthrough for setting up your system.

Last edited by Chih Long Liu on November 18, 2008 anno Domini