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