This section discusses the installation of MAExplorer as a stand-alone application on a variety of computers. Since Java is portable between Microsoft Windows (95/98/NT/2000/XP), Macintoshes, Linux, Solaris, etc., it is possible to freely download and install MAExplorer and Cvt2Mae on your computer and run it as an application program.

There is a discussion on using it with other arrays (Appendix C) that requires editing data files for use with MAExplorer. An array data conversion tool is being constructed which will automate this process in the future.

1. Stand-alone applications can utilize huge amounts of memory (for example, we were able to use >80Mb on a 128Mb Windows NT system). This means that an analysis of large numbers of hybridizations and complex statistical computations could be done locally.

2. The stand-alone version can do local disk I/O. This means that data-mining sessions may be saved and restored locally to continue a data-mining session at a latter time. Plots may be saved as GIF (.gif) files, and text windows as ASCII text (.txt) files. Hybridized sample quantification files slowly downloaded from a microarray database Web server may be cached on the local machine - saving time when the data session is resumed at a later time. Users could then add GIPO conforming hybridized sample quantification files on their desktop and perform a data-mining analysis of hybridized data from multiple sources - mixing data from public servers as well as private data. This latter option would be most useful using commercial arrays.

3. Users may download a self-extracting Java application. This is available on the MAExplorer Web site for a variety of computer systems and includes a Java Virtual Machine (JVM) for your operating system. [The JVM is only available on the installers on the LECB/NCI web site, it is not available on the SourceForge Web site because of space considerations. However, if by some chance your computer does not have a JVM, this should not be a problem since the JVMs (called JDK's) are available at various Web sites.] This JVM does not interfere with any other JVMs you may already have installed. However, it guarantees optimal operation of MAExplorer. This makes the stand-alone application more robust than the Applet as well as being simple to install.

4. Having more memory implies allows taking advantage of more sophisticated statistical, clustering and data-mining methods, as well as working with large numbers of samples with larger numbers of spots. Some Web browsers will not give you access to large amounts of memory - even if it is available on your computer.

5. Having the stand-alone version on the user's computer allows them to configure a local database for their own data.

Figure D.1 Web page showing options for installing MAExplorer as a stand-alone application. Installers are available for Windows95/98/NT/2000/XP, Mac OS, Solaris, Linux, Unix, and other Java enabled platforms.

D.2 Downloading MAExplorer for stand-alone use with other arrays

This installation process uses a commercial "Java Installer" (InstallAnywhere^(TM) by ZeroG Inc.) that requests you "Grant" it permission to save the installation on your computer. It will suggest where to install it or you can install it wherever you want. For example, in Windows it may suggest saving it in C:\Program Files\MAExplorer\ - you can specify an alternative directory if the default disk does not have much free space left.

1. Go to download MAExplorer to begin the installation.
2. With Netscape, Click on "Grant" to questions "Starting programs stored on your computer" and "Reading, modification, or deletion of nay of your files". With Internet Explorer, click on "Yes" in response to the popup window "Do you want to install and run ...". [All data files are kept in the same directory tree where the MAExplorer program is kept. MAExplorer does not use any other directories on your computer and does not affect other Java programs on your computer.]
3. Either click on the default "Download ..." button that was automatically determined for your machine or scroll down and click on a "download" hypertext link for the operating system you want to download. If it is the latter, it pops up a "Save as" window for you to select a temporary directory in which to put the "installMae.exe" (Windows), "installMae.bin" (MacOS and Unix systems), etc. In Windows this could be "C:\Temp" or in Unix "/var/tmp", etc. After you have installed MAExplorer, you can delete this file.
4. After the file was downloaded on your machine, go to that directory and start that file (e.g. click on it on a Windows or MacOS system). [If you wish, you may exit your Web browser at this point since it is no longer needed].
5. When the installer starts, it pops up a window "Preparing to Install" and gives you the option of selection a language. Click on the "OK" button.
6. It then pops up an "Introduction" window. Click on "Next".
7. It then pops up a "Choose Install Folder". You have the option of specifying a different directory. E.G. (on Windows) if it says: C:\Program Files\MAExplorer and you don't have space on disk C: but do on disk E: and want to put it into its own directory, you could specify it as E:\MAExplorer. Then click on the "Install" button.
8. It then pops up a new window with "Install Complete". Click on the "Done" button. You are now ready to run MAExplorer.

D.2.2.1 Subsequent updating of only the MAExplorer JAR file from the MAExplorer server

1. Download just the MAExplorer.jar file.
2. Use this to replace the previous version of the MAExplorer.jar file on your system with this file.

Additional instructions for Installing MAExplorer on Sun Solaris

  http://sunsolve.Sun.COM/pub-cgi/show.pl?target=patches/patch-access

1. Download Solaris version of MAExplorer by clicking on the correct link.
2. After downloading, open a shell or xterm window then, cd to the directory where you downloaded the installer.
3. At the prompt type: "sh ./installMAExplorer.bin". this will run Install Anywhere.
4. The InstallAnywhere program should now be running, follow the instructions to install MAExplorer.
5. After MAExplorer is installed click on the Exit key to end the Install Anywhere program. Then cd to the directory where it was installed and type "MAExplorer&" to run MAExplorer.
6. To uninstall MAExplorer: cd into /UninstallerData subdirectory and at the Unix prompt type Uninstall_MAExplorer. This will bring up a window to prompt you to uninstall MAExplorer. Click on uninstall button.

D.2.2 Enabling MAExplorer to fetch data from a microarray Web server

Table D.2.2 Parameters specifying Web database access. These optional parameters may be used for control access to a microarray Web database. The example values are shown for the MGAP database.

D.3 Starting MAExplorer by clicking on a .mae file

   (installation path)/MAExplorer MAE/(some startup file).mae

   set path = ($path <MAExplorer installation path>)

   MAExplorer MAE/(some startup file).mae

There is a set of sample MGAP .mae files in the MAE subdirectory in the downloaded installation.

D.4 The data file format for .mae startup files

The .mae startup files are simply tab-delimited ASCII files with a .mae file extension. These could be created or edited either manually (e.g. using Microsoft Excel and saving the file as a tab-delimited file) or by various database programs (eg. the NCI/CIT mAdb program, the MAExplorer Cvt2Mae program being developed). They may also be generated by MAExplorer (File:Database:Save as file DB). The .mae file form consists of two tab-delimited columns containing fields Name and Value. These field names appear in the first row. This is followed by instances of the various parameters. A simple .mae file is shown in the following table Table D.4 using a 4 sample Lactation database subset from the MGAP database. Although any of the configuration file values can be specified in the .mae file, we list some of the more common optional parameters are indicated in Table D.4.1.

Table D.4 The Minimum data required entries for .mae startup files. These entries are shown with example values from some of the data in the MGAP demonstration database. Each sample is specified by an imagei name.

Table D.4.1 Some of the common optional entries for .mae startup files. These entries are shown with example values for the 4 samples in Table D.4. See (Appendix C.5 for lists of many other options.

D.5 Using MAExplorer as an Applet on your computer

1. Create a a sub-directory dir/ in your htdocs/ Web server tree (where dir/is what you called the directory).
2. Create dir/Config and dir/Quant sub-directories.
3. Copy the MAExplorer.jar file into dir/.
4. Edit configuration files and copy them to dir/Config sub-directory.
5. Copy quantification files into the dir/Quant sub-directory.
6. Add HTML Web pages containing <APPLET> code (see example below).

The following is a simple example of HTML code containing an applet which will invoke MAExplorer. You may add other options with PARAMs in the Applet (or for that matter in the the .mae startup file) that overide any options normally specifed in the Configuration file (See Appendix C.5).

<HTML>
<HEAD>
<TITLE>MAExplorer Startup: C57B6 Pregnancy vs Lactation</TITLE>
</HEAD>

<BODY>
<H2>MAExplorer Startup: C57B6 Pregnancy vs Lactation</H2>

This startup database will start the MAExplorer. It contains a subset
of the database consisting of four C57B6 mammary development
hybridized samples (HP): two each for pregnancy and lactation.

<APPLET CODE=MAExplorer.class  ARCHIVE=MAExplorer.jar
        WIDTH=10 HEIGHT=10 ALIGN=absmiddle>
  <PARAM NAME=configFile VALUE=MaExplorerConfig-MGAP.txt>
  <PARAM NAME=dbSubset VALUE="C57B6 pregnancy vs lactation">
  <PARAM NAME=image1 VALUE=C57B6-p13.1>
  <PARAM NAME=image2 VALUE=C57B6-L1-30min>
  <PARAM NAME=image3 VALUE=C57B6-p13.2poly-A>
  <PARAM NAME=image4 VALUE=C57B6-L1-total>
  <PARAM NAME=Xlist VALUE=1,3>
  <PARAM NAME=Ylist VALUE=2,4>
  <PARAM NAME=Elist VALUE=1,3,2,4>
  <PARAM NAME=classNameX VALUE=Pregnancy>
  <PARAM NAME=classNameY VALUE=Lactation>
(Sorry, you need a Java-capable browser to view this.)
</APPLET>
</BODY>
</HTML>