Downloads for The MicroArray Explorer Project

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Program downloads   |   Update programs   |   Update jar file   |   Installation hints

The table below lists the various types of downloads: program installer, source code file, jar file, and information on installing the programs.

Types of download files available

You may download program installers for your particular computer for both ProtPlot. Click on the entries to download the installer or files.

Access of ProtPlot from the Web server

Program Installer
Update Program
Jar Version
Jar file(s) Source PRP data
ProtPlot 0.39.6 0.39.6 ProtPlot ProtPlot.jar N.A. yet PRP data

Upgrading the ProtPlot JAR program file after the initial installation

If you want to upgrade your installation to the latest JAR files, simply download the JAR files and save them wherever you have installed the programs replacing the previous jar files. For example, in a typical Windows OS installation, the ProtPlot.jar is installed in C:\Program Files\ProtPlot\ folder. Alternatively, an easier way is to update the Jar file when running ProtPlot as described in the next paragraph.

Updating the ProtPlot JAR file from the running programs

You can use the new "Update ProtPlot" command in the Files menu to quickly download and install just the JAR file. This first prompts you to verify that you want to update your program. Then it will: (1) backup the current ProtPlot.jar file as ProtPlot.jar.bkup; (2) copy the latest ProtPlot.jar file from the TMAP Web site and replace your ProtPlot.jar file in your installation directory. Then when you restart ProtPlot, it will use the new version of the program.

Hints on downloading the stand-alone ProtPlot program

You may freely download and install the current stable release of the stand-alone version of the MAExplorer program. You are free to use or redistribute ProtPlot (see disclaimer). We also include a subset of CGAP derived data. in the PRP subdirectory which is loaded by ProtPlot when you run it.

After you have first installed ProtPlot, run it and do an update of the latest jar file by going into the (File menu | Update | Update ProtPlot from TMAP ProtPlot server). This will get the latest version of the software. Note: you may do this anytime so you do not have to do the full re-installation to update the program data.

If you want to update your copy of the PRP database, then go into the (File menu | Update | Update PRP data files from TMAP ProtPlot server). This will get the latest version of the database. Note: you may do this anytime. [This will not be updated for a while, but we expect to automate its update and will then make it available.]

Figure. Web page showing options for installing ProtPlot as a stand-alone application. Installers are available for Windows95/98/NT/2000/XP, MacOS-8/9, MacOS-X, Solaris, HP-UX, Linux, Unix, and other Java enabled platforms. [Click on the figure to see a high resolution version.]

Distribution contents

  1. We recommend including the Java Virtual Machine (JVM) for a more robust installation.
    This will not affect any of your other Java applications or Web browsers as it is used only with ProtPlot.
  2. The distribution includes:
    • The ProtPlot Java stand-alone application,
    • A set of PRP samples data derived from DB.
    • Support files for your operating system - possibly including the JVM which you may optionally download.

1. Procedure for downloading and installing ProtPlot on your computer

1. Click here to select the current installer for your operating system. This Web page allows you to select the operating system you are using. If you have problems downloading the installer with Netscape 4.7x or later, then try Internet Explorer 5.0. It could be a Mime/type problem with your browser setup.

2. You start the download process when you click on the installer for your computer platform. (You may alternatively use the default installer discussed below.) Follow the directions it provides as you download the installer. It also provides instructions in the "View" hyperlink adjacent to the operating system you selected that tells you what to do after you finished the download. Part of the installation consists of telling the installer where you want to 1) put the executable installer (a temporary directory where you have lots of room is a good choice), and 2) the "installation" directory where you will typically leave the distribution after the installer unpacks it.

We use the commercial InstallAnywhere(TM) program to create the installers. It provides installers for:

Other systems will be added as installers become available through InstallAnywhere (

1.1 The Default Installer

Alternatively, you can use the default installer that is selected for your computer. If you want to control where the files are saved on your computer, then use the explicit installer for your particular platform described above.

The default installer will put the installer executable in a fixed directory and the installed ProtPlot files in another fixed directory.

1.2 Installation Notes

Currently, the Windows, Linux, MacOS-X installers are robust. We have had mixed success with MacOS-8/9 Solaris.

Note that the installers (where possible) will include a copy of a recent Java Virtual Machine (JVM) from InstallAnywhere(TM) to make running ProtPlot on your computer more robust. This is used locally and only affects the running of ProtPlot. It will not affect any other Java applications on your computer. In the case of Mac OS, if you have an older version of the MRJ JVM, it will ask you if you want to upgrade to the newer version (MRJ-2.4.5) - however you do not have to unless you want to.

1.3 Downloading just the ProtPlot.jar file after initial install

If you have previously done an installation. you may avoid a complete re-installation download by getting just the latest Java ProtPlot.jar file. You should replace the old version of this file on your system with the one you are downloading. This will work if the new ProtPlot.jar file does not depend on any new changes in the data files files (which generally the case - try it and see what happens). If necessary, try doing a complete re-installation where you uninstall the old version first.

1.4 Starting ProtPlot Using a ".prpstate" startup state file

If you are on Windows 95/98/NT/2000/XP system, simply click on the particular .prpstate file you want to use. These files reside in the state folder where you have installed ProtPlot.Hint: you might put a short-cut to the installation-directory on your desk-top to make it more convenient to find the .prpstate files.

If you are on a Macintosh system, then start ProtPlot and then run the startup .prpstate file you want by going to the (File menu | State | Change state) command. Then browse your disk and then open up the startup state file of interest.

If you are on a Unix system, then you supply the state startup file explicitly in the command line. You might consider adding the "installation" directory to your UNIX $PATH or $path variable to have UNIX automatically find the executable binary.

  cd installation-directory/
  ProtPlot.bin myLastSession.prpstate

1.5 Problems installing ProtPlot on some operating systems

  1. The MacOS installer is available, but may not work with older versions of MacOS. In addition, there may be problems if file names are longer than 32 characters. For now, the solution is to use short file names. There may also be problems if your data files have embedded carriage returns in addition to line feeds. For now, the solution is to strip the CRs out of the data file.

  2. On Solaris, and possibly other Unix systems, you may have problems with the stack limits. Do a "man limit" to read about the command for your particular Unix shell. We have found that the following seems to work. For the Unix C-shell (csh), add the following to your .cshrc startup file.
       limit stacksize unlimited
    In addition, we have set the default stack size that ProtPlot uses to 96Mbytes. If your computer has less physical memory, it will page. You may also increase this number as well if you have more memory and want to use it. The solution is to edit the ProtPlot.lax file found where you installed ProtPlot. Change the two instances of memory allocation from 96000000 to a smaller number that is less than your actual memory size.
  3. On Solaris, if you download the version with the JVM, unless your Solaris system has been updated recently, it may not be able to find the version required by the JVM. Try downloading the non-JVM version or update your Solaris system.
  4. If you have problems with the Sun installer, you may need to update your Solaris OS system patch set. It is not a single patch. It is the latest Recommended Patch Cluster from Sun. We STRONGLY recommend having your SysAdmin do this for you if you have not done this before. Point your Web browser to:
    and choose the appropriate patch set for the version of Solaris (2.6, 7, or 8) that you are running. Do not choose any of the x86 versions unless you are running Solaris x86. Click on either the Download HTTP option or Download FTP option, and click the GO button to download the patch set.

1.6 FAQ of problems using ProtPlot on Mac OS8/9 users

Q: How many characters can I use in array names for data read by ProtPlot?

A: For MacOS-X, with 256 character file names, this is not a problem. For MacOS 8 and 9 with 32 character file names it may be a problem. Because ProtPlot uses file extensions (eg. ".prpstate"), you are currently limited to 25 characters or less. We will be modifying the system to remove this limit.

Q: How do I start ProtPlot on my data automatically by double-clicking a protplot.prpstate file on my Mac.

A: There is no easy way to do this at this time. Use the (File menu | State | Change state) command to popup a browser to specify the new .prpstate file.

1.7 Sun Solaris (or other Unix system) Memory Problems

We have on occasion seen the following types of memory errors. This discusses how to handle them.

ProtPlot Stack size Memory Error on Sun Solaris

Running ProtPlot on a Solaris (or other Unix system) may produce this error:

  % ProtPlot
  Stack size of 97664 Kb exceeds current limit of 8192 Kb.
  (Stack sizes are rounded up to a multiple of the system page size.)
  See limit(1) to increase the stack size limit.
If the Sun (under Solaris) is slow in loading ProtPlot or has memory errors (shown above) one should first see what the memory limits are set to on your machine using the "limit" command. If they are too small they should be increased or set to "unlimited" (see
in 1.5 above

1.8 ProtPlot LAX file

If the problems persist, one might have to edit the ProtPlot.lax file found in the ProtPlot directory (see example below). The default memory settings in the ProtPlot.lax file (found in the installation directory) should be no larger than the total memory of the machine or paging problems will occur. For instance, if you have 64Mb of memory in your Sun, edit the "" and "" options to be under 64Mb. You can use any text editor to do this. More memory may be needed to be installed on your Sun to run ProtPlot with very large datasets.

Default Lax settings
The Lax file is a startup file generated by InstallAnywhere when we packaged ProtPlot. It is used when ProtPlot starts up on your computer. We currently set the memory limits to 96Mbytes. If you have more memory, you can edit the Lax file to have it use more memory.

  #   -------------------------------------
  #   ---------------------------------------- 

NOTE: this software is undergoing Beta-testing.

Djamel Medjahed, in the LMT, SAIC-Frederick
Peter Lemkin, LECB, NCI-Frederick

Revised: 08-26-2004