Downloading the stand-alone MicroArray Explorer (current release)

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 MAExplorer (see disclaimer). We also include a subset of 50 Mammary Genome Anatomy Program (MGAP) hybridized sample data to run stand-alone on your computer platform. These are may also be downloaded directly as:

This data may be used for learning about MAExplorer with the tutorials and for investigating some of the stages of normal and mouse-model mammary development. The MAExplorer reference manual may be viewed in your browser from the Web from this Web site. Alternatively, you may download the full manual as a Acrobat MaeRefMan.pdf PDF file (> 5Mb).

If you have problems with the installation, then you might want to read the rest of this section and also the part of the manual which discusses installation (Appendix D) and using it with your arrays (Appendix C). The latter requires editing your data files for use with MAExplorer. The Cvt2mae is a "wizard" array data conversion tool automates this process.

If you have previously installed MAExplorer and you want to update just the MAExplorer.jar file (the actual program), you can do this as described in Section 1.3. Alternatively, you can use the new "Update MAExplorer" command in the Files menu. This will (1) backup the current MAExplorer.jar file as MAExplorer.jar.bkup; (2) copy the latest MAExplorer.jar file from the maexplorer.sourceforge.net Web site and replace your MAExplorer.jar file in your installation directory. Then when you restart MAExplorer, it will use the new version of the program.

After initially, installing MAExplorer (or the Cvt2Mae for that matter), you can simply download the latest .jar file and overwrite the previous version you had when you installed the program. The MGAP demo data can be downloaded separately.
SourceForge Download MAExplorer Installer

Figure. Web page showing options for installing MAExplorer 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.] NOTE: the MacOS installer is currently not available. If you have problems with the Sun installer, you may need to update your Solaris OS system patches (see below).

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 MAExplorer.
  2. The distribution includes:

1. Procedure for downloading and installing MAExplorer 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 (www.ZeroG.com).

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 MAExplorer files in another fixed directory.

1.2 Installation Notes

Currently, the Windows and Linux installers are robust. We have had mixed success with Mac OS and Solaris.

Note that the installers (where possible) will include a copy of a recent Java Virtual Machine (JVM) from InstallAnywhere(TM) to make running MAExplorer on your computer more robust. This is used locally and only affects the running of MAExplorer. 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.

The MAExplorer Reference Manual describes the details of MAExplorer as well as showing a number of screens illustrating various data-mining operations. Several tutorials are available and are discussed in the Reference Manual.

1.3 Downloading just the MAExplorer.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 MAExplorer.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 MAExplorer.jar file does not depend on any new entries in the configuration files (which generally the case - try it and see what happens).

Update MAExplorer Program from maexplorer.sourceforge.net

As of version 0.96.21 of MAExplorer, it is now possible to update the MAExplorer program from the program itself - rather than having to download the complete installer and then running the installer. Press the "Update MAExplorer" button at the lower left of the corner of MAExplorer when it is running. It asks if you want to update MAExplorer. Answer yes. This will then (1) backup the current MAExplorer.jar file as MAExplorer.jar.bkup in the directory where you had initially installed MAExplorer; (2) it then copies the latest MAExplorer.jar file from the maexplorer.sourceforge.net Web site and replaces your working MAExplorer.jar file in your installation directory. You must restart MAExplorer for this to take effect. It will then use the new version of the program. This is a much less time consuming alternative than doing an entire download and reinstallation from the Web site.

2. Description of Sample MGAP Datasets in the Distribution

The MGAP data is supplied in three directories. The installer leaves other directories and files in the "installation" directory needed to run MAExplorer as a stand-alone application. These include MAExplorer.jar, MAExplorer.exe (.bin if UNIX or Mac), Uninstall-MAExplorer.exe (.bin), etc. The lax files, and jre, resource directories are used by InstallAnywhere and you do not need to be concerned with their contents. The MGAP data directories are listed here and are discussed in detail in Appendix D of the Reference Manual:
  1. /Config - contains database configuration and samples tables for this database
  2. /Quant - contains 50 quantified hybridized sample spot lists
  3. /MAE - contains MAExplorer ".mae" startup files

2.1 List of MGAP demo data MAExplorer ".mae" Startup Files in the /MAE Directory

The table lists the startup files provided for the MGAP database. Some good sets of data to try initially are the Lact1vs10-38probes.mae, Preg13VsLact1-38probes.mae, and Preg13day-C57vsStat5a-38probes.mae startup files.

.mae startup file Data set contents
Lact-C57vsStat5a-5probes.mae 5 probes. (X,Y) is lactation day 1 (C57B6, Stat5a(-,-))
Lact-C57vsStat5aCEBPnull-19probes.mae 19 probes. (X,Y) subset is lactation day 1
(C57B6, Stat5a(-,-) + CEBP-null)
Lact1-C57vsStat5a-38probes.mae 38 probes. (X,Y) subset is lactation day 1 (C57B6, Stat5a(-,-))
Lact1vs10-38probes.mae 38 probes. (X,Y) subset is C57B6 lactation day (1,10)
MAEstartupDefault.mae No initial samples loaded
Preg-C57vsStat5a-4probes.mae 4 samples. (X,Y) is pregnancy (C57B6, Stat5a(-,-))
Preg-C57vsStat5a-8probes.mae 8 samples. (X,Y) is pregnancy (C57B6, Stat5a(-,-))
Preg13VsLact1-38probes.mae 38 samples. (X,Y) subset is pregnancy (C57B6, Stat5a(-,-))
Preg13day-C57vsStat5a-19probes-cache.mae 19 samples from MGAP Web server. (X,Y) subset is
pregnancy (C57B6, Stat5a(-,-))
Preg13day-C57vsStat5a-19probes.mae 19 samples. (X,Y) subset is pregnancy (C57B6, Stat5a(-,-))
Preg13day-C57vsStat5a-38probes.mae 38 samples. (X,Y) subset is pregnancy (C57B6, Stat5a(-,-))
Preg13day-Stat5aVsCEBP-null-38probes.mae 19 samples. (X,Y) subset is pregnancy (Stat5a(-,-),CEBP-null)
reuseXY-Preg-C57vsStat5a-8probes.mae Same as other startup, but uses XY coordinates of 1st sample
reuseXY-Preg13day-C57vsStat5a-38probes.mae Same as other startup, but uses XY coordinates of 1st sample
C57vsDevModels-15probes-cache.mae 15 samples from MGAP cache. (X,Y) subset is
(C57B6, knock-outs)
C57vsDevModels-15probes.mae 15 samples. (X,Y) subset is (C57B6, knock-outs)
C57vsDevModels-38probes.mae 38 samples. (X,Y) subset is (C57B6, knock-outs)
MGAP-50samples.mae 50 samples. All of the public samples sorted alphabetically

2.2 Starting MAExplorer Using a ".mae" Startup File

If you are on Windows 95/98/NT/2000/XP system, simply click on the .mae file you want to use. Hint: you might put a short-cut to the installation-directory\MAE\ directory on your desk-top to make it more convenient to find the files.

If you are on a Macintosh system, then start MAExplorer and then run the startup .mae file you want by going to the File menu and then the Databases submenu. Use the "Open disk DB" option to browse your disk and then open up the startup file of interest.

If you are on a Unix system, then you supply the MAE 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/
  MAExplorer.bin MAE/Preg13VsLact1-38probes.mae

2.3 The MAExplorer Error Log File

Each time you run MAExplorer, it creates or overides the previous error log file called MAEerr.log in the installation-directory. If you are experiencing major problems, this file is useful to us in helping figure out what is wrong. Otherwise, just ignore it.

2.4 Problems installing MAExplorer 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 your 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 MAExplorer uses to 256Mbytes. 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 MAExplorer.lax file found where you installed MAExplorer. Change the two instances of memory allocation from 256000000 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 libCrun.so.xxx 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: 
      http://sunsolve.Sun.COM/pub-cgi/show.pl?target=patches/patch-access
    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.

2.5 FAQ of problems using MAExplorer on Mac OS for NCI/CIT mAdb users

Q: How many characters can I use in array names for data to be donwloaded to MAExplorer?

A: For Mac-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 MAExplorer uses file extensions (eg. ".quant"), you are currently limited to 25 characters or less. We will be modifying the system to remove this limit.

Q: I tried unsuccessfully to open NCI/CIT mAdb data (nciarray.nih.gov) on a Mac OS system. I generated a .zip file using mAdb "BETA Formatted Array Data Retrieval Tool" , then decompressed this .zip file using "Stuffit Expander" on my Mac. The Start.mae file could not be opened by MAExplorer, what can I do to fix this?

A: Stuffit Expander (default settings) removes a form feed character from decompressed text files, this prevents the Start.mae (and other text files used by MAExplorer) to be read by MAExplorer. To fix this you need to set Stuffit Expander so that it will keep the form feed characters when it decompress text files: 

Open Stuffit Expander by double clicking its icon
Click on menu File -> Preferences
Click on "Cross Platform"
Click on "Never" button of 'Convert text file to Macintosh format:'
Your .zip will be decompressed properly and the text files from your mAdb data can now be open by MAExplorer.

Q: How do I start MAExplorer on my data automatically by double-clicking a Start.mae file on my Mac.

A: There is no easy way to do this at this time. Use the File menu, Databases, Open Disk DB browser to specify the Start.mae file.

2.6 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.

MAExplorer Stack size Memory Error on Sun Solaris

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

  % MAExplorer
 
  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 MAExplorer 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 2.4 above

MAExplorer LAX file

If the problems persist, one might have to edit the MAExplorer.lax file found in the MAExplorer directory (see example below). The default memory settings in the MAExplorer.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 192Mb of memory in your Sun, edit the "lax.nl.java.option.native.stack.size.max" and "lax.nl.java.option.java.heap.size.max" options to be under 192Mb. You can use any text editor to do this. More memory may be needed to be installed on your Sun to run MAExplorer with very large datasets.

Default Lax settings
The Lax file is a startup file generated by InstallAnywhere when we packaged MAExplorer. It is used when MAExplorer starts up on your computer. We currently set the memory limits to 256Mbytes. If you have more memory, you can edit the Lax file to have it use more memory. 

 
  #   LAX.NL.JAVA.OPTION.JAVA.HEAP.SIZE.MAX
  #   -------------------------------------
  lax.nl.java.option.java.heap.size.max=256000000
 
 
  #   LAX.NL.JAVA.OPTION.NATIVE.STACK.SIZE.MAX
  #   ----------------------------------------
  lax.nl.java.option.native.stack.size.max=256000000