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 |
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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).
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:
The default installer will put the installer executable in a fixed directory and the installed MAExplorer files in another fixed directory.
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.
.mae startup file | Data set contents |
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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 |
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
limit stacksize unlimitedIn 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.
http://sunsolve.Sun.COM/pub-cgi/show.pl?target=patches/patch-accessand 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.
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.
% 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
# 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