GCAT Microarray Data Analysis Workshop

Software Installation Instructions


In the GCAT Microarray Data Analysis Workshop, you will gain hands-on experience with several analytical techniques and two software packages: MagicTool and SAM.  If you are bringing a laptop computer, you will need to install the software packages on your computer before the workshop begins.  You should also plan to attend a special session for checking software installation at 8:00 a.m. on the first day of the workshop.


Disclaimer: Many of the details of this process vary from one operating system to another.  We have tried to cover the many systems that participants are bringing, but cannot guarantee we have identified every variation.  To be safe, you should back up important files before proceeding with these instructions.


Technical Support:  If you have difficulties with this software installation process, we will provide technical assistance prior to the workshop.


For questions about MagicTool or Java installation, please contact Laurie Heyer at laheyer@davidson.edu or 704-894-2267.


For questions about SAM installation, please contact Jo Hardin at jo.hardin@pomona.edu or (909) 607-8717.



Please follow the steps outlined below for installing each package.   Note that SAM will only run on Windows computers.



Updating your computer


Before installing anything, sure you have an up-to-date operating system (Mac users need at least OS X 10.2.6 and should accept and install security and Java updates from Software Update; Windows users visit http://windowsupdate.microsoft.com).



Installing Java


You may already have Java installed, but it is important that you have the right version(s).  MagicTool and SAM require different versions of Java, but the two versions co-exist peacefully in our tests on Windows XP.


  1. If you intend to install MagicTool on your computer, you will need the Sun version of Java.
    1. On a PC, go to http://java.com, and click on “Get It Now”.  The correct version of the code should download and begin to install automatically.  Complete installation instructions, with screen shots, are at http://java.com/en/download/help/win_auto.jsp .
    2. On Mac, Java is already included.  (OS X 10.2.6 or later is required.)

  2. If you intend to install SAM on your computer (Windows systems only; see instructions below), you will need the old Microsoft version of Java.  Microsoft no longer provides it (because of legal difficulties with Sun) but you can find it on the internet by Googling msjavx86.exe.  Alternatively, our own copy of this file is attached to this email as a zipped archive.  Double click on it to extract the .exe file, then double click the .exe to install Java.



Installing MagicTool


  1. Create a folder called magictool on your computer. 
    1. On a PC, we recommend that you place this folder directly under the C: drive, or a folder within the C: drive that has no spaces in its name.  This specifically excludes, for example, the Desktop (which is under “Documents and Settings”) or “Program Files.”
    2. On a Mac, we recommend that you place this folder in any convenient place, but not under a folder that contains spaces in its name.
  2. Go to www.bio.davidson.edu/magic, and follow the links to download the software, or go directly to http://www.bio.davidson.edu/projects/magic/agreement.html

  3. Download the file called MagicTool.jar to the magictool folder you created in step (1).

  4. On most operating systems, you can now run MagicTool by simply double-clicking on the file MagicTool.jar.  You will know it is starting when the magic wand waves across the MagicTool logo on the screen.  If the jar file does not start the program, it may be because Java is not installed properly on your machine.  Be sure you have completed the instructions for Installing Java before proceeding to step (5).

  5.  This step sets up a script so you can run MagicTool with extra memory.  This is important for working with large data files.
    1. On a PC:

                                                               i.      Download the file called Magic_launch.bat to the magictool folder.

                                                             ii.      Double click on Magic_launch.bat.  This should cause a DOS command window to open, then MagicTool should start.

    1. On a Mac:

                                                               i.      Download the file called Magic_Launch.txt

                                                             ii.      Open Script Editor (this program is under the Applications, AppleScript folder).

                                                            iii.      In Script Editor, go to Open Script… under the File menu.  Select the file Magic_Launch.txt.  The text from the file should now appear in the lower window in Script Editor.

                                                           iv.      In Script Editor, go to Save As under the File menu, remove the .txt extension from the filename, select Application under the Format menu, and select the magictool folder as the destination.

                                                             v.      Open a finder window and open the magictool folder, but do not use favorites, shortcuts or the multicolumn finder display.  (In other words, use View as Icons or View as List.)  Double click on Magic_Launch, which should start MagicTool.



Installing SAM (Windows users only)


1.      Go to http://www-stat.stanford.edu/~tibs/SAM/index.html and register for the SAM software.  You must certify that you will use the software for academic purposes, and provide your email address and additional contact information.  Upon completing the registration, you will receive an email with a password and instructions for downloading SAM.


2.      While you are at the SAM web site, you might wish to read the FAQ.  The following guides you through the installation, but more detailed information is available in the FAQs.  You can read further instructions and browse the user manual in the file sam.pdf.


3.      Download SAM (as a zipped file) to a convenient location on your computer.


4.      Double click on the file you downloaded.  Depending on your operating system and configuration, you may see the contents of the zipped file in a normal-looking window, or in a WinZip or other zip file-handling program.  Extract all files to a convenient folder.


5.      Close whatever programs you have running.  Go to the folder to which you extracted the files and double-click on the file Setup.exe


6.      Setup will ask you a few questions.  You should be able to accept the default answer for each one.  When Setup is finished, SAM is on your computer, but not fully installed.


7.      Open Microsoft Excel.  Go to Add Ins… under the Tools menu.  Select Browse.  Navigate to where Setup put SAM, which should be C:/Program Files/SAMVB, then go into the Addin folder, and double-click on the SAM file.  Hitting return finishes the process of installing SAM by added it into Excel.  The SAM  and SAM Plot Control buttons should now show in the Excel toolbar, signaling that SAM is ready to use.