We have different GOALIE packaging alternatives, but the one that you have most likely downloaded now will guide you through a series of simple steps before showing you the actual user interface. This choice was done to simplify the start-up procedure for simple cases. In the following we will illustrate these steps. Eventually the actual user interface will be visible on the screen.
Note: sometimes, you will see various dialog displaying the name GOALNET; this is the name of the internal library at the core of GOALIE.
GOALIE can be started by double clicking on the goalie.exe icon or by typing in goalie.exe at the command line. This will bring up the splash screen.
Depending on your configuration (Windows version, GOALIE release, and GOALIE initialization file setup), GOALIE may complain about a missing GO database connection. Assuming that you do have installed a GO database instance on your machine, GOALIE will tell you about the error it detected and whether you want to continue.
If you choose Yes, then GOALIE will ask you to set up a connection to the GO database via the ODBC that you should have saved beforehand. The DB Connection Dialog serves this purpose.
Please fill in the appropriate values for your connection and click Ok. You can also access the Windows ODBC Driver Manager from the dialog and set up your ODBC connection from there.
If the GO database connection is properly setup, GOALIE will ask you whether you want to load a Complete Cluster Set Script File. These files contain a description of where to find several bits and pieces of an experiment, e.g. its raw quantitations and its clusters arranged in windows.
You really do not have a choice here (this is by design); just click on the OK button.
GOALIE will open up a file chooser dialog. Note that the dialog is set on the goalie/data directory of your installation.
The picture shows the content of our data directory. You will probably have only the Yeast-Cell-Cycle-data and the Yeast refined directories, depending on the date of your download. Let's navigate to the Yeast refined sub-directory.
The organization of each data sub-directory has not been agreed
upon yet, but in general, at the top level you will see a number of
sub-folders and a number of .gcss (GOALIE Cluster Set Script)
files and/or .lisp files, which contain more or less the same
information.
In the Yeast refined sub-directory there should be at
least the following files.
| ycc-alpha-w5o2-wcd.lisp |
| ycc-elu-w5o2-wcd.lisp |
The first file contains a description of the set of files to be loaded in order to reconstruct the set of cluster windows for the well known Yeast Cell Cycle alpha data-set in GOALIE. The second file contains a description of the set of files to be loaded in order to reconstruct the set of cluster windows Yeast Cell Cycle elutriation data-set. The file names have the following structure ycc is the "Yeast Cell Cycle" acronym, the alpha and elu tags distinguish the two experiments and the w5o2 tells us the the window size used to break up the time course is 5, while the overlap between windows is 2. The wcd is there for historical reasons and will disappear in the future.
The bibliographical reference for this data-sets is [P. T. Spellman, G. Sherlock, M. Q. Zhang, V. R. Iyers, K. Anders, M. B. Eisen, P. O. Brown, D. Bolstein and B. Futcher, Comprehensive Identification of Cell Cycle-Regulated Genes of the Yeast Saccharomyces Cerevisiae by Microarray Hybridization, Molecular Biology of the Cell, 9:3273-3297, 1998]. How the data-sets were manipulated to get the set of clusters is described here.
Let's select ycc-alpha-w5o2-wcd.lisp file. GOALIE will load all the data (it may take a while) and then it will pop up the main interface with one extra question.
Answering No will leave the main interface up, while answering Yes will make GOALIE compute all the cross relationships among clusters and their related summaries using the default method (an application of the Fischer Exact Test).
Let's choose Yes and postpone a discussion of the main interface. After a possibly long while (it may take on the order of 15 or 20 minutes for the Yeast Cell Cycle data-set) you will be presented with the Experiment View.
Note: depending on the configuration of the system, GOALIE may seem to be "not responding" for a while. Do not worry and let the computation come to an end. If GOALIE were truly stuck, the operating system would be able to signal this to you.
If you want to skip ahead you can look at how to compare two experiments.