MAExplorer - Microarray Exploratory Data Analysis

2.1 File menu

The File menu operations includes options and submenus providing access to database data from disk and Web servers, state saving, and groupware to share states between collaborators.

In stand-alone mode, the user may select the database subset to be loaded from either a Web server or a local file system. When used as an applet, this is pre-determined by the Web page where MAExplorer is started. Opening a disk DB, 'Open disk DB', also restores any user defined gene sets and other parts of the exploratory state that were present when the 'Save ... disk DB' was invoked.

In the following menus, selections that are sub-menus are indicated by a ' Indicates the menu
entry has a submenu '. Selections prefaced with a '' and indicate '' indicate that the command is a checkbox that is enabled and disabled respectively. Checkbox menu items have a "[CB]" at the end of the command. Selections prefaced with a '' and indicate '' indicate that the command is a multiple choice "radio button" that is enabled and disabled respectively, and that only one member of the group is allowed to be on at a time. Radio button menu items have a "[RB]" at the end of the command. Selections prefaced with a '#' indicate that the commands are available only when MAExplorer is run in the stand-alone mode. Selections prefaced with a '*' commands requires access to the backend Web server [Future]. Selections that are not currently available will be grayed out in the menus of the running program.

When used as an applet connected to a Web database server, databases may be divided into public and collaborator projects. Users accessing protected collaborator projects will be required to log-in to the server and a popup login request will appear.

Databases - open and save databases of hybridized samples
Exploratory 'state' - save and restore the user's data-mining explorations
Groupware - share some exploration states with collaborators [Future]
Update MAExplorer from maexplorer.sourceforge.net - 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. The much more time consuming alternative is to do an entire download and reinstallation from the Web site.
Update Plugins from maexplorer.sourceforge.net - This will determine the list of new MAExplorer Plugins available. It will prompt you on whether you want to update each default plugin one by one. If you are running one of these plugins, you must first Unload it and then Load it again (see Plugin menu).
Update RLO methods from maexplorer.sourceforge.net - This updates RLO methods available from the server. RLO methods consist of pairs of R scripts and RLO files. To use these methods, R must be installed on your computer (www.r-project.org. When MAExplorer is restarted these downloaded RLO methods will be available in the (Plugins | RLO methods) submenu.
Quit - exit MAExplorer

2.1.1 Databases menu

The Databases submenu is currently available only in stand-alone mode and contains the following selections for opening and saving databases.

[In the future], each user will be able to save the state of their exploration into a password protected directory of named states on a Web server (e.g. doing a 'Save ... Web DB' command. Later, they could restore that state from the Web server by doing an 'Open Web DB' command). Users would be required to register with that server to set up a unique state-saving area. Once this facility was setup, users may selectively allow other user's to view selected data implementing a groupware environment for improving collaboration.

# New project - assign new project .mae database file. This assigns a project to either a local disk directory (or to a Web DB [Future]).

# Set project directory - change the project directory and then do an "Open disk DB" command (or "Open Web DB"). Note: used with "New project" [Future].

# Open disk DB - open an existing disk .mae database file

# Open Web DB - open MAExplorer database with Web server that supports MAExplorer. [Future]

# Save disk DB - save current database as a .mae startup disk file

# Save as disk DB - save current database as a new .mae startup disk file

# Save Web DB - save current database as a .mae startup Web DB file [Future]

# Save as Web DB - save current database as a new .mae startup Web DB file [Future]

Starting an existing MAExplorer database using the file browser with 'Open file DB'

Figure 2.1.1 Example of the "Open file DB" command. The file browser is opened in the current project directory with the name of the currently opened file. You may select another .mae startup database file to load in the current project. You may also "cruise" the file system and load an .mae file from a different project directory. The "Set project" command makes this easier since it gives you a list of available projects that you may change directly. The projects must have been setup on your computer previously. The "New project" command can be used for setting up new projects or projects.

Saving the current session in a new MAExplorer startup database file using the 'SaveAs file DB'

Figure 2.1.2 Example of saving a user session in a new startup file using the "SaveAs DB" command. The file browser is opened in the current project directory with the name of the currently opened file. You may enter another .mae file name to save your current session. Then when you restart MAExplorer using this new file, it will restore the data mining state to where you left off (except that no popup windows are opened).

2.1.2 Exploratory state menu

The Exploratory 'state' submenu contains the following selections for saving and later using the user's state of the exploration. If MAExplorer is being run on a local computer, no login is required.

* Register - register your login name and request a password so you may login in the future [Future]
* Login - log on to the MAExplorer web server. This is used for accessing protected projects and for saving accessing your "state" data [currently only used for MGAP DB]
* Open user's state - restore a user's previously saved exploratory state file [Future]
* Save user's state - save the user's current exploratory state in a file on the server [Future]
* Directory of user's states - list the user's named exploratory states [Future]
* Delete user's state - delete a particular user state file [Future]

2.1.3 Groupware facility for sharing user states menu [Future]

The groupware facility allows users to share their state data with other users. However, If MAExplorer is being run on a local computer, then groupware may not be available since it depends on using specific Web servers with MAExplorer-specific groupware services available. [We first developed these concepts in the context of 2D protein gels. They include: WebGel (Lemkin et al., 1999b) for Internet exploration of 2DE databases, Xconf (Lemkin et al., 1993) an early X-windows based image conferencing similar to CU-See-Me or ALO Instant messenger for sharing images in a conference over the net, Flicker (Lemkin, 1997) an image comparison over the internet using a a Java applet, and GELLAB-II (Lipkin and Lemkin, 1981) a system for data mining - see GELLAB-II Poster on the Web) that embody many of the concepts used in MAExplorer.] The Groupware submenu contains the following selections:

* Open another user's state - read another user's exploratory state file if they granted you access [Future]
* Share user state - allow another user to access a particular exploratory state [Future]
* 'Unshare' user state - disallow another user access a particular exploratory state [Future]

Saving the state and databases on the local file system

The current state of an exploratory data analysis session may be saved on the local file system. The state consists of: gene sets; HP-X and HP-Y hybridized sample sets; HP-E hybridized sample lists; thresholds and switch setting preferences; etc. The user may save their current state and restore a previous state at any time. Restoring the state will overide the current database.

Groupware sharing of intermediate exploratory results [FUTURE]

Each registered user will be able to save the current state of their exploration of the data in named User State files on the back-end Web server using the Save user's state command. The user may keep multiple named states on the back-end secure server where they be accessed to restore the state at a future time using the Open user's state command. The user can request a list of their states with the Directory of user's states command. They may remove a particular state with Delete user's state.

A registered user may allow another registered user to access their state or states (using the Open another user's state command) if the user owning the data had granted them permission. The Share user state and Unshare user state commands control these permissions. There are two special share-users defined: public to allow unlimited read-only access to the state they specify, and private to disallow all access to a user state.