ALES - A Lineage Evaluation System

Downloads

Main program

ALES.dmg 1.4 MB (Mac OS X disk image, Mac OS 10.4 or greater required)
ALES.jar 1.6 MB (All platforms, Java™ 5.0 or greater required)

ALES uses and bundles part of the Colt library. Colt License Agreement:

Permission to use, copy, modify, distribute and sell this software and its documentation for any purpose is hereby granted without fee, provided that the above copyright notice appear in all copies and that both that copyright notice and this permission notice appear in supporting documentation. CERN makes no representations about the suitability of this software for any purpose. It is provided "as is" without expressed or implied warranty.

Data sets

pma.alm 20 KB Pellioditis marina cell lineage (data from Houthoofd et al., 2003)
maleV6Lpap.alm 16 KB Caenorhabditis elegans male V6L.pap sublineage

(for a description of the .alm file format see Braun et al., 2003)

Installation

Mac OS X

Locate in Finder the ALES.dmg file that you downloaded and double-click it to open and mount the image. When the disk image mounts, a Finder window will open that contains the Ales application icon. Simply drag this icon to your Applications folder (or wherever you would like to keep it) to install.

All (other) platforms

Save the ALES.jar to a directory of your choice. On some platforms you can double-click the downloaded ALES.jar file to start the program. Otherwise, open a command line, change to the directory where you saved the ALES.jar file and type:

    java -jar ALES.jar

Usage

Ales consists of two windows, a main application window and a smaller results window (see Screenshots). The main application window displays the cell lineage and the results window lists general information about the lineage and results from analyzing the lineage.

Opening a Lineage

Choose Open Lineage... from the File menu or use the corresponding button () in the toolbar. In the file dialog that opens select an .alm file. The cell lineage is loaded from the file and displayed in the main application window. The number of cells in the lineage, the currently used classification and the number of cell fates using that classification are displayed in the results window.

Creating a New Lineage

Choose Create New Lineage... from the File menu or use the corresponding button () in the toolbar. In the dialog that opens one of the following algorithms for creating new random cell lineages can be chosen:

Permute Current Lineage
If a cell lineage has been already loaded or created this algorithm creates a new lineage by permuting the cell fates of the terminal cells without changing the topology of the cell lineage.
Generate New Markovian Random Lineage
This algorithm creates a new random lineage using the Markovian model (Braun et al., 2003). Fates and number of cells per fate can either be taken from the already open lineage or arbitrary ones may be specified in the dialog.
Generate New Density Random Lineage
This algorithm creates a new random lineage using the density-dependent model (Braun et al., 2003). Fates and number of cells per fate can either be taken from the already open lineage or arbitrary ones may be specified in the dialog.
Generate New Gene Network Lineage
This algorithm creates a new random lineage based on a gene network model (Lohaus et al., 2007). Number of genes in the gene network, connectivity of the gene network and maximum depth of the lineage can specified in the dialog.

The generated cell lineage is then displayed in the main application window. New random cell lineages using the selected algorithm can then easily be generated by choosing Create Lineage from the Experiments menu or by using the corresponding button (

) in the toolbar.

Viewing a Lineage

After a cell lineage has been loaded or generated the complete lineage is displayed in the main application window. The cell fates of the terminal cells are shown and the inner nodes of the lineage can be drawn using different styles (Display -> Set Lineage Style menu).
The cell lineage display can be zoomed using Zoom In, Zoom Out and Original Size from the Display menu or the corresponding buttons (, , ) in the toolbar.
The display of the cell lineage can also be changed by limiting the visible depth of the lineage tree (Visible Depth spinner in the toolbar), i.e. collapsing all sublineages below the selected depth treshold.

Analyzing a Lineage

The open cell lineage can be analyzed using three different metrics: determination events (DE, see Braun et al., 2003), reduced rules (RR, see Azevedo et al., 2005 and Braun et al., 2003) and reduced rules 2 (RR2, see Lohaus et al., 2007).
To analyze the lineage choose the metric from the Analysis -> Set Lineage Metric menu and choose the classification for which the metric should be calculated from the Analysis -> Set Classification menu. The currently selected metric is displayed on the right side of the toolbar.
To finally perform the analysis, choose Run from the Experiments menu or use the corresponding button () in the toolbar. The calculated metric value (number of DEs, number of RRs or number of RR2s) is listed in the results window and the display of the cell lineage is updated showing the DEs, RRs or RR2s within the lineage. The display style can be switched from the Display -> Set Lineage Style menu.
A list of the individual DEs, RRs or RR2s can be displayed in the results window choosing List DE, List RR or List RR2, respectively, from the Experiments menu or using the corresponding button () in the toolbar.

Saving a Lineage

Choose Save Lineage or Save Lineage as... from the File menu or use the corresponding button () in the toolbar to save a newly created or modified cell lineage as an .alm file. To save a screenshot of the cell lineage display in the main application window in PNG format choose Save Screenshot... from the File menu.