CytoGEDEVO tutorial

Installation

The easiest way is to use the Cytoscape App Manager to install the most current version.

CytoGEDEVO should be in the list of apps available for download.

Alternatively, download CytoGEDEVO manually, then click on the "Install from File..." button and select the downloaded JAR file:

When CytoGEDEVO is successfully installed, a new entry will be added to the Apps menu.

Setup

CytoGEDEVO requires no further setup.

Note that after installation or after starting Cytoscape, CytoGEDEVO is inactive. To load it, select the "Load CytoGEDEVO" entry from the Apps menu.

This will make a new tab appear in the left panel, and add pair layout methods to the Layout menu.

Note that the "Load CytoGEDEVO" menu entry is removed afer it is clicked -- CytoGEDEVO will stay enabled until Cytoscape is closed.

Basic usage

To get started, make sure that at least two networks are loaded. Either import some or load one of the prepared example sessions (*.cys files).

Select the two networks to be aligned in the "Basic" sub-panel.

For first use, keep all settings at their default values. The default configuration performs a purely topological alignment, forces all edges to be undirected edges, finishes reasonably fast, and opens a graphical overview when it is done with the alignment.

You may want to generate a results file for further examination or keep the alignment data cached for the next step, but this is not necessary and will work without.

Note that you can hover the mouse over almost all settings to open an explanation tooltip.

While the alignment is performed, the job can be accessed in the "Job List" panel. A spinner in the tab indicates that at least one job is running.

Note that you can continue working and add more alignment jobs if you want to let it run overnight -- Cytoscape's user interface is not blocked.

It is normal that the progress bar is "jumpy" -- in the default configuration, it will reach 100% (and finish) after some iterations without improvement. If the alignment is improved, the progress bar resets to zero.

If you are impatient, you can let it run for some iterations and then force it to get done by clicking the "Finish Now" button. Results will not be as good as they could be but since we made no effort at parameter tuning this is fine for now.

Note that CytoGEDEVO uses an evolutionary algorithm -- the longer it runs, the better the results.

After the alignment is done it will take a few more seconds since it was set to open a graphical view and perform a network layout.

The default pair layout arranges both networks side-by-side, so that it is easy to see which nodes are mapped.

You can try the coloring options on the "Common tasks" panel at this point.

Note that in order to create an alignment result, the two source networks are combined into one, which will also appear in the "Networks" tab.

Now it is time to improve parameters a bit. Select the combined network as input for CytoGEDEVO.

The second network will grey out since the first network essentially already contains two, and CytoGEDEVO can continue an alignment that was started earlier.

In order to produce a less "forceful" alignment and only map nodes that match quite well, set the "Null pairing penalty" to something lower.

Continue the alignment.

If the "Keep data..." box was ticked last time, it will initialize much faster. This is especially noticeable for large networks.

After letting it run for some iterations, force it to finish and highlight Graph edits.

It shows the steps that are necessary to transform the first network into the second one. Deletions are colored in brown, additions in green.

There are more options to highlight scores. Since no extra scores were imported from an external data source, only topological ones are available. The pair score is the combined score of all contributions that made GEDEVO align this pair. All internal scores are distances and topological, but if more scores were supplied you can color them accoring to their type (distance, similarity, or E-value). E-value is a distance, but the the visible range is compressed to specially highlight nodes with an E-value of < 0.05.

A node and its mapped partner will always have the same score, and thus, the same color.

To layout the two networks in a different way, use Layouts > GEDEVO pair layouts > .... Side by side mode is recommended unless your networks are reasonably small.

Note that overlapped mode changes node alpha (makes them half transparent), you need to change that back manually if you do not want it.

The default pair layout uses Cytoscape's default (in side-by-side mode), which is "Prefuse force directed layout". It is selected as follows from the Layout menu:

Note that Cytoscape's default layout methods do not know the notion of a pair of networks -- if you do not use the pair layout for a network pair, it is nearly impossible to see aligned partners of nodes at a glance.

Adding prior knowledge

To impose restrictions to the alignment process it is possible to map nodes by hand, which will then be kept aligned. The easiest way to do this is to enable mapping mode, then click the first node in one network, then its intended partner in the other network. This will draw a fixed mapping edge between them that will stay, even through re-alignments.

This concludes the basic tutorial.

Read the description of table columns for advanced usage.

Feel free to write email for questions or comments.