Gene Expression Data

Enable BiNA to use gene expression data

Be sure that you have installed the ExpressionExperiment plugin. (Directory "org.bina.bcp.controller.interaction.mapping.expression_mapping" should be in your plugins-directory.)

There are two ways to integrate expression data into BiNA. The first one uses a epd file, the second one needs gene expression data into your BN++ database.

How to load gene expression data from a file?

The package org.bnplusplus.model.expressions contains the class ExpressionPlatforms:

public class ExpressionPlatforms {
    public static ExpressionPlatform readFromFile(InputStream is) throws IOException { ... }
    public static LinkedList<ExpressionPlatformInformation> getAvailablePlatformsInDB(BiNAEngine engine) { ... }
}

The readFromFile-method reads an epd-file and stores the content in the returning ExpressionPlatform.

Example:

try {

	File f = new File("gpl96.epd");
	FileInputStream fis = new FileInputStream(f);

	ExpressionPlatform ep = ExpressionPlatforms.readFromFile(fis);

} catch (IOException e) {
	System.err.println("Error: " + e.getMessage());
} 

How to load gene expression data from the database?

The second method returns all available ExpressionPlatforms in the database, associated with the given BiNAEngine:

public class ExpressionPlatforms {
    public static ExpressionPlatform readFromFile(InputStream is) throws IOException { ... }
    public static LinkedList<ExpressionPlatformInformation> getAvailablePlatformsInDB(BiNAEngine engine) { ... }
}

An ExpressionPlatformInformation is a helper class which contains information about the ExpressionPlatform, without loading the whole data from the database.

public static class ExpressionPlatformInformation {
    public ExpressionPlatform loadPlatform() { ... }
    public ExpressionData loadData(int dataId) { ... }
}

Example:

LinkedList<ExpressionPlatformInformation> list = ExpressionPlatforms.getAvailablePlatformsInDB( engine );

if (list == null || list.size() == 0)
	return;

// take the first one
ExpressionPlatformInformation epi = list.getFirst();
EypressionPlatform ep = epi.loadPlatform();

// get available datasets
Integer id = epi.getData().getFirst().first;

// load the first dataset
epi.loadData(id);