BioLayout Express 3D is a powerful program for Windows that provides you with an open source visual analytics platform. It is engineered to assist you in the interpretation of large and complex biological datasets, represented in the form of networks.

Principle of operation

The tool is capable of generating projects derived from any table containing numeric or discrete data values. As a result, you are presented with intricate graph structures. You can also analyze any data that is already in the form of a network or model pathway activity via a stochastic Petri net algorithm.

During the processing stage, the utility iterates through each entity, searching for and associating a suitable shape for that type. Subsequently it generates a corresponding graph node. Following this, the application establishes connections by creating edges to represent elements.

Create gene visualizations

After a visual scheme has been defined, the node shapes and colors are mapped to entity types. There is support for the import of mEPN pathway models saved as GraphML files. Once visualized, the concepts are translated into equivalent 2D or 3D shapes.

In order to explore the graph, you can use the Class Viewer. This component enables your data to be subcategorized into classes, based on node type. You also have the option to open a search dialog and locate pathways that involve the genes of interest. To visualize ORF sequences, you may try a program called SnapGene.

Features

free to download and use;
compatible with modern Windows versions;
you can create and visualize gene networks;
there is support for many input data formats;
enables you to export the analysis results.