Paint4Net description

Paint4Net (Paint for Network) is an open source (under the GPL v3 license) the COBRA Toolbox extension for visualization of constraints-based reconstruction and analysis (COBRA) models and reconstructions in the MATLAB environment starting from releases of 2009.

The Paint4Net uses the Bioinformatics toolbox to visualize COBRA models and reconstructions as a hypergraph.

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Paint4Net Sample Files

Sample pack

This sample pack contains:

  • The MATLAB workspace with saved original model (test_model_old_notation.xls) and flux balance analysis (FBA) results
  • Sample model stored in Excel (test_model.xls) file
  • Sample model stored in old notation in Excel (test_model_old_notation.xls) file
  • Artificially modified model stored in old notation in Excel (test_model2_old_notation.xls) file for visualization of Type III-extreme pathways and isolated parts of the model
 

Paint4Net Download and Installation

The Paint4Net was developed in MATLAB as script files. The Paint4Net and other necessary files can be downloaded from the list below. Paint4Net versioning consider two part notation, where the first part represent important new functionality and the second part represent some small changes and improvements of already existing functionality. Paint4Net versioning starts from version 1.0.

Latest version

Release date 03.10.2012.

  • A new optional input argument save added for automatic iterative visualization saving as jpeg files.
  • A new optional input argument closev added for automatic iterative closing of Biograph Viewer windows.
  • A new output deadRxns added to return a list of dead reactions.
  • FVA included for dead reactions identification and marking by red.
  • Task start time, end time and total time notifications added.
  • Exchange reactions are marked by diamonds.
 

Older versions

 

Installation

The installation of the extension consists of unpacking the archived scripts (M files) to desired location and setting a path to these files in MATLAB.

The Paint4Net is tested on several versions of MATLAB and it works starting from versions of 2009.

Required additional software