Paint4Net

A software tool SpaceAnalyzer (SAnalyzer) is developed in Matlab environment for automatic generation of pathways. This tool can be used for the metabolic pathway supergraph construction using reactions taken from KEGG database.

SAnalyzer tool is a set of algorithms for metabolic pathways construction. SAnalyzer reads all necessary data from KEGG database REST web service and processes it in the real time. Algorithms are realized in M scripts that can be places on the local PC and launched from the Matlab command windows. The construction algorithm of possible metabolic pathways construction is independent software that can return nodes and edges of constructed graph. The tree construction proceeds recursively, beginning from the starting metabolite, i.e. initial substrate of the pathway of interest given by industrialist, as a root of a tree. We can call it “super graph” which contains all possible pathways from the input substrate for fixed levels count. Construction is performed based on the graph theory methods.

 

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.

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.

 
 

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

Institute of Microbiology and Biotechnology, University of Latvia Jelgavas iela 1, Riga
LV-1004, Latvia

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