MCMC for metabolic networks

    (c) 2010 István Miklós , Eszter Friedman

    Metabolic networks are under continous evolution. Most organism have a common set of reactions as a part of their metabolic networks that relate to essential processes but a large proportion of the reactions present in different organisms are specific to the needs of individual organisms or tissues. The regions of metabolic networks corresponding to these non-essential reactions are under continuous evolution.

    In our model the evolution is characterized by gain and loss of reactions connecting two metabolites and can be described as a discrete space continuous time Markov process.

    The input has to contain the input networks. These networks will occur as the leafs of a tree. The input network can be chosen from the networks of KEGG database. It is also possible to load your own input in fasta format. The program will simulate the evolution.

    Each step of the Markov chain includes three types of change on the tree:

    • Metropolis Hasting on a random egde.
      A random egde of the tree is chosen, and the path on that egde is changed. A change can be an addition of a hyperedge, a deletion of a hyperedge or a permutation of the process. The networks obtained during the change defined by the path can not have more components as the original network.
    • Metropolis Hasting on parameters.
      A random hyperedge of the reference network is picked, and the selected hyperedge's lambda or mu value is changed.
    • Metropois Hasting on a node.
      A random inner node of the tree is picked. The network at this node will be changed. A random hyperedge will be added or deleted.

    McmcNetwork is written in Java 1.6. You do not need to install the program, on the other hand, you need a Java Virtual Machine (JVM) 1.6 or higher. If you do not have such JVM installed onto your computer, please, visit www.sun.com for a free download.

    You can click to the jar file (or left-click and Open with Sun Java 6 Runtime) to start the program. You can also run the program from command line, no parameters are needed. Type: java -jar mcmcNetwork.jar

    If you would like to download the jar file only (contains everything you need for running the program, but no source code), use this link.

    To run the mcmcNetwork.jar file you need input data. You can either use our toy network in fasta format, or you can download the xml file corresponding to the reference network of pentose phosphate pathway and further xml files of this pathway in certain species from here. These xml files were originally downloaded from the KEGG database. Further xml files can be downloaded from KEGG's ftp site.

    The help page of the program is available from here

    The package with full documentation and source code can be downloaded from here .

    The package contains the source code in the mcmc/ folder, documentation in the doc/ folder and some auxiliary data in a few other folders.

    The documentation of the classes can be found here