The command-line version of moderator. The last version Without GUI.
Features of ModeRator 2.2
- can compare COBRA models (xls) and SBML models (xml)
- can compare using (according to user's will):
- neutral formulas
- charged formulas
- reaction synonims (program can download them from BRENDA)
- is a commandline application (no GUI & fully scriptable)
- can check reactions balance
- can visualize the comparison results in a graph
- written in Python
ModeRator was designed to analyze reactions and thereby to compare two reconstructions. Originaly the tool has been developed to compare and analyze genome-scale reconstructions stored as COBRA models, but it also works with SBML models. Its main purpose is to detect the inconsistencies, like, duplicate reactions of complex reconstructions and to compare them.
Installation & dependencies (ModeRator 2.2)
The complete set of features uses of the following software packages:
- xlrd (http://www.lexicon.net/sjmachin/xlrd.htm) - package for extracting data from Excel files;
- libSBML (http://sbml.org/Software/libSBML) - open-source programming library to manipulate SBML files;
- NetworkX (http://networkx.lanl.gov/index.html) - package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks;
- Graphviz (http://graphviz.org/) - open-source graph visualization software.
From Python repositories additional packages are required:
- SOAPpy - required to download synonyms from BRENDA
- matplotlib - required by NetworkX
- pyparsing - used in balance check
However, full set of the additional software is not obligatory. If the user is not going to ever visualize comparison results, NetworkX and Graphviz may remain uninstalled. The same with xlrd and libSBML - the functionality provided by these libraries are used only to import the data.
Fig. Comparison of two reconstructions of Zymomonas Mobilis. Red dots indicate common reactions.
PhD student Martins Mednis (link to profile »»)