Online Suite of Web-tools to Process Stoichiometric Network Analysis: Tools-4- Metatool

Stoichiometric network analysis (SNA) is a powerful approach to study complex metabolic networks. SNA provides fundamental information on the structure of the network, as it is: the stoichiometric matrix, the convex basis, elementary modes or extreme currents, and enzyme subsets. Metatool is one of the most popular tools to perform SNA. Metatool output is hard to process and visualize, especially for users who have no experience with this software.
In this communication we present the web-tool called Tools-4-Metatool (t4m) (http://solea.quim.ucm.es/t4m/) as an online platform that analyses, parses, and manipulates files related with Metatool. It has two major options: Analysis and Compare.
Analysis facilitates the visualization of the results of the SNA. This option has five tools:
- MDigraph: that draws bipartite directed graphs of Metatool’s metabolic network, its subsets and the subsets’ pathways;
- MetaMatrixTXT: visualizes the convex basis and elementary modes of Metatool’s output in function of subsets, in vectorial or matrix format;
- CBGraphs: draws bipartite directed graphs of Metatool’s convex basis and its pathways;
- EMGraph: draws bipartite directed graphs of Metatool’s elementary modes and its pathways;
- SortEModes: orders Metatool’s elementery modes that contain a given metabolite (or a list of metabolites) in a certain side of its reaction.
Compare was developed to compare different Metatool’s results from two species, using subsets or elementary modes comparison. It is composed by:
- Compara: tool that matches up distinct Metatool’s outputs and shows the identical subsets;
- ComparaSub: compares different Metatool’s outputs and shows the first output in function of the subsets of the second;
- ComparaEM: compares distinct Metatool’s outputs and shows the identical elementary modes.
The suite t4m also include scripts that generate Metatool’s input based on COBRA SBML files, Cobra2Metatool, or based on a Metatool’s output file that is filtered by a list of convex basis’ enzymes, Cbasis2Metatool. Besides, t4m has a script, called CheckMIn, that checks Metatool input file format and its consistency.
All these tools have been tested with several metabolic networks. In this contribution we will present some examples to illustrate the use and t4m possibilities.