iMet: A graphical user interface software tool to merge metabolic networks

Abstract

Nowadays, studying microorganisms has become faster and deeper than the last decades, thanks to the modeling of genome-scale metabolic networks. Completed genome sequencing projects of microorganisms and annotating these sequences have provided a worthwhile platform for reconstructing and modeling genome-scale metabolic networks. The genome-scale metabolic network reconstruction is a laborious and time-consuming task which needs an extensive study and search in different types of databases. Furthermore, it also requires an iterative process of creating and curating the obtained network, particularly with experimental methods. Hence, different types of reconstructions and models of a targeted microorganism can be found with different qualities, as the goal and need of researchers differ. Due to these circumstances, scientists have to continue with only one of the reconstructed metabolic networks of each microorganism and ignore the rest in their in silico works. It is clear that having a tool which merges different metabolic networks of a single organism can be a useful and effective way to study them with minimal cost and time. To meet this need, we have developed iMet , the standalone graphical user interface (GUI) software tool to merge multiple reconstructed metabolic networks of microorganisms. As a case study, we merged three reconstructed metabolic networks of a cyanobacterium using iMet, and then all of them (including the new merged one) became modeled. The results of our evaluations including Flux Balance Analysis (FBA), revealed enhancing metabolic network coverage as well as increasing yield of desired products in the new obtained model.

mergem: merging and comparing genome-scale metabolic models using universal identifiers

“…iMET is a standalone graphical user interface that can semi-automatically merge metabolic networks in the SBML file format [11]. The algorithm uses features such as metabolite name and KEGG ID to compare pairs of metabolites after which it assigns a similarity score to each pair.…”

“…mergem does not use reaction identifiers and instead compares the participating reactant and product metabolites to find matching reactions, bypassing completely the identifier mapping problem for reactions. iMET is a standalone graphical user interface that can semi-automatically merge metabolic networks in the SBML file format [11]. The algorithm uses features such as metabolite name and KEGG ID to compare pairs of metabolites after which it assigns a similarity score to each pair.…”

“…modelBorgifier [10] is a MATLAB toolbox for matching and comparing, semi-automatically, two given genome-scale reconstructions by merging metabolites and reactions based on a set of parameters such as metabolite name, KEGG ID, reaction name and the number of reactants and products in reaction. iMet [11] is a graphical user interface software that merges metabolic networks in a semi-automatic fashion. The MetaNetX web-interface [12] provides tools for combining models and identifying common and unique components between pairs of models.…”