AntND: A java framework for curation and optimization of metabolic networks.

Abstract

Summary: Metabolic modeling is a widely used tool for the study and prediction of cell metabolism. High-quality metabolic models are needed for accurate metabolic simulations and predictions. The database BioModels (Juty 2015) hosts 2641 whole-genome stoichiometric models created using pathway information from KEGG or MetaCyc. The curation of a whole-genome metabolic model to make it functional and able to predict experimental data is a tedious process (Thiele 2010). AntND is a software framework that enhances the manual curation, analysis, visualization and optimization of metabolic models. It contains modules for reading and writing files in SBML format, easily editing the models, extracting subnetworks based on pathway information or based on the shortest path search, performing FBA and flux optimizations, visualizing and analyzing the metabolic networks. The visualization of the models is one the most powerful modules in AntND. It allows to extract and create layouts using GML (Graph Modeling Language) format, easily expand the network and coloring the nodes.

Avaliability and implementation: AntND is implemented using java and is distributed freely under GNU General Public Licence. It’s code is hosted in github.

Contact: sandra.castillo@vtt.fi