Integrated network reconstruction, visualization and analysis
Roland Schwarz, Chunguang Liang and Thomas Dandekar
Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
YANAsquare is a user friendly software package for the analysis of metabolic networks. It is capable of performing elementary mode analysis on those networks and incorporates new algorithms for mapping elementary mode activities to enzyme activities and vice versa. It features automatic extraction of metabolic networks from KEGG and visualization of metabolic networks as bipartite graphs.
YANAsquare was written in Java and is available for Windows and Unix systems. It includes a graphical user interface for the easy editing of metabolic networks and is capable of reading and writing the METATOOL file format as well as the SBML Level 2 file format (http://www.sbml.org).
Note: The latest YANAsqaure requires the JRE 1.6 (http://java.sun.com/javase/downloads/index.jsp) to run.
YANAsqaure is distributed under the GNU General Public License (GPL). For more information, see http://www.gnu.org/copyleft/gpl.html or the LICENSE file which comes with the download archive.
YANAvergence is an important extension to YANAsquare software, which allows integrating more expermental data to inspect the adaptation of metabolic network under different stresses, conditions.
YANAsquare GUI software package - Download
YANAvergence demo - Supplementary files for flux computation:
1. List of processes in the strain-specific models and comparison: suppl_1_processes.xls
3. Tutorial on the use of the program YANAvergence: yanavergence_demo.rar
5. Proteome data set: suppl_2_proteins.pdf
6. Condensed Model in SBML format: suppl_0_sac_model.sbml
Requirement for YANAvergence: GNU R under windows/Linux/Mac system with MASS libraries installed.