Analysis of synthetic metabolic pathways solution space

Author

Meitalovs, Jurijs ; Stalidzans, Egils

Author_Institution

Dept. of Comput. Syst., Latvia Univ. of Agric., Latvia

fYear

2013

fDate

4-6 July 2013

Firstpage

183

Lastpage

187

Abstract

The size and the number of available genome scale metabolic models and reconstructions of different organisms is growing rapidly. Various computational methods and tools are developed in the last decades for metabolic network construction, analysis and optimization in the interdisciplinary scientific branches of systems biology and synthetic biology. A software tool SpaceAnalyzer (SAnalyzer) is developed in Matlab environment for automatic generation of pathways to new metabolites. The necessary time for a metabolic pathway supergraph development using reactions from KEGG database is analyzed. The construction of all the up to 15 reactions long pathways for glucose, glycerol and xylose takes about 11 000 seconds involving about 5500 metabolites from totally 17 000 available metabolites in the KEGG data base. Availability: www.biosystems.lv/sanalyzer.

Keywords

biology computing; genomics; optimisation; software tools; KEGG data base; KEGG database; Matlab environment; SAnalyzer; SpaceAnalyzer; genome scale metabolic models; glucose; glycerol; interdisciplinary scientific branches; metabolic network construction; metabolic pathway supergraph development; metabolites; optimization; software tool; synthetic biology; synthetic metabolic pathways solution space; systems biology; xylose; Biochemistry; Bioinformatics; Biological system modeling; Databases; Genomics; Organisms; Substrates; metabolic pathway construction; metabolism; solution space; synthetic biology;

fLanguage

English

Publisher

ieee

Conference_Titel

System Science and Engineering (ICSSE), 2013 International Conference on

Conference_Location

Budapest

ISSN

2325-0909

Print_ISBN

978-1-4799-0007-7

Type

conf

DOI

10.1109/ICSSE.2013.6614656

Filename

6614656