Development of algorithms and methods for analysis and visualization of biochemical networks (2013 – 2016)

Grant No. 258/2013 (Latvian Council of Science)

 

Source of funding: Latvian Council of Science


Project period: 01.01.2013 – 31.12.2016

Project costs:  66 000 EUR (17 000 EUR for CSBG)

Project coordinator: Professor Juris Viksna, Institute of Mathematics and Informatics, University of Latvia

Project coordinator from our group: Professor, Egils Stalidzans, egils.stalidzans@lu.lv

Project objective:

Development of a software tool for comparison and reconciliation of genome-scale stoichiometric models and reconstructions of metabolic networks. Structural analysis of intersections of models has to be performed.

 

Project summary:

The main tasks of the project are related  with the development of software tools BINESA (promotion work of Tatjana Rubina) and ModeRator (promotion work of Martins Mednis).

 

Biosystems Group, Latvia University of Life Sciences and Technology (Egils Stalidzans)

 

 

Results

Software tools BINESA and MODERATOR have been developed and applied for the structural analysis of model pairs of the same organism and their intersections. Different structural parameters can be determined to find out the parameters that give indications about the quality of intersection models. Those parameters can be used for fast analysis of intersections of models assessing the quality of intersection and level of agreement between the compared models.

The algorithm implemented in MODERATOR analyses the similarity of chemical formulas and names of metabolites. In the case of identical formulas and names, the metabolites are automatically considered to be identical. In the remaining cases a similarity rate is calculated and manual curation is needed.

 
 

Institute of Microbiology and Biotechnology, University of Latvia Jelgavas iela 1, Riga
LV-1004, Latvia

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