System biology modelers from Latvia visits Iceland

Our researchers were in Iceland from November 28 until December 4, 2010. Week began with the analysis of Korean Zymomonas mobilis metabolic model. In consultation with colleagues in Latvian the model bottleneck localization was made. The model first level debugging was carried out.


With the help of Iceland University Systems Biology experts metabolites mass and charge balancing was conducted. Icelandic COBRA toolbox latest addition "Reconstruction tool" was viewed. When you create a computer model of organism metabolism a lot of time is spent researching metabolites chemical formulas (neutral and charger) on internet databases. Often, information on metabolites and enzymes are fragmented and not available in one or two databases. However, there is no single database that contains information about all metabolites. Furthermore, if metabolite is in the particular database, there is no guarantee, that information is complete. It was quite usual situation that there was no charge available in a database - only visual structure. Often there are occasions when a specific metabolite has no information. In such cases, experience of foreign colleagues in metabolic modeling is very useful.