Software and Modelling

Development of high throughput analytical methods to quantify transcriptome, proteome and metabolome together with massively parallel cultivation procedures generate an enormous amount of data. Analysis and presentation of the data in the real time in simultaneously with carrying out cultivation experiments requires development of new type of models allowing full comprehensive quantitative analysis of physiology of growing cells. Modeling technology is developed based on a new whole-cell models (SCM) that enable describing quasi-stationary physiological states and metabolism of microbial cells including cell-cycle and geometry.

CFFT supplements cell models with additional biological systems –regulatory mechanisms and networks, enzyme kinetics and metabolite concentrations – and to create integrated software platform enabling real-time data analysis and modeling.

The two most important novelties of the data handling and modeling part of the systems-biology/synthetic-biology platform are:

a) the use of novel SCMs which make possible ab initio design of bacterial cells, and

b) development of the software environment suitable for the near-real-time modeling and analysis of data from advanced cultivation (e.g. A-stat) experiments to understand steady state cell physiology.

At the moment, model organisms are L. lactis, E. coli and S. cerevisiae. New modeling technology is applied for media design, growth space scanning, mutant design, screening of strains, etc.

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