Optimization protocol of biochemical networks for effective collaboration between industrialists, biologists and modellers

Due to the growing number and size of biochemical network computer models an efficient co-operation among experts industrialists, biologists and modellers in industrial biotechnology is becoming a topical issue. In order to speed up the introduction of systems biology achievements into production an organism independent universal collaboration protocol is necessary incorporating a sequence of actions starting with a choice of criterion and model up to industrial tests. Protocol of cooperation of industrialists, biologists and modellers engineering the performance of a microorganism using systems biology approach to improve the efficiency of biotechnological process is developed. Method is described in form of an algorithm that consists of four consecutive stages starting with determination of the product of interest and optimization criteria and ending by an estimation of industrial process feasibility analysis taking into account the features of the available industrial equipment. Application of protocol in yeast glycolysis optimization is given as example. The protocol facilitates efficient resource usage and time savings in biochemical network optimization process due to rational sequence of operations and reduction of optimization duration.