Abstract

Various experimental approaches including also isotopic tracer information were proposed paving the way for quantitative modeling and detailed in vivo studies of biological systems. Accordingly, for the underlying modeling approaches a diversity of in silico tools have been developed. The full exploitation of this potential to ad-dress metabolic processes is hampered by mainly three principal issues.  First, not all currently realizable experiments are covered by these tools. Secondly, an easy switching between exist-ing tools allowing for a flexible description of different experimental states is not possible. The third item addresses the universality of underlying modeling concepts which usually have a restricted focus. We propose a general modeling concept which allows modeling and simulation of all combinations of metabolically and isotopically variants in their stationary and dynamic states and which is embedded in an unique software platform.  The basic idea is to build up dynamic metabolic networks relying on mass balances for intermediate labeling pools. A workflow is presented that allows the automatized gener-ation of models of any size and complexity specially tai-lored for the experiment of choice. Within the software framework, the application of sophisticated methods for statistical analysis and interpretation of simulation results are realized.