A scientific workflow framework for 13C metabolic flux analysis

Metabolic flux analysis (MFA) with C-13 labeling data is a high-precision technique to quantify intracellular reaction rates (fluxes). One of the major challenges of C-13 MFA is the interactivity of the computational workflow according to which the fluxes are determined from the input data (metabolic network model, labeling data, and physiological rates). Here, the workflow assembly is inevitably determined by the scientist who has to consider interacting biological, experimental, and computational aspects. Decision making is context dependent and requires expertise, rendering an automated evaluation process hardly possible. Here, we present a scientific workflow framework (SWF) for creating, executing, and controlling on demand C-13 MFA workflows. C-13 MFA-specific tools and libraries, such as the high-performance simulation toolbox 13CFLUX2, are wrapped as web services and thereby integrated into a service-oriented architecture. Besides workflow steering, the SWF features transparent provenance collection and enables full flexibility for ad hoc scripting solutions. To handle compute-intensive tasks, cloud computing is supported. We demonstrate how the challenges posed by C-13 MFA workflows can be solved with our approach on the basis of two proof-of-concept use cases. (C) 2015 Elsevier B.V. All rights reserved.