2.1. PCI-32765 order FiatFlux-Headless In order to prepare FiatFlux for use from within a workflow environment, we developed a “headless” version of the software, which comprised three major aspects: (1) Enabling programmatic access: Being developed as interactive software, the code has not been designed for invocation from the outside. FiatFlux-Headless makes the functionality of the FiatFlux code base accessible for external invocation (without using Inhibitors,research,lifescience,medical the graphical user interfaces (GUIs)). (2) Emulation of user interaction: As the abstract 13C flux analysis process depicted in Figure 1 shows, the computations require several

user interactions via the GUIs. In FiatFlux-Headless the user interactions that are required at specific points of the original software Inhibitors,research,lifescience,medical are emulated by purpose-built methods. (3) Visualization support: FiatFlux comprises functionality for exporting the flux analysis results in different textual formats. As graphical presentations of metabolic flux distributions inside network diagrams are more accessible, FiatFlux-Headless furthermore exports the results in a format that can later be used in network visualization software. Details on the development of FiatFlux-Headless are given in the following sections. 2.2. Enabling Programmatic Access FiatFlux consists of the two main modules ratio and netto containing the GUI for steering the flux Inhibitors,research,lifescience,medical ratio and the

net flux distribution computation, respectively. Some other Inhibitors,research,lifescience,medical modules provide additional GUI components, for instance for the setting of different experimental parameters, for editing the weights of amino acid fragments that are considered in the flux ratio computation, or for writing the analysis results into text files. Basically, inactivation of the GUI in these

modules was achieved by rigorously removing all code Inhibitors,research,lifescience,medical for graphical components and replacing invocations from the GUI with (parameterized) functions. These changes made it possible to access the basic FiatFlux functions from external program code and to transfer data between the different analysis steps, which are prerequisites for integration into a workflow environment. Edoxaban Another useful functionality that we adopted from FiatFlux is the possibility to upload custom network models instead of using the standard networks provided by the system. The required information has to be provided as a text file following a defined syntax. Also within this file, the user can specify new metabolic flux ratios complementary to those calculated in the ratio module. The values of such additional ratios have to be provided together with the analytical equations in the model file. Furthermore we extended the FiatFlux outputs with some additional information on the analysis procedure: Initially, results could be exported to text files that contain the data in tab-separated format and can thus be directly imported into spreadsheet programs like MS Excel or OpenOffice Calc.