README.rtf

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{\author marco fondi}}\paperw11904\paperh16836\margl1440\margr1440\vieww19340\viewh13180\viewkind0
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This is a README file for the computational pipeline described in the manuscript \'93A synthetic ecosystem for the multi-level modelling of heterotroph-phototroph metabolic interactions\'94, by Marco Fondi and Francesca Di Patti.
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\cf0 The code is structured into 4 main folders:
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- \'93Code\'94 contains the code for the generation and the constraint-based analysis of the phototroph-heterotroph metabolic reconstruction (plus some additional figures that have not been included in the manuscript). In particular, the MATLAB script \'93DFBA_lab_pipeline.m\'94 launches all the scripts necessary to load the two reconstructions, parse (using bash scripts and MetaNetX databases and xref files) and combine them in a single reconstruction, run FBA and dFBA on such integrated model. To run the code just enter the \'93Code\'94 folder and then execute \'93DFBA_lab_pipeline\'94 from the MATLAB command line. Editing the \'93DFBA_lab_pipeline.m\'94 script on lines 39-41 allows chosing among:
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\f0 \cf0 1) modelling co-culture behaviour with standard parameters (\'93main_function\'94)
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\f0 2) modelling co-culture behaviour at different DOM release ratio (\'93main_function_DOM_fraction\'94)
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\f0 3) modelling co-culture behaviour at D/B dilution rates (\'93main_function_DilutionCombinations\'94, memory demanding)
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\f0 \cf0 The dFBA part of this pipeline relies on the DFBAlab toolbox (Gomez et al. 2014) so you need to have installed and its location included in the MATLAB path. The code inside this folder was used to produce Figures 3 and 4 in the manuscript. 
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- \'93ODE_model\'94 contains the code for running the ODEs-based model of the phototroph-heterotroph metabolic reconstruction. This folder is accessed by the \'93DFBA_lab_pipeline.m\'94 during its execution so, in principle, there should be no need to modify anything inthere. 
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- \'93Stochastic_simulations\'94 contains the code used to analyze the stochastic simulations of the co-culture behavior at different phosphate inflow concentration and plot the results. The results of the stochastic simulations related to the results presented in the manuscript are already inside the folder (*.dat files). Such files have been generated using the code \'93stochasticSimulation.c\'94. The code inside this folder was used to produce Figure 5 in the manuscript.To run the code and generate the figures just enter the \'93Code\'94 folder and then execute \'93Main_stochastic\'94 from the MATLAB command line.
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\f0 \cf0 - \'93Stochastic_simulations_dilution_rate\'94 contains the code used to analyze the stochastic simulations of the co-culture behavior at different dilution rates of phototroph and heterotroph cells and plot the results. The results of the stochastic simulations related to the results presented in the manuscript are already inside the folder (*.dat files). Such files have been generated using the code \'93stochasticSimulation.c\'94. The code inside this folder was used to produce Figure 6 in the manuscript. To run the code and generate the figures just enter the \'93Code\'94 folder and then execute \'93Main_stochastic\'94 from the MATLAB command line.
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\f0 Question and bugs to 
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\f0 Marco Fondi, {\field{\*\fldinst{HYPERLINK "mailto:marco.fondi@unifi.it"}}{\fldrslt \ul \ulc0 marco.fondi@unifi.it}} 
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\f0 twitter: @mrcfnd
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