Experimental data, and modelling and analysis source code for the paper 'Combining SIMS and mechanistic modelling to reveal nutrient kinetics in an algal-bacterial mutualism'

Experimental data and source code files for the paper 'Combining SIMS and mechanistic modelling to reveal nutrient kinetics in an algal-bacterial mutualism'.

The zipped folder 'ExperimentData.zip' contains data files with the data obtained from Secondary Ion Mass Spectrometry (SIMS), Isotope Ratio Mass Spectrometry (IRMS), growth measurements and the B12 bioassay as described in the paper.

The zipped folder 'MatlabCode.zip' contains the Matlab source code and data files that were used to solve the model equations and to run the global parameter optimisations for the axenic cultures and the co-culture. The file 'odefun.m' defines the model ODEs and the file 'model_run.m' specifies the solver used to solve the model ODEs. The file 'Gf_global_optimisation.m' runs the global parameter optimisation with the objective function being minimised defined by the file 'Gf_obj_function.m' and the non-linear constraints defined by the file 'nonlconstraints.m'. The file 'initial_conditions.m' specifies the initial conditions for the culture and the file 'parameters.m' specifies the model parameter values. The folders 'growth' and 'SIMSdata' contain the relevant Matlab data files needed for the parameter optimisations. The output of the global parameter optimisations can also be found in the relevant folders.

The zipped folder ‘PythonCode.zip’ contains the source code files used for the global parameter optimisation in Supplementary Figure S5. The file ‘experimental_data_global_import_result.npz’ is a NumPy array containing all the experimental results from which the fit is based. The file ‘data_global_fit.py’ is the main fit script that launched 32 basin-hoppers to optimize the fit to the data. It thus loads the data (which clarifies what the previous file contains), defines the cost functions and runs the fit. The file ‘utils.py’ is a small utilities file, which contains two functions for saving figures and files. It is used by the global fit file, so is submitted here for completion. The file ‘cysolver2.pyx’ is the finite difference solver called by the main fitting script in order to evaluate the co-culture model forward in time given initial conditions and parameters. It is in Cython, the C-based python for fast calculation. The folder ‘basin_hopping_result.zip’ is an archive containing the 32 Numpy files that correspond to the 32 results obtained on 22nd of March 2017 when the solver was run. The result used for Supplementary Figure S5 is #6 (from #0 to #31).

Below is a list of the labels used to help identify the cultures relevant to the isotope labelling experiments in the paper.

List of cultures:

A: preliminary experiment, algal pre-culture (unlabelled)

Aii: main experiment, algal pre-culture (unlabelled)

Bii: main experiment, bacteria pre-culture (unlabelled)

1: preliminary experiment, algal pre-labelling culture

1ii: main experiment, algal pre-labelling culture

2: preliminary experiment, algal data for the labelled co-culture

2ii: main experiment, the labelled co-culture

3: preliminary experiment, unlabelled axenic culture of algae

4: preliminary experiment, unlabelled co-culture

5: preliminary experiment, axenic bacteria with 0.1% glycerol

5ii: main experiment, axenic bacteria with 0.1% glycerol

6: main experiment, axenic bacteria with no glycerol

7: main experiment, axenic bacteria with 0.01% glycerol

8: main experiment, axenic bacteria with 0.001% glycerol