Data and code NTS pathway in Accumulibacter

Description

Here we make available all the data, input files, scripts, and functions required to reproduce our analyses regarding the glycolytic pathways available in Candidatus Accumulibacter. Additionally, the same data and files can be freely downloaded at https://github.com/kolavarria/NTS_pathway. Instructions for the creation of a Python environment suitable for reproducing our analyses are included.

Steps to reproduce

To reproduce our analyses, place the following files in a known folder in your computer: custom_plot_functions.py equilibrator_custom_functions.py equilibrator_custom_functions_my.py input C13 data.xlsx input physiologic data during labeling.xlsx input_data_bioreactor.csv input_MW_values.csv input_kinetic_parameters_database.csv input_metabolite_ranges_default.csv input_proteomics.xlsx script_01_processing_proteomic_and_physiology_data.ipynb script_02_FBA_stoichiometric_model_maker.ipynb script_03_plotting_labeling_data.ipynb script_04_FBA_metabolic_fluxes_labeling.ipynb script_05_MDF_metabolic_fluxes_labeling.ipynb script_06_FBA_pathway_maker.ipynb script_07_MDF_pathways.ipynb script_08_FBA_generating_file_for_ECM.ipynb script_09_ECM_calculations.ipynb Our analyses combined Flux Balance Analyses with thermodynamic calculations. To facilitate the reproducibility of our analyses, we strongly recommend the reproduction, in your computer, of the Python environment we created to perform these analyses. To facilitate the reproduction of this environment in another computer, we created a file named "cobra_and_equilibrator.yml". To reproduce in your computer the environment we created for our analyses, place the file named "cobra_and_equilibrator.yml" in an easy-to-find folder in your computer. Launch Anaconda prompt in your computer and navigate to the folder where you placed the file "cobra_and_equilibrator.yml". Then just type in the Anaconda prompt: conda env create -f cobra_and_equilibrator.yml This command enables the creation of an environment named "cobra_and_equilibrator" in your computer. Once the environment is created, you should activate this environment by typing in the Anaconda prompt: conda activate cobra_and_equilibrator Once the environment "cobra_and_equilibrator" is active, launch Jupyter Notebook by typing in the Anaconda prompt: jupyter notebook Once Jupyter Notebook is launched, navigate to the folder in your computer where you previously saved the provided files. Then you can perform the execution of the scripts inside Jupyter Notebook. The successful running of a given script depends on the existance of input files. Some of these input files are provided by us in the github "https://github.com/kolavarria/NTS_pathway" or are created with a script that you should run before. Therefore, you should execute the provided scripts by their numerical order, i.e., first the script named "script_01_processing_proteomic_and_physiology_data.ipynb", then the script named "script_02_FBA_stoichiometric_model_maker.ipynb" and so on.

Institutions

• Technische Universiteit Delft

  Zuid-Holland, Delft

Categories

Funders

• Dutch Research Council

  South Holland, The Netherlands

  Grant ID: NWO-BBE.2017.013
• Fundação de Amparo à Pesquisa do Estado de São Paulo

  São Paulo, Brazil

  Grant ID: FAPESP-2017/50249-6
• Ministry of Education, Science and Culture

  Mecklenburg-Vorpommern, Germany

  Grant ID: Gravitation grant 024.002.002

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