SPOREme contains all the information and building scripts required to construct a ME-model for B. subtilis sporulation (SporeME2) based on BACILLUSme (iJT964-ME), which was based on COBRAme. See the COBRAme github and documentation for further instructions on how to build and solve ME-models. Minor changes were necessary for COBRAme to function with this organism, so find the modified COBRAme we used for iJT964-ME here.

SporeME2 files and model are available in bacillusme/analysis/spore. The notebooks are listed in numerical order and reproduce the reconstruction and findings of the manuscript.

If you are using BACILLUSme or iJT964-ME, please cite doi:10.1038/s41540-022-00259-0.

If you are using SporeME2, please cite doi: 10.1038/s41467-024-55586-z.

1. clone the repository
2. run python setup.py develop --user

Note: You will need to manually download and install some necessary requirements: COBRApy 0.5.11, COBRAme (modified), and solveME. solveME requires qMINOS, a quad-precision solver that is available upon request to Prof. Michael A. Saunders at Stanford University

1. Clone repository and navigate to sporeme/
2. docker build --file "./Dockerfile-Python3.7" . -t "python3.7-cobrame"
3. docker run --detach -p 10000:8888 python3.7-cobrame
4. In your browser, go to localhost:10000

There are two main folder locations that correspond to the two main steps of this project: (1) Reconstruction of ME-models, including updating iJT964-ME, and reconstructing the forespore and mother cell ME-models, and (2) Reconstruction and analysis of the ME2-model of B. subtilis sporulation, SporeME2. The layout is as follows:

1. Reconstruction of ME-models: Location: sporeme/bacillusme/

   • Notebooks 1, 2, and 3 reconstruct the updated ME-model of B. subtilis, and individual the ME-models of the mother cell and forespore, respectively.
   • The data used for ME-model building (following previously used formatting and structure, see ECOLIme and BACILLUSme), is in building_data. Notebooks 1 and 2 generate input files used for ME-model building (already provided in building_data/, so there is no need to re-run).
   • The output models are stored in me_models, as solution.pickle, solution_mother.pickle, and solution_spore.pickle.

2. Reconstruction of SporeME2: Location: sporeme/bacillusme/analysis/spore/

   • Notebooks are numbered in logical order. The first steps (Notebooks 1.) reconstruct SporeME2, while the subsequent ones load it to analyze metabolic mechanisms (Notebooks 2.) as well as proteome-wide protein essentiality (Notebooks 3.).
   • Notebook 1.1: Estimates biomass composition corrections to the B. subtilis biomass reaction from various reports.
   • Notebook 1.2: Merges the ME-models of the mother cell and the forespore, implements special constraining from literature, and generates SporeME2.
   • Notebook 1.3: Visualizes the properties of SporeME2.
   • Notebook 2.1.1: Estimates ATP supply mechanisms to the forespore.
   • Notebook 2.1.2: Estimates ATP supply mechanisms to the forespore if direct ATP transport is allowed.
   • Notebook 2.2: Analyzes the amino acid supply mechanisms to the forespore.
   • Notebook 2.3: Analyzes NTP supply mechanisms to the forespore.
   • Notebook 2.4: Visualizes the activity and cell-specific expression of the QA channel.
   • Notebook 3.1.1.: Runs the calculation of the cell-specific protein essentiality analysis.
   • Notebook 3.1.2.1.: Reads and analyzes the results of the protein essentiality analysis.
   • Notebook 3.1.2.2.: Analyzes the output of the GO enrichment analysis.
   • Notebook 3.1.3.: Runs conditional activity/inactivity analysis to identify proteome-wide effects of protein depletions.
   • Notebook 3.1.4.: Visualizes results from the conditional activity/inactivity analysis and prepares inputs for visualization in Cytoscape.
   • Notebook 3.2.1.: Runs the calculation of the cell-specific protein essentiality analysis in the naive SporeME2 (containing no cell-specific depletion constraining).
   • Notebook 3.2.2.: Analyzes the results of the protein essentiality analysis on the naive model.
   • Notebook 3.2.3.: Runs conditional activity/inactivity analysis on the naive model.
   • Notebook 3.2.4.: Visualizes results from the conditional activity/inactivity analysis in the naive model and prepares inputs for visualization in Cytoscape.