E.coli FBA

Analyze E. coli code and heat response with FBA

1. Install cobrapy and associated packages.

sudo apt-get install libglpk-dev
sudo pip install cobra --pre
sudo pip install python-libsbml
sudo pip install numpy,scipy

Note: Many other packages need to be installed to use python libsbml.

2. Modify the model to fit for E. coli BW225113

Include reactions: ARAI, RBK_L1, RMPA, LYXI, RMI, RMK, and LACZ. Gap filling:

python read_ecoli2011.py

3. Set constraints for LB media/culture

Following:http://2013.igem.org/Team:KU_Leuven/Project/Glucosemodel/MeS/Modelling-FBA

python read_ecoli2011.py

4. Gene Knockout

Based on data from Phenotypic Landscape of a Bacterial Cell, mmc2.xlsx E. coli gene mapping is downloaded from supplementary file of

Riley, et al. Escherichia coli k-12: a cooperatively developed annotation snapshot2005. NAR, 34(1):1–9, 2006

Mapping genes to reactions, change constraints based on protein abundance data from PaxDb.

python Gene2React.py

5. Flux balance analysis

python ./fba/Ecoli_FBA.py

6. Map fitness to growth rates

python ./fva/colonySize2GrowthRate.py

7. Flux variability analysis

python ./fva/Ecoli_FVA.py

8. Draw graphs

./sample_heatmap/plot.sh # Draw heatmaps for sample mutants

./temp/var_analysis.py  # Draw histogram for mutants using mean of flux variances
./temp/plot_10bins.py # Draw 10 bin bar chart.

./temp/cold_10bins/cold_10bin.sh #check essentiality and dispensability in each 10 bins
./temp/cold_10bins/disp_var_max.py # used to find maximum variance reactions

./temp/cold_10bins/pathways/cytoscape_data.py # prepare data for cytoscape
./temp/cold_10bins/pathways/top100_rxn_max.py # Find top100 reaction ids for mutants, draw heatmaps for reactions

charlesxu90/Ecoli_FBA