# iColonEpithelium
This is a part of the CyberGut project, aiming at constructing a tissue-specific GEM of colon epithelium .
Each folder contains code corresponding to the method steps described in the methods section of the manuscript.

## Step 1
### Download datasets used in this project refered to the file "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/Input_datasets/Human colon epithelium transcriptome datasets.xlsx"

## Step 2
### Follow the code "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/Input_data_process/Gene_expression_data_process_code.R" to processed the downlaod datasets

## Step 3
### Follow the tutorial of the corss-platfram normalization tool Shambhala2 (https://github.com/BorisovNM/Shambhala2) to normalize all datasets, which will produce the file "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/Input_data_process/geneset_final.csv" 

## Step 4
### Follow the code "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/Input_data_process/Ubiquity_score_calculation.R" to calculate Ubiquity score and Expressionset, which will produce file "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/Input_data_process/Ubiquity_Score.txt" and "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/Input_data_process/Expressiondata.csv"

## Step 5
### Follow the tutorial of iMAT&tINIT (https://github.com/BioSystemsUM/troppo), CORDA (https://github.com/resendislab/corda) and pymcadre(https://github.com/draeger-lab/pymCADRE) to manually prepare input files for these four tools, which were save at "Draft_reconstruction_inputs/"

## Step 6
### Follow the code in "Code_of_Draft_Reconstructions/" to build 4 draft reconstructions and code "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/Code_of_Consensus_Reconstruction/Consensus_Reconstruction.ipynb" to build consensus reconstruction.

## Step 7
### Follow code "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/Code_of_Metabolic_Task_Testing/metabolic_task.ipynb" to run metabolic task test of the consensus reconstruction and manually corate the consensus reconstruction to build our iColonEpithelium reconstrction 

## Step 8
### Download two dataset for case study: Crohn's Disease (CD: GSE164985) and ulcerative colitis (UC: Single Cell Portal (SCP259)), and follow code "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/Code_of_Case_Studies/CD.R" and "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/Code_of_Case_Studies/UC.R" to process single cell RNAseq data, extract colonocyte data and prepara input for iMAT the same as Step 5;

## Step 9
### Follow code "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/Code_of_Case_Studies/Context-specific_reconsturctions_imat.m" to build  reconstructions

## Step 10
### Follow code "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/Code_of_Case_Studies/Case_sutdy.ipynb" to analyze reconstructions obtained in the previous step.

## Step 11
### Follow code "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/Code_of_Host_Microbiome_Integration/Integration_example.ipynb.ipynb" to try the toy model integrating iColonEpithelium reconstruction and a MICOM model