GEMcon

Pipeline for fetching expression /proteomic abundance data and building context-specific human metabolic models (Human-GEM based)

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Overview

GEMcon integrates data from:

• scRNA-seq (Human Cell Atlas)
• bulk RNA-seq (GTEx) -->proposed
• proteomics (PaxDB)

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Quick Start

1. Clone the repository

git clone https://github.com/ToruOkadaOi/GEMcon.git
cd GEMcon

2. Create necessary environments

conda env create -f envs/scanpy_env.yml
conda env create -f envs/cplex_env.yml
conda env create -f envs/gecko_env.yml

3. Usage

# Inside GEMcon directory
python scripts/cli.py --branch <transcriptomic|proteomic> [--task <annotate|metabolic>] [--algo <algorithm>] [--input <file>]

• --branch is required
• --algo is optional. Choices:
  • gimme
  • tinit
  • fastcore (testing)
  • imat (testing)
• --input is optional

Optional

# Use as CLI instead
pip install -e . # install

gemcon --branch <transcriptomic|proteomic> [--task <annotate|metabolic>] [--algo <algorithm>] [--input <file>] # run!

4. Results

results/ && data_processed/

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Status

In the works

TODOs

GTex integration
env. reproducibility

Docker

# pull the image
docker pull toluene123/gemcon:latest

docker run -it toluene123/gemcon:latest bash # add --rm if you want post-exit deletion; -v for mounting a volume.

# check the config.yaml && ## run!
gemcon --help