Recon3D

A 3-Dimensional View of Human Metabolism and Disease

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GEM-PRO (Recon3D_GP)

GEM-PRO for the H. sapiens Recon3D metabolic model.

Instructions

Requirements

• Jupyter notebook installation and Python 2/3
• ssbio

Installing nglview and ssbio

pip install nglview
pip install ssbio

Cloning

git clone https://github.com/SBRG/Recon3D

Opening

• Launch the notebook Recon3D - Loading and Exploring the GEM-PRO.ipynb from a Jupyter instance

Updating

• Launch and run the notebook Recon3D - Updating the GEM-PRO.ipynb from a Jupyter instance

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Single gene deletion simulations (sgd)

The description of these simulations is made available through the Supplementary Information.

Instructions

Requirements

• MATLAB R2015B+
• Mosek v.7+
• RAVEN v.1.08+
• R 3.4.0 and R libraries gplots (3.0.1) and RColorBrewer (1.1-2)

Workflow

• Set /sgd as working directory
• Convert Recond3D model into RAVEN-format and save it to models/Recon3d_toRaven.mat) by running convertRecon3toRaven.m
• Simulate in silico library of sgds for HMR2, Recon3d, and HMR2-derived GBM models under Ham's medium composition (described in media/) by running main.m. Medium-constrained wild-type models are saved in models/constrained/.
• Analyze in silico sgd results by running main.R. Plots are saved in /plots

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Citation

The manuscript for Recon3D can be found and cited at:

Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlić A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO. 2018. Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat. Biotechnol. http://dx.doi.org/10.1038/nbt.4072.