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haowang-bioinfo merged 4 commits into from
Nov 6, 2018
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Update readme to adapt to new repo name #61

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feat: update the README.md for new repo name
haowang-bioinfo Oct 29, 2018
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fix: improve document
haowang-bioinfo Oct 30, 2018
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doc: minor fixation
haowang-bioinfo Oct 30, 2018
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Merge pull request #59 from SysBioChalmers/changeRepoName
haowang-bioinfo Oct 31, 2018
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20 changes: 11 additions & 9 deletions README.md
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# Human-GEM
# human-GEM: The generic genome-scale metabolic model of _Homo sapiens_

- Brief Model Description

This repository contains the latest version of the generic Human Metabolic model, humanGEM, which is a genome-scale metabolic model of the generic human cell.
This repository contains the latest version of metabolic model human-GEM, which is a genome-scale model of the generic human cell.

- Abstract:

Human genome-scale metabolic models (GEMs) are an important tool for the study of human health and disease, providing a scaffold upon which many different types of data can be analyzed in an integrative manner. Despite advancements in the size and complexity of human GEMs, there currently exists the need for a highly accurate, standardized, and manually curated model of human metabolism. Here, we update the previous version of the Human Metabolic Reaction model (
2) to humanGEM, in a process that includes the addition of new reactions, metabolites, and genes, followed by extensive curation. The objective of humanGEM is to serve as a continually maintained “gold-standard” of generic human GEMs, further enabling integrative and mechanistic studies of human metabolism.
Human genome-scale metabolic models (GEMs) are important tools for the study of human health and diseases, by providing a scaffold upon which many different types of data can be analyzed in an integrative manner. Despite advancements in the size and complexity of human GEMs, there currently exists the need for a highly accurate, standardized, and manually curated model of human metabolism. Here, we update the previous version of the Human Metabolic Reaction (HMR2) model to human-GEM, in a process that includes the addition of new reactions, metabolites, and genes, followed by extensive curation. The objective of human-GEM is to serve as a community maintained “gold-standard” of generic human GEMs, further enabling integrative and mechanistic studies of human metabolism.

- Model KeyWords:

**GEM Category:** Species; **Utilisation:** Predictive simulation; **Field:** Metabolic-network reconstruction; **Type of Model:** Reconstruction; **Model Source:** HPA, HMR, iHepatocytes2322; **Omic Source:** Proteomics; **Taxonomy:** _Homo sapiens_; **Metabolic System:** General Metabolism; **Condition:** Generic metabolism;
**GEM Category:** Species; **Utilisation:** Predictive simulation; **Field:** Metabolic-network reconstruction; **Type of Model:** Reconstruction; **Model Source:** HPA, HMR2, iHepatocytes2322, Recon3D; **Omic Source:** Proteomics; **Taxonomy:** _Homo sapiens_; **Metabolic System:** General Metabolism; **Condition:** Generic metabolism;

- Reference: n/a

Expand All @@ -35,15 +34,18 @@ This repository is administered by Jonathan L. Robinson ([@JonathanRob](https://
## Installation

### Required Software:
* You need a functional Matlab installation of **Matlab_R_2015_b** (MATLAB 7.3 and higher)
* The [RAVEN](https://github.com/SysBioChalmers/RAVEN) toolbox for MATLAB. An up-to-date version from COBRA GitHub repository is strongly recommended . Add the directory to your Matlab path, instructions [here](https://se.mathworks.com/help/matlab/ref/addpath.html?requestedDomain=www.mathworks.com)
* A functional Matlab installation (MATLAB 7.3 and higher).
* The [RAVEN toolbox](https://github.com/SysBioChalmers/RAVEN).
* The [COBRA toolbox](https://github.com/opencobra/cobratoolbox).


### Dependencies - Recommended Software:
* libSBML MATLAB API (version [5.13.0](https://sourceforge.net/projects/sbml/files/libsbml/5.13.0/stable/MATLAB%20interface/) is recommended).
* The libSBML MATLAB API (version [5.13.0](https://sourceforge.net/projects/sbml/files/libsbml/5.13.0/stable/MATLAB%20interface/) is recommended).
* [Gurobi Optimizer](http://www.gurobi.com/registration/download-reg) for any simulations.


### Installation Instructions
* Clone [model](https://github.com/SysBioChalmers/) branch from [SysBioChalmers GitHub](https://github.com/SysBioChalmers)
* Clone the model from [master](https://github.com/SysBioChalmers/) branch from [SysBioChalmers GitHub](https://github.com/SysBioChalmers)
* Add the directory to your Matlab path, instructions [here](https://se.mathworks.com/help/matlab/ref/addpath.html?requestedDomain=www.mathworks.com)


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