https://github.com/bblodfon/colomoto-gupta
A reproducibility study using the Colomoto notebook
https://github.com/bblodfon/colomoto-gupta
colomoto-docker logical-modeling reproducibility reproducible-research
Last synced: 7 months ago
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A reproducibility study using the Colomoto notebook
- Host: GitHub
- URL: https://github.com/bblodfon/colomoto-gupta
- Owner: bblodfon
- Created: 2018-11-19T13:32:57.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2018-11-22T10:19:40.000Z (over 7 years ago)
- Last Synced: 2025-01-30T13:22:53.052Z (over 1 year ago)
- Topics: colomoto-docker, logical-modeling, reproducibility, reproducible-research
- Language: HTML
- Homepage:
- Size: 756 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# colomoto-gupta
## Intro
This repo has the necessary files to reproduce the analysis on the boolean model presented in [Gupta et al. (2018)](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6053189/), titled '*Modeling the role of microRNA-449a in the regulation of the G2/M cell cycle checkpoint in prostate LNCaP cells under ionizing radiation*'. The present reproducibity analysis was the project of the PhD course **Logical Modeling for Experimental Design in Current and Future Biotechnology and Biomedicine**, offered by NTNU during the Autumn of 2018.
## Run notebook
First, you need to install the [colomoto-docker](https://github.com/colomoto/colomoto-docker). Then:
```
git clone https://github.com/bblodfon/colomotoGupta.git
cd pathTo/colomoto-docker
python colomoto_docker.py -V 2018-08-17 --bind /pathTo/colomotoGupta
```
The [gupta_john_zobolas.ipynb](https://github.com/bblodfon/colomotoGupta/blob/master/gupta_john_zobolas.ipynb) is the main notebook file.