MALBoost: a web-based application for Gene Regulatory Network Analysis in Plasmodium falciparum

[![MIT License][license-shield]][license-url]

MALBoost web application

Source code behind the MALBoost web applicaiton

Table of Contents

1. About The Project
   • Built With
2. Getting Started
   • Prerequisites
   • Installation
3. Usage
4. License
5. Contact
6. Acknowledgements

## About The Project [![Product Name Screen Shot][product-screenshot]](http://malboost.bi.up.ac.za) MALBoost as web application which allows researchers to construct Gene Regulatory Networks (GRNs) based on the [Arboreto](https://doi.org/10.1093/bioinformatics/bty916) library in python. The web framework constructs GRNs through a supervised approach using either GRNBoost2 or GENIE3. The application is intended for *Plasmodium spp.* GRN construction, howerver the algorithm is in no way organisms specific. ### Built With This section should list any major frameworks that you built your project using. Leave any add-ons/plugins for the acknowledgements section. Here are a few examples. * [Python3](https://www.python.org) * [Flask](https://flask.palletsprojects.com) * [Celery - Distributed Task Queue](https://docs.celeryproject.org/en/stable/index.html) * [Redis](https://redis.io) * [SQLite](https://www.sqlite.org/index.html) ## Getting Started The application is built using python-flask, redis and celery worker. The data is stored and managed using SQLite. It's recommended to use a python virtual environment. ### Prerequisites This is an example of how to list things you need to use the software and how to install them. #### Python virtual environment * python virtual environment ```sh python3 -m venv env source env/bin/activate ``` #### Redis * install redis macOS ```sh brew install redis ``` * install redis linux ```sh wget http://download.redis.io/redis-stable.tar.gz tar xvzf redis-stable.tar.gz cd redis-stable make ``` Please see documentation for [Redis](https://redis.io) more detail #### SQLite * install SQLite linux ```sh sudo apt update sudo apt install sqlite3 ``` ### Installation 1. Clone the repo ```sh git clone https://github.com/roelof89/malboost.git ``` 2. Install python packages ```sh pip install -r requirements.txt ``` ## Usage Use the launch shell script to start the application, this will run redis, celery and then flask. Check port configurations and nginx for hosting on web. * create .env file with the following variables ```sh app_url='http://url:port' CELERY_BROKER_URL='redis://localhost:6380' # match launch CELERY_RESULT_BACKEND='redis://localhost:6380' SQLALCHEMY_DATABASE_URI='sqlite:///data/YOURDATABASE.db' ``` * start app ```sh ./launch.sh ``` * stop app ```sh ./kill.sh ``` ## License Distributed under the MIT License. See `LICENSE` for more information. ## Contact Rudi - roelofvanwyk89@gmail.com ## Acknowledgements * [TUKS: Centre for Bioinformatics and Computational Biology](https://www.up.ac.za/centre-for-bioinformatics-and-computational-biology) * [Arboreto](https://arboreto.readthedocs.io/en/latest/) * [Aertslab](https://github.com/aertslab/arboreto) * [Choose an Open Source License](https://choosealicense.com) * [GitHub Pages](https://pages.github.com) * [Bootstrap](https://stackpath.bootstrapcdn.com) [license-shield]: https://img.shields.io/github/license/othneildrew/Best-README-Template.svg?style=for-the-badge [license-url]: https://github.com/othneildrew/Best-README-Template/blob/master/LICENSE.txt [product-screenshot]: static/img/product-sh.png