Biostar Central

Software for better science.

Biostar Central is a Python and Django based collection of web applications that support scientific practice and education.

The goal of the project is to produce software with straightforward installation and minimal dependencies that works on any computing platform that supports Python. For each app the philosophy is that of decentralization and self hosting. We write code to allow others to recreate the same services that we run.

Each web application may be deployed individually or in combination with the others. The following applications are currently feature complete:

• recipes a web app that can runs data analysis scripts via a web interface, see: Bioinformatics Recipes
• forum a web app that runs a Q&A forum inspired by StackOverflow, see: Biostars Q&A

Note: The public biostars.org site runs the code from the biostar2016 branch. The master branch is the development version that we will migrate the main server to in the future.

Installation

The code in Biostar Central requires Python 3.6 or above.

Our installation instructions rely on conda though other alternatives for managing python environments are equally viable.

# Create a virtual environment.
conda create -y --name engine python=3.6

# Activate the python environment.
conda activate engine

# Clone the source server code and the recipe code.
git clone https://github.com/ialbert/biostar-central.git

# Switch to the biostar-engine directory.
cd biostar-central

# Install server dependencies.
pip install -r conf/pip_requirements.txt

The installation is now complete.

All server management commands are run through make.

Testing the code

To test the recipes app run:

make recipes test

To test the forum app run:

make forum test

Running the demo server

To run the demonstration version of the recipes app execute:

make recipes_demo

To run a demonstration version of the forum app execute:

make forum_demo

Visit http://127.0.0.1:8000/ to view the site.

Executing multiple tasks

The Makefile has several tasks that demonstrate the commands that may be chained together:

Initialize and run an empty recipes app.

make recipes init serve

Initialize and run an empty forum app.

make forum init serve

Documentation

Additional documentation for:

• Documentation for the recipes app
• Documentation for the forum app