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 our 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:

• forum

  a web app that runs a Q&A forum inspired by StackOverflow, see: Biostars Q&A

• recipes

  a web app that can runs data analysis scripts, see: Bioinformatics Recipes

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/requirements.txt

The installation is now complete.

All server management commands are run through

make

Demo server

To run the demonstration version of the

recipes

make recipes demo

To run a demonstration version of the

forum

make forum demo

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

Default users

All users listed in the

ADMINS

settings.py

DEFAULT_ADMIN_PASSWORD

[email protected]

Use this username and password combination to log into the site as an administrator. Change the

DEFAULT_ADMIN_PASSWORD

Running the site

The Makefile has several tasks that demonstrate the commands that may be run. Typically a series of

make

Initialize and run a new

recipes

make recipes serve

Initialize and run a demo version of the recipes app:

make recipes demo

Initialize and run an new

forum

make forum serve

Valid tasks

• forum

  ,

  recipes

  : selects the app to run. It must be the first task in the list.

• demo

  : runs a demonstration version

• init

  : initializes the database schema

• serve

  : runs the app on the default port (

  localhost:8080

  )

• save

  : saves the current database content as a JSON fixture file

• load

  : loads the last database save file from a JSON fixture

• reset

  : resets the database (deletes all database content)

• hard_reset

  : runs

  reset

  then deletes all files in the media/spool folder

Testing

To run all tests type:

make test

To test the

recipes

make recipes test

To test the

forum

make forum test

Documentation

Additional documentation for:

• Documentation for the

  recipes

  app
• Documentation for the

  forum

  app