BioStar codebase is a Python and Django based Q&A web software modeled after the StackOverflow Q&A engine.

Our primary goal is to create a simple, generic, flexible and extendeable Q&A framework.

The software requires only Python (2.6 or higher) to run. All other libraries are included in the distribution. The code will run with no changes on any operating system that supports Python.

The test version of this site can be seen at: http://test.biostars.org

Unpack the source code archive. If you don't have django installed then switch to the libs directory and unpack the django.zip archive (included for convenience):

$ cd libs
$ unzip django.zip
$ # switch back to the source directory
$ cd ..

From the command line execute:

$ biostar.sh init populate run

Visit the http://localhost:8080 to view your site. Enjoy!

Note The Windows version of the biostar.sh manager has not yet been written. The site will work just fine on Windows but for now users will need to manually invoke the commands present in the biostar.sh run manager.

There is a main run manager in the root directory:

$ biostar.sh 

Execute it with no parameters for information on usage. This run manager can take one or more commands. For example to initialize the database then populate it with the test data and to run the server one would invoke it in the following way:

$ biostar.sh init 
$ biostar.sh populate
$ biostar.sh run

Alternatively one may run all these commands all at once:

$ biostar.sh init populate run

Note: If database models change you must reset and reinitialize the database:

$ biostar.sh delete init populate

The biostar.sh run manager to pulls in environment variables to allow you to customize locations/test fixtures, etc. Edit the biostar.sh script to override the various settings.

The default server will bind the all IP adapters (0.0.0.0) and port 8080. Visit http://localhost:8080 to see interact with your version of the test server.

Warning: The default settings will create an application with a default admin user and password! Make sure to change the passwords in the django settings file!

To migrate content from a StackExchange 1 XML datadump one needs to import the data via the import/migrate.py script. This script will need to be able to import the django settings module as well. Run this script with the -h flag to see the flags it can take:

$ python import/migrate.py -h

To facilitate the re-import the best practice is to dump the data into a data fixture after an import takes place. A data fixture may be reused via the populate command. Thus to create a new migration one would do the following:

$ biostar delete init import

This may be followed by a run command or deployment. Alternatively one may dump the data for easier reuse:

$ biostar.sh dump $ biostar.sh delete init populate

The ALLOW_MIGRATION setting will enable a single automatic account migration based on the email provided by the OpenID provider. Only the information from a subset of well known OpenID providers are trusted enough to automatically merge accounts. For other users manual migration of accounts will be required.

Users in ADMINS settings will automatically obtain full administration privileges and may log into the admin site using the SECRET_KEY as their password.

All messages are private, only users can see them.

The Python code, templates, static content (css, images, javascript) and default database are found in the main directory. There is partial datadump of the existing BioStar content in the import folder. The populate command will load this data into the current database.

Biostar is built with open source libraries. The following software packages are included with BioStar:

• JQuery for javascript and
• markitup as rich text javascript editor.
• markdown python library to parse the content
• django_openid_auth and python_openid for openid authentication
• pygments for source code highlighting
• django_mptt to provides the hierachical data model to keep track of
• whoosh provides fast full text searching

• Purple: #8F2C47
• Green: #75845C