isoformQuantify can be used to compute relative abundances of different transcripts belonging to the same gene and visualize the result.

1. install Django (https://www.djangoproject.com/download/)

2. install scipy (http://www.scipy.org/SciPy)

3. install samtools (http://sourceforge.net/projects/samtools/files/samtools/0.1.18/)

4. clone the project repository to the location where you want to put

   git clone https://github.com/jaxcs/charlie.git

5. change line 20, 28, 29 in /isoformQuantifyApp/getIsoformAbund.py to appropriate directories in your server

6. copy data files in the /isoformQuantifyApp/data/ directory to the same directory in the server (right now, data files have been ignored by git repo commit)

7. use command like python manage.py runserver 0.0.0.0:8080 to kick off web service in the root folder that contains manage.py

• isoformQuantify: configuration files for Django (Please refer to https://docs.djangoproject.com/en/1.4/)
• isoformQuantifyApp: actual project code locates

• *.py: Python scripts that implement algorithm and do scientific computation
• /static/: contains javascripts for visualization, css styling files
• /templates/: index.html (our homepage)

• "views.py": respond to web request (which function responds to which request is determined by /isoformQuantify/urls.py)
• "models.py": stores Python objects used in algorithm
• "getIsoformAbund.py": calculate relative abundances of transcripts (main script that implements the algorithm)
• "test.py": auto generated file by Django (demonstrates how to write a test)