What is visbio?

But, for now, 

it's all about the 

maps.

Why I am doing this?

Human metabolism:

Is this better?

KEGG

Specialized figures are the most informative:

Lehninger, Principles of Biochemistry, 4th Ed.

And some nice tools exist

to build them:

Omix

SimPheny is one

of the best!

• Load SimPheny maps 
  
• Apply any dataset
• Build features on the fly
• Share in any browser, including mobile browsers
• Run from Python and IPython notebooks (& NBViewer)

How does import work?

Demo time!

• v0.3.0    
  
  
• Metabolic maps in Python, IPython, & web
  
  
  

1. Web-based metabolic map
   
   
2. Knockout + FBA
   
   
3. IPython notebook
   
   
4. Bonus: Interactive scatter plots

McCloskey, D. et al. Biotechnology and Bioengineering. 1–31 (2013).

Coming Soon! 

• v0.4.0 
  
  
• View and edit maps
  
  
• Direct import from BIGG database
  
  
  

1. Web-based map viewer & builder
   

Let's share the maps

What do you think?

Getting started

a) Download

b) Install Python package

> python setup.py install 

In Python and IPython, you can:

import visbio
map = visbio.Map()
map.create_standalone_html()
map.view_browser()

More instructions at  github.com/zakandrewking/visbio

c) Run local server

The only dependencies are Python, tornado, and cobrapy.

 > python server/tornado_main.pyserving directory /Users/zaking/www/visbio-public on port 7777

What's next: