visbio

Metabolic maps for the masses


Zak King, Ali Ebrahim, Niko Sonnenschein
Winter retreat
Dec. 19, 2013

What is visbio?



A collection of web visualizations for systems biology.


Heat maps,
interactive scatter plots,
dendrograms, ...

But, for now, 

it's all about the 

maps.

Why I am doing this?


Visualizing metabolism is hard

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!


But what about data integration?
Customized figures for publication?
Sharing?



  • 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)

maps + any feature you can think of

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

  • We have 828 maps from SimPheny
  • We could curate and share the collection online
  • Community development = free features


What do you think?




Getting started


a) Download


  1. Go to github.com/zakandrewking/visbio/releases 

  2. Download source code


Or,
> git clone git@github.com:zakandrewking/visbio.git

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
More instructions at github.com/zakandrewking/visbio

What's next:


  • Gathering interest
    • Senior design group:  Visualizing isotope-tracing
      • With Dr. Metallo's group
    • Alex:  Interactive dendrogram + heatmap
    • Jon:  Web-based reconstruction tool

  • Make a plan for release v 1.0.0

  • Suggestions?

  • If you're excited,  fork & pull !

visbio: Metabolic maps for the masses

By zakandrewking

visbio: Metabolic maps for the masses

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