Network Analysis and Modeling for Python
These modules are currently under development at Sanford-Burnham Medical Research Institute and collaborating groups in support of the investigation of viral/host interactions,
especially flu-omics: www.fluomics.org
and hint: http://hint.org
Prereqesites: Basic operation: scipy/numpy ID mapping: bioservices
Why?
Basically, I've started to develop a small tool targeted to:
- performing efficient analyses on networks and omics data
- take advantage of the many Python packages available and being developed by others
- integrate established network analysis methods
- object oriented & flexible to facilitate inegrating new omics data types as they become available
- create a framework to inspire the development of other applications
Hopefully others in the community will find this useful. This is a work in progress and I'll try to develop it as best as possible as a stable tool as my research progresses. Please contact me if you are interested in contributing.
"NAMpy" seems shameless, albeit apt, it will probably change when I am feeling more creative.
I recommend starting with the example for now, that is stable.
You may notice similarities with the open source COBRApy project: Ebrahim, A., Lerman, J., Palsson, B. O., & Hyduke, D. R. (2013). COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC systems biology, 7(1), 74. doi:10.1186/1752-0509-7-74
Note there is a module included to convert to COBRA models here but isn't fully tested/debugged yet.
Release history
Release Date Notes
a0.0.0 11.21.2013 Working draft!!