Analysis of Flow Networks
This repository provides a series of Python scripts to extract relevant data from flow networks generated by code from a related repository and some R scripts for their analysis and plotting.
Please follow the relevant documentation for the installation of external packages.
This package can be installed like any other Python package but if you only use the
extract_data.py script, it doesn't have to be.
sudo python setup.py install
If you don't want to make a system-wide installation, you can simply add the location of the package to the path variable.
import sys sys.path.append("/home/you/location/rfn-analysis") import rfn_analysis as ra
With the class definitions imported, you can unpickle the networks.
import networkx as nx net = nx.read_gpickle("standard/node_robust/sim1025_final.pkl")
- extraction and storage of network characteristics in HDF5 files pytables
- reading HDF5 files in R with rhdf5
|||Kaluza, P., Ipsen, M., Vingron, M. & Mikhailov, A. S. Design and statistical properties of robust functional networks: A model study of biological signal transduction. Physical Review E 75, 15101 (2007).|
|||Kaluza, P. & Mikhailov, A. S. Evolutionary design of functional networks robust against noise. Europhysics Letters 79, 48001 (2007).|
|||Kaluza, P., Vingron, M. & Mikhailov, A. S. Self-correcting networks: function, robustness, and motif distributions in biological signal processing. Chaos 18, 026113 (2008).|