The prospective resilience of (protein) networks

Python code for calculating the resilience and the prospective resilience in networks. This code accompanies the recent paper:

Resilience and evolvability of protein-protein interaction networks. by Brennan Klein, Ludvig Holmér, Keith M. Smith, Mackenzie M. Johnson, Anshuman Swain, Laura Stolp, Ashley I. Teufel, and April S. Kleppe. (2020).

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<p align="center"> <img src="figs/pngs/resilience_intro.png" alt="Resilience calculation" width="95%"/> </p>

<p align="center">Fig. 1: Schematic of network resilience.</center>

<p align="center"> <img src="figs/pngs/erdos_renyi_p_resilience.png" alt="Resilience of E.R. networks" width="95%"/> </p>

<p align="center">Fig. 2: The effect of network density on resilience.</center>

<p align="center"> <img src="figs/pngs/attachment_mechanisms.png" alt="Attachment mechanisms" width="95%"/> </p>

<p align="center">Fig. 3: Different node attachment mechanisms for prospective resilience.</center>

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Analysis Notebooks

1. 01_Intro_Network_Resilience
2. 02_Protein_Network_Resilience
3. 03_Prospective_Resilience

Installation and Usage

In order to use this code, first clone/download the repository. Please feel free to reach out if you find any bugs, have any questions, or if for some reason the code does not run.

Requirements <a name="requirements"/>

This code is written in Python 3.x and uses the following packages:

• NetworkX
• Scipy
• Numpy
• And for replicating figures, you will need:
  • matplotlib
  • Pandas

The colormaps in the paper are from https://matplotlib.org/cmocean/ and the named colors are from https://medialab.github.io/iwanthue/.

Citation <a name="citation"/>

If you use these methods and this code in your own research, please cite our paper:

Klein, B., Holmér, L., Smith, K., Johnson, M., Swain, A., Stolp, L., Teufel, A., and Kleppe, A. (2020). Resilience and evolvability of protein-protein interaction networks.

Bibtex:

@article{klein2020presilience,
  title = {Resilience and evolvability of protein-protein interaction networks},
  author = {Klein, Brennan and Holmér, Ludvig and Smith, Keith M. and Johnson, Mackenzie M.
            and Swain, Anshuman and Stolp, Laura and Teufel, Ashley I. and Kleppe, April S.},
  journal = {bioRxiv preprint 10.1101/2020.07.02.184325v1},
  year = {2020}
}

See also:

• Zitnik, M., Sosič, R., Feldman, M.W., and Leskovec, J. (2019). Evolution of resilience in protein interactomes across the tree of life. Proceedings of the National Academy of Sciences. 116, 10, 4426–4433. doi: 10.1073/pnas.1818013116.
  • recent work introducing the network resilience measure used here, showing that the resilience of protein-protein interactomes increases across the tree of life.