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Pathway Reconciliation

This repo contains code for the following paper:

Reconciling Signaling Pathway Databases with Network Topologies. Tobias Rubel, Pramesh Singh, and Anna Ritz. Pacific Symposium on Biocomputing (PSB) 2022. PSB Proceedings Link.

Directory Contents

  • src: source code

  • networks: parsed networks, null model networks, and interactomes.

  • graphlets: orbit, graphlet, and rho values for networks.

  • regression: regression files (ground truth and predictions).

  • out: output visualization and analysis files.

Reproducibility

To reproduce plots in paper, as well as all attendant data, just run bash pipeline.sh. Run these commands first:

git submodule init
git submodule update
cd src/graphlets/ORCA/orca/
g++ -O2 -std=c++11 -o orca.exe orca.cpp

See the README.md file in orca/ for more info.

Developer Notes

Code repo ported from graphlet-tools

Some code related to parsing datasets ported from pathway-connectivity and pathway-parsers.