Accompanying code for Cook et al 2020 The connectome of the Caenorhabditis elegans pharynx
All questions or requests for data should be directed to sjc2153 at columbia dot edu
Multiple versions of MATLAB, 2009a and later are functional
The following python dependcies were used:
Python 2.7
matplotlib 2.0.0
networkx 2.2
numpy 1.16.5
pandas 0.24.2
Figure 2: .cys file is included to reproduce wiring diagrams shown Figure 6: Code provided is modified from Varshney et al 2011 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3033362/ and were also used in Jarrell et al 2012 https://science.sciencemag.org/content/337/6093/437. Figure 7: Code provided is modified from Jarrell et al 2012 https://science.sciencemag.org/content/337/6093/437. Figure 8: aux_1.py is a renamed version of aux.py for compatability with Windows OS. Code for extracting adjacencies from reconstructed TrakEM2 files is available at https://github.com/cabrittin and is related to the preprint https://www.biorxiv.org/content/10.1101/485771v1.abstract. Figure 10: Data and analysis for neurotransmitter and neurotransmitter receptor expression is related to the preprint https://www.biorxiv.org/content/10.1101/676312v1.abstract.