Replication in Brain 2 of C. elegans models

Replication of two computational models of locomotion of Caenorhabditis elegans in Brian 2.

Code generated for the thesis ‘Brain-Inspired Computing’

Experiments from Izquierdo et al. (2018)

E. O. Olivares, E. J. Izquierdo and R. D. Beer, ‘Potential role of a ventral nerve cord central pattern generator in forward and backward locomotion in Caenorhabditis elegans’, Network Neuroscience, vol. 2, no. 3, pp. 323-343, 2018. DOI: 10.1162/netn_a_00036.

1-neuron experiments

• Files:
  • AVA_neuron.py
  • AVA_rectangles.py
  • RMD_neuron.py
  • RMD_rectangles.py
• Import:
  • aux_functions.py

3-neuron circuit

• File: Izq_3_neurons.py
• Imports: aux_functions.py

Evolutionary optimization

• File:
  • Izq_CPG_gen_alg.py
• Imports:
  • Izq_CPG_fitness_func.py
  • Izq_model.py
  • aux_functions.py
  • genetic_functions.py

Experiments from Kunert et al. (2014)

J. Kunert, E. Shlizerman and J. N. Kutz, ‘Low-dimensional functionality of complex network dynamics: Neurosensory integration in the Caenorhabditis elegans connectome’, Phys. Rev. E, vol. 89, p. 052805, 5 May 2014. DOI: 10.1103/PhysRevE.89.052805.

5-neuron circuit

• File:
  • Kunert_5neurons_Iconst
• Imports:
  • aux_function.py
  • Wicks_model.py

Whole connectome experiments

• File:
  • Kunert_top5
• Imports:
  • aux_function.py
  • Brian2_experiment.py
  • Wicks_model.py
  • /connectome_data

Bifurcation

• File: Kunert_bifurcation.py

Singular-value decomposition

• File: Kunert_SVD.py

Ablations

• File: Kunert_ablation.py