ASCENT
v1.1.0

Contents:

  • Metadata required to model an in vivo experiment using the ASCENT pipeline
  • Installation
  • ASCENT data hierarchy
  • Your first run
  • Helper Scripts
  • Template for methods reporting
  • Enums
  • JSON configuration files
  • JSON file parameter guide
  • Python utility classes
  • Submitting NEURON jobs
  • Morphology Files
  • Python MockSample class for creating binary masks of nerve morphology
  • Python classes for representing nerve morphology (Sample)
  • Creating sample specific nerve morphologies in COMSOL
  • Micro Leads cuff measurements
  • Library of part primitives for electrode contacts and cuffs
  • Creating custom preset cuffs from instances of part primitives
  • Creating new part primitives
  • Cuff placement on nerve
  • Fiberset
  • Implementation of NEURON fiber models
  • Simulation Protocols
  • ModelWrapper Class
  • Making geometries in COMSOL (Part class)
  • Control of medium surrounding nerve and cuff electrode
  • Java utility classes
  • Defining and assigning materials in COMSOL
  • Definition of perineurium
  • Data interchange between COMSOL and NEURON
  • Python simulation class
  • NEURON launch.hoc
  • NEURON Wrapper.hoc
  • Data analysis tools
  • Convergence analysis example
  • Sim4Life validation
  • Comparison of MRG fit to Bucksot 2019
  • ASCENT Troubleshooting Guide
  • Paper References
ASCENT
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© Copyright 2021, Duke University. Revision bc1f3332.

Musselman ED, Cariello JE, Grill WM, Pelot NA. ASCENT (Automated Simulations to Characterize Electrical Nerve Thresholds): A Pipeline for Sample-Specific Computational Modeling of Electrical Stimulation of Peripheral Nerves. PLoS Comput Biol [Internet]. 2021; Available from: https://doi.org/10.1371/journal.pcbi.1009285

ASCENT software available from: https://github.com/wmglab-duke/ascent