Welcome to ASCENT’s documentation!
Please check out the associated publication in PLOS Computational Biology!
Cite both the paper and the DOI for the release of the repository used for your work. We encourage you to clone the most recent commit of the repository.
- Cite the paper:
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
- Cite the code (use the DOI for the version of code used):
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, DOI: 10.5281/zenodo.5500260
- Cite the code (use the DOI for the version of code used):
ASCENT is an open source platform for simulating peripheral nerve stimulation. To download the software, visit the ASCENT GitHub repository.
Contents:
- Metadata required to model an in vivo experiment using the ASCENT pipeline
- Installation
- ASCENT data hierarchy
- Your first run
- Helper Scripts
- Command-Line Arguments
- 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