Microconnectomics of motor cortex: a multiscale computer model

Investigators
Salvador Dura-Bernal, Samuel Neymotin, Ben Suter, Craig Kelley, Joseph Graham, Donald Doherty, Gordon MG Shepherd, William Lytton
Contact info (email)
bill.lytton@downstate.edu; salvador.bernal@downstate.edu
1. Define context(s)
identify/explore new therapies
reveal new biological insights
Current Conformance Level / Target Conformance Level
Extensive
Primary goal of the model/tool/database

- Reveal cellular and circuit mechanisms of dynamics in M1. The model reproduced in vivo experimental data, and provided insights into oscillatory dynamics, molecule-to-behavior links, neuronal avalanches, information flow, and other neural coding mechanisms.

- Serve as a template for development of cortical circuit models in other areas.

- Public resource for cortical simulations.

 

Biological domain of the model
Neuroscience
Structure(s) of interest in the model
Mouse primary motor cortex (M1)
Spatial scales included in the model
Molecular, subcellular, cellular, circuit (um to cm)
Time scales included in the model
Milliseconds to minutes
Other uses for the model (optional)

- Extension to lower reaction diffusion scale and higher multi-columnar scales.

 

2. Data for building and validating the model
Data for building the model Published? Private? How is credibility checked? Current Conformance Level / Target Conformance Level
in vitro (primary cells cell, lines, etc.) Yes Yes Extensive
ex vivo (excised tissues)
in vivo pre-clinical (lower-level organism or small animal)
in vivo pre-clinical (large animal)
Human subjects/clinical
Other: ________________________
Data for validating the model Published? Private? How is credibility checked? Current Conformance Level / Target Conformance Level
in vitro (primary cells cell, lines, etc.)
ex vivo (excised tissues)
in vivo pre-clinical (lower-level organism or small animal) Yes Yes Extensive
in vivo pre-clinical (large animal)
Human subjects/clinical
Other: ________________________
3. Validate within context(s)
Who does it? When does it happen? How is it done? Current Conformance Level / Target Conformance Level
Verification Modelers using NetPyNE tool During model development Extensive
Validation Modelers using NetPyNE tool After first model version completed; and after any updates Extensive
Uncertainty quantification
Sensitivity analysis Modelers using NetPyNE tool After model version completed Adequate
Other:__________
Additional Comments
4. Limitations
Disclaimer statement (explain key limitations) Who needs to know about this disclaimer? How is this disclaimer shared with that audience? Current Conformance Level / Target Conformance Level
Homogeneity of cells within cell class
Only 2-6 compartments for many cell models
Long-range inputs simulated as spike generators with fixed rates
5. Version control
Current Conformance Level / Target Conformance Level
Extensive
Naming Conventions? Repository? Code Review?
individual modeler Yes Github Yes
within the lab Yes Github Yes
collaborators
6. Documentation
Current Conformance Level / Target Conformance Level
Code commented? Adequate
Scope and intended use described? Adequate - in README files and associated publications
User’s guide? Adequate - extensive for modeling tool used (NetPyNE)
Developer’s guide? Adequate - extensive for modeling tool used (NetPyNE)
7. Dissemination
Current Conformance Level / Target Conformance Level
Extensive
Target Audience(s): “Inner circle” Scientific community Public
Simulations https://doi.org/10.1101/201707
Models https://doi.org/10.1101/201707
Software DOI: 10.7554/eLife.44494
Results https://doi.org/10.1101/201707
Implications of results https://doi.org/10.1101/201707
8. Independent reviews
Current Conformance Level / Target Conformance Level
Adequate
Reviewer(s) name & affiliation: Padraig Gleeson
When was review performed? 2018-2019
How was review performed and outcomes of the review? Conversion to NeuroML format and upload to OSB
9. Test competing implementations
Current Conformance Level / Target Conformance Level
Adequate
Yes or No (briefly summarize)
Were competing implementations tested? Implementation in NeuroML and similar version inNEST
Did this lead to model refinement or improvement? Yes
10. Conform to standards
Current Conformance Level / Target Conformance Level
Extensive
Yes or No (briefly summarize)
Are there operating procedures, guidelines, or standards for this type of multiscale modeling? Yes - NeuroML, SONATA, ModelDB
How do your modeling efforts conform? Conforms to all standards listed above