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 |