Investigators
William Lytton, Salvador Dura-Bernal, Ben Suter, Gordon MG Shepherd, Cecilia Romaro, Fernando Araujo Najman, Antonio Carlos Roque
Contact info (email)
wwlytton@yahoo.com
1. Define context(s)
reveal new biological insights
Current Conformance Level / Target Conformance Level
extensive
Primary goal of the model/tool/database
Reveal sources of cortical dynamics in M1.
Serve as a template for development of cortical models in other areas.
Public resource for cortical simulations.
Note: Assessment needs further updating (please review after May 10, 2020)
Biological domain of the model
Neuroscience
Structure(s) of interest in the model
mouse motor neocortex
Spatial scales included in the model
molecular (ion channels) to "Column" (1e4-1e6 cells)
Time scales included in the model
ms to min
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.) | y | |||
| 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.) | y | |||
| ex vivo (excised tissues) | ||||
| in vivo pre-clinical (lower-level organism or small animal) | ||||
| in vivo pre-clinical (large animal) | y | |||
| 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 | good | |||
| Validation | good | |||
| Uncertainty quantification | good | |||
| Sensitivity analysis | good | |||
| 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 |
|---|---|---|---|
| single compartment models for many cell types | |||
5. Version control
| Current Conformance Level / Target Conformance Level |
|---|
| git github |
| Naming Conventions? | Repository? | Code Review? | |
|---|---|---|---|
| individual modeler | yes | ||
| within the lab | yes | ||
| collaborators | pending |
6. Documentation
| Current Conformance Level / Target Conformance Level | |
|---|---|
| Code commented? | excellent |
| Scope and intended use described? | excellent |
| User’s guide? | excellent |
| Developer’s guide? | excellent |
7. Dissemination
| Current Conformance Level / Target Conformance Level |
|---|
| excellent |
| Target Audience(s): | “Inner circle” | Scientific community | Public |
|---|---|---|---|
| Simulations | y | ||
| Models | y | ||
| Software | y | ||
| Results | y | ||
| Implications of results | y |
8. Independent reviews
| Current Conformance Level / Target Conformance Level |
|---|
| excellent |
| Reviewer(s) name & affiliation: | course students |
|---|---|
| When was review performed? | January 2020 |
| How was review performed and outcomes of the review? | useable |
9. Test competing implementations
| Current Conformance Level / Target Conformance Level |
|---|
| comparable simulation run in NEST |
| Yes or No (briefly summarize) | |
|---|---|
| Were competing implementations tested? | yes |
| Did this lead to model refinement or improvement? | no |
10. Conform to standards
| Current Conformance Level / Target Conformance Level |
|---|
| ModelDB submission standards pending |
| Yes or No (briefly summarize) | |
|---|---|
| Are there operating procedures, guidelines, or standards for this type of multiscale modeling? | y |
| How do your modeling efforts conform? | excellent |
11. (optional) Additional information to support items 1-10
Note: Assessment needs further updating (please review after May 10, 2020)