Investigators
William W Lytton, Srdjan D. Antic, Joseph Graham
Contact info (email)
bill.lytton@downstate.edu
1. Define context(s)
identify/explore new therapies
Current Conformance Level / Target Conformance Level
adequate
Primary goal of the model/tool/database
-Develop models of neural networks based on available experimental data and morphologies to test activity patterns of Layer 5 pyramidal cells
Biological domain of the model
Neuroscience
Structure(s) of interest in the model
Mammalian neocortex, pyramidal neurons
Spatial scales included in the model
Molecular, cellular, subcellular, microcircuit
Time scales included in the model
1ms to 10sec
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 | adequate | ||
| ex vivo (excised tissues) | ||||
| in vivo pre-clinical (lower-level organism or small animal) | ||||
| in vivo pre-clinical (large animal) | ||||
| Human subjects/clinical | ||||
| Other: ________________________ | by user of the software | adequate |
| Data for validating the model | Published? | Private? | How is credibility checked? | Current Conformance Level / Target Conformance Level |
|---|---|---|---|---|
| in vitro (primary cells cell, lines, etc.) | yes | adequate | ||
| ex vivo (excised tissues) | ||||
| in vivo pre-clinical (lower-level organism or small animal) | ||||
| in vivo pre-clinical (large animal) | ||||
| Human subjects/clinical | ||||
| Other: ________________________ | by user of software | adequate |
3. Validate within context(s)
| Who does it? | When does it happen? | How is it done? | Current Conformance Level / Target Conformance Level | |
|---|---|---|---|---|
| Verification | users and developers | |||
| Validation | ||||
| Uncertainty quantification | ||||
| Sensitivity analysis | ||||
| 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 |
|---|---|---|---|
| This is a special purpose model, focusing on phenomenology of dendritic plateaus in the context of basilar and oblique dendrites. | Everyone | adequate | |
5. Version control
| Current Conformance Level / Target Conformance Level |
|---|
| adequate |
| Naming Conventions? | Repository? | Code Review? | |
|---|---|---|---|
| individual modeler | GitHub | ||
| within the lab | GitHub | ||
| collaborators |
6. Documentation
| Current Conformance Level / Target Conformance Level | |
|---|---|
| Code commented? | partial |
| Scope and intended use described? | adequate |
| User’s guide? | partial |
| Developer’s guide? | partial |
7. Dissemination
| Current Conformance Level / Target Conformance Level |
|---|
| adequate |
| Target Audience(s): | “Inner circle” | Scientific community | Public |
|---|---|---|---|
| Simulations | |||
| Models | |||
| Software | |||
| Results | doi.org/10.1101/828582. | ||
| Implications of results |
8. Independent reviews
| Current Conformance Level / Target Conformance Level |
|---|
| partial |
| Reviewer(s) name & affiliation: | Student review |
|---|---|
| When was review performed? | |
| How was review performed and outcomes of the review? |
9. Test competing implementations
| Current Conformance Level / Target Conformance Level |
|---|
| inadequate |
| Yes or No (briefly summarize) | |
|---|---|
| Were competing implementations tested? | |
| Did this lead to model refinement or improvement? |
10. Conform to standards
| Current Conformance Level / Target Conformance Level |
|---|
| adequate |
| Yes or No (briefly summarize) | |
|---|---|
| Are there operating procedures, guidelines, or standards for this type of multiscale modeling? | |
| How do your modeling efforts conform? |