Investigators
Salvador Dura-Bernal
Contact info (email)
salvador.bernal@downstate.edu
1. Define context(s)
reveal new biological insights
other
Current Conformance Level / Target Conformance Level
adequate
Primary goal of the model/tool/database
Development, simulation, parallelization, analysis, and optimization of multiscale biological neuronal networks
Biological domain of the model
Neuroscience
Structure(s) of interest in the model
Nervous systems
Spatial scales included in the model
Molecular, subcellular, cellular, microcircuit, network, brain region
Time scales included in the model
Microseconds to minutes
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.) | ||||
| 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 the 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.) | ||||
| 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 the user of the 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 | constantly | testing | adequate |
| 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 |
|---|---|---|---|
| As with any simulation, the output is only as good as the input | Everyone | adequate | |
5. Version control
| Current Conformance Level / Target Conformance Level |
|---|
| adequate |
| Naming Conventions? | Repository? | Code Review? | |
|---|---|---|---|
| individual modeler | yes | GitHub | yes |
| within the lab | yes | GitHub | yes |
| collaborators | yes | GitHub | yes |
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 | https://doi.org/10.7554/eLife.44494 | ||
| Results | |||
| Implications of results |
8. Independent reviews
| Current Conformance Level / Target Conformance Level |
|---|
| insufficient |
| Reviewer(s) name & affiliation: | |
|---|---|
| When was review performed? | |
| How was review performed and outcomes of the review? |
9. Test competing implementations
| Current Conformance Level / Target Conformance Level |
|---|
| adequate |
| Yes or No (briefly summarize) | |
|---|---|
| Were competing implementations tested? | Yes, regular comparisons of output from pure NEURON are compared with results from NetPyNE |
| Did this lead to model refinement or improvement? | Yes, any differences have been and will continue to be eliminated |
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? | Yes, including NeuroML and SONATA |
| How do your modeling efforts conform? | They conform to these standards and can import/export to them |