Investigators
David Carlson
Contact info (email)
david.carlson@duke.edu
1. Define context(s)
reveal new biological insights
Current Conformance Level / Target Conformance Level
Adequate
Primary goal of the model/tool/database
The primary goal of this tool is to learn electrical connectome networks of activity from multi-region brain recordings. The inferred networks vary in strength over time, are consistent between animals in a mouse model, and are relevant to neuropsychiatric disorders (e.g., in a mouse model of depression).
Biological domain of the model
Neuroscience; modeling of electrophysiological signals
Structure(s) of interest in the model
Multiple brain regions
Spatial scales included in the model
Multiple brain regions
Time scales included in the model
.5s-5s
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) | Yes | Currently; will be released at the conclusion of the grant/study. | The data is scanned by a trained bench scientist, and results are checked with cross-validation. | Adequate |
| 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 | Currently; will be released at the conclusion of the grant/study. | Cross-validation techniques. | Adequate |
| 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 | Results and code are reviewed by computational and bench scientists. | Throughout development | Adequate | |
| Validation | Developers have done validations. | Throughout development | Adequate | |
| 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 |
|---|---|---|---|
| Has only been tested on multi-region local field potential recordings. | Partial | ||
5. Version control
| Current Conformance Level / Target Conformance Level |
|---|
| Partial |
| Naming Conventions? | Repository? | Code Review? | |
|---|---|---|---|
| individual modeler | Yes | Yes | Partial |
| within the lab | No | Yes | |
| collaborators | No | Yes | Partial |
6. Documentation
| Current Conformance Level / Target Conformance Level | |
|---|---|
| Code commented? | Partial |
| Scope and intended use described? | Partial |
| 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 | http://papers.nips.cc/paper/7260-cross-spectral-factor-analysis;https://arxiv.org/abs/2004.05209 | ||
| Software | https://github.com/carlson-lab/encodedSupervision | ||
| Results | https://www.sciencedirect.com/science/article/pii/S0092867418301569 | ||
| Implications of results | https://www.jneurosci.org/content/38/7/1601.abstract |
8. Independent reviews
| Current Conformance Level / Target Conformance Level |
|---|
| Partial |
| 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 |
|---|
| Insufficient |
| 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 |
|---|
| Partial |
| Yes or No (briefly summarize) | |
|---|---|
| Are there operating procedures, guidelines, or standards for this type of multiscale modeling? | No, we are not aware of any for this specific area. We are attempting to follow best practices on documentation and dissemination. |
| How do your modeling efforts conform? |