Investigators
Shaul Druckmann
Contact info (email)
shauld@stanford.edu
1. Define context(s)
reveal new biological insights
Current Conformance Level / Target Conformance Level
Partial
Primary goal of the model/tool/database
Neural representations of for instance task-relevant information are often distributed across multiple brain areas. These representations could have independent dynamics, or could influence each other. Our tool uses latent dynamical system models to assess the degree of influence of dynamics in one brain area on another by correlating the sub-single trial fluctuations of brain areas.
Biological domain of the model
Neuroscience
Structure(s) of interest in the model
Neurons, brain areas
Spatial scales included in the model
From single cells to brain areas
Time scales included in the model
from one millisecond to hours
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) | X | Field best practices | 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) | X | Out of sample prediction | Partial | |
| 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 | Our group | Ongoing | Tests on synthetic data | Partial |
| Validation | Our group | Ongoing | Out of sample prediction | Partial |
| Uncertainty quantification | Our group | Ongoing | Testing different model approaches | Partial |
| Sensitivity analysis | Our group | Ongoing | Across animal differences | Partial |
| 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 |
|---|---|---|---|
| Tested extensively on data, but only data from two brain areas | Researchers | In the description of our results and validation | Partial |
5. Version control
| Current Conformance Level / Target Conformance Level |
|---|
| Partial |
| Naming Conventions? | Repository? | Code Review? | |
|---|---|---|---|
| individual modeler | In progress | Yes | Yes, but not professional |
| within the lab | In progress | Yes | Yes, but not professional |
| collaborators | Yes |
6. Documentation
| Current Conformance Level / Target Conformance Level | |
|---|---|
| Code commented? | Partial |
| Scope and intended use described? | Partial |
| User’s guide? | Insufficient |
| Developer’s guide? | Insufficient |
7. Dissemination
| Current Conformance Level / Target Conformance Level |
|---|
| Insufficient. Work still in progress. |
| Target Audience(s): | “Inner circle” | Scientific community | Public |
|---|---|---|---|
| Simulations | |||
| Models | |||
| Software | |||
| Results | |||
| Implications of results |
8. Independent reviews
| Current Conformance Level / Target Conformance Level |
|---|
| Insufficient. Work still in progress. |
| 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 |
|---|
| Partial. Work still in progress |
| 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 |
|---|
| Insufficient. |
| Yes or No (briefly summarize) | |
|---|---|
| Are there operating procedures, guidelines, or standards for this type of multiscale modeling? | No |
| How do your modeling efforts conform? |