Investigators
Michael A. Henson, Erik D. Herzog, Yannis Kevrekidis
Contact info (email)
yannisk@jhu.edu
1. Define context(s)
reveal new biological insights
Current Conformance Level / Target Conformance Level
Extensive
Primary goal of the model/tool/database
The goal of this project is to combine modeling, experiment and computation to unravel the effects of environmental conditions on the network topology, synchronization behavior and entrainment properties of the mammalian circadian clock. The project leverages our expertise in experimental determination of functional connectivity across circadian neuron populations, multicellular modeling of the circadian clock with heterogeneous networks of coupled neural oscillators and new computational tools for efficiently simulating large populations of networked heterogeneous cells.
Biological domain of the model
Biological oscillators
Structure(s) of interest in the model
Synchronized oscillators
Spatial scales included in the model
Genes to neural population
Time scales included in the model
Minutes to weeks
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 | No | Replicates | Extensive |
| ex vivo (excised tissues) | ||||
| in vivo pre-clinical (lower-level organism or small animal) | Yes | No | Replicates | Extensive |
| 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.) | Yes | No | Replicates | Extensive |
| ex vivo (excised tissues) | ||||
| in vivo pre-clinical (lower-level organism or small animal) | Yes | No | Replicates | 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 | PhD Student | Weekly | Testing with different scenarios | Extensive |
| Validation | PhD Student | Monthly | Comparison with data | Adequate |
| Uncertainty quantification | ||||
| Sensitivity analysis | PhD Student | Monthly | Sensitivity calculations | Adequate |
| 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 |
|---|---|---|---|
| Limited to VIP and GABA neurotransmission and constant darkness conditions | Users | In papers and code distribution | Partial |
5. Version control
| Current Conformance Level / Target Conformance Level |
|---|
| Adequate |
| Naming Conventions? | Repository? | Code Review? | |
|---|---|---|---|
| individual modeler | Yes | No | Yes |
| within the lab | Yes | No | Yes |
| collaborators | No | No | Yes |
6. Documentation
| Current Conformance Level / Target Conformance Level | |
|---|---|
| Code commented? | Yes |
| Scope and intended use described? | Yes |
| User’s guide? | No |
| Developer’s guide? | No |
7. Dissemination
| Current Conformance Level / Target Conformance Level |
|---|
| Partial |
| Target Audience(s): | “Inner circle” | Scientific community | Public |
|---|---|---|---|
| Simulations | Private Box folder | Papers | None |
| Models | Private Box folder | Papers now, Biomodels soon | None |
| Software | Private Box folder | Papers | None |
| Results | Private Box folder | Papers | None |
| Implications of results | Skype meetings | Papers | None |
8. Independent reviews
| Current Conformance Level / Target Conformance Level |
|---|
| Adequate |
| Reviewer(s) name & affiliation: | Stephanie Taylor, Colby College |
|---|---|
| When was review performed? | Summers, 2018 and 2019 |
| How was review performed and outcomes of the review? | Verbal feedback leading to code changes |
9. Test competing implementations
| Current Conformance Level / Target Conformance Level |
|---|
| Insufficient |
| Yes or No (briefly summarize) | |
|---|---|
| Were competing implementations tested? | No |
| 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? | None generally accepted |
| How do your modeling efforts conform? | We use MATLAB |