Investigators
Jason Haugh
Contact info (email)
jason_haugh@ncsu.edu
1. Define context(s)
reveal new biological insights
Current Conformance Level / Target Conformance Level
Comprehensive/Comprehensive
Primary goal of the model/tool/database
The primary goal of these models is to explain and predict how signal transduction pathways and regulation of the F-actin cytoskeleton are polarized in cells responding to chemo- and hapto-tactic gradients, which evolve dynamically and thus program the collective movements of cells during wound healing.
Biological domain of the model
Mammalian cell, wounded tissue (skin)
Structure(s) of interest in the model
Cell scale: plasma membrane, cytosol; Tissue scale: dermis, wound clot
Spatial scales included in the model
1e-7 - 1e-2 m
Time scales included in the model
1 - 1e6 s
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.) | X | Peer reviewed literature | Comprehensive/Comprehensive | |
| ex vivo (excised tissues) | ||||
| in vivo pre-clinical (lower-level organism or small animal) | X | Peer reviewed literature | Comprehensive | |
| 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) | ||||
| 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 | In house. | Prior to publication of the model. | By varying the discretization of the model equations. | Extensive/Extensive |
| Validation | In house. | Either prior to or after publication of the model. | By performing experiments designed to test model predictions. | Insufficient/Comprehensive |
| Uncertainty quantification | ||||
| Sensitivity analysis | In house. | Prior to publication of the model. | By systematic variation of model parameters. | Extensive/Extensive |
| 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 |
|---|---|---|---|
| The model is not comprehensive with respect to the mechanisms and cell types considered. | Biologists and clinicians seeking to understand wound healing. | By addressing the limitations in publications. | Comprehensive/Comprehensive |
5. Version control
| Current Conformance Level / Target Conformance Level |
|---|
| Adequate/Extensive |
| Naming Conventions? | Repository? | Code Review? | |
|---|---|---|---|
| individual modeler | X | X | X |
| within the lab | X | ||
| collaborators | X |
6. Documentation
| Current Conformance Level / Target Conformance Level | |
|---|---|
| Code commented? | Extensive/Extensive |
| Scope and intended use described? | Extensive/Extensive |
| User’s guide? | N/A |
| Developer’s guide? | N/A |
7. Dissemination
| Current Conformance Level / Target Conformance Level |
|---|
| Extensive/Extensive |
| Target Audience(s): | “Inner circle” | Scientific community | Public |
|---|---|---|---|
| Simulations | https://www.imagwiki.nibib.nih.gov/resources/models-tools-databases/polarization-plcpkc-pathway-chemotactic-gradient-sensing | https://www.imagwiki.nibib.nih.gov/resources/models-tools-databases/polarization-plcpkc-pathway-chemotactic-gradient-sensing | |
| Models | https://www.imagwiki.nibib.nih.gov/resources/models-tools-databases/polarization-plcpkc-pathway-chemotactic-gradient-sensing | https://www.imagwiki.nibib.nih.gov/resources/models-tools-databases/polarization-plcpkc-pathway-chemotactic-gradient-sensing | |
| Software | |||
| Results | https://www.imagwiki.nibib.nih.gov/resources/models-tools-databases/polarization-plcpkc-pathway-chemotactic-gradient-sensing | https://www.imagwiki.nibib.nih.gov/resources/models-tools-databases/polarization-plcpkc-pathway-chemotactic-gradient-sensing | |
| Implications of results | https://www.imagwiki.nibib.nih.gov/resources/models-tools-databases/polarization-plcpkc-pathway-chemotactic-gradient-sensing | https://www.imagwiki.nibib.nih.gov/resources/models-tools-databases/polarization-plcpkc-pathway-chemotactic-gradient-sensing |
8. Independent reviews
| Current Conformance Level / Target Conformance Level |
|---|
| N/A |
| 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 |
|---|
| N/A |
| 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 |
|---|
| Extensive/Extensive |
| Yes or No (briefly summarize) | |
|---|---|
| Are there operating procedures, guidelines, or standards for this type of multiscale modeling? | Yes |
| How do your modeling efforts conform? | There are standards for verifying numerical accuracy as noted above. |