Multiscale Modeling of Wound Healing

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.