Investigators
Adrian Buganza Tepole
Contact info (email)
abuganza@purdue.edu
1. Define context(s)
aid in clinical trial design
reveal new biological insights
Current Conformance Level / Target Conformance Level
Adequate
Primary goal of the model/tool/database
The goal of the model is to predict skin growth in response to stretch during tissue expansion. Tissue expansion is a widely known clinical procedure to grow skin in situ for large reconstructive procedures. The most common application of tissue expansion is for breast reconstruction after mastectomy. However, even though the technique is widely used and its unique applicability for resurfacing large skin lesions is recognized, in practice it leads to complications such as unnecessary expansion, undesired shape of the grown flap, tissue damage. To fix these problems, we propose a computational model backed by a porcine animal model of tissue expansion. An initial model has been developed and continues to be improved. Some data is available and we continue to collect more data to validate the model.
Biological domain of the model
Skin mechanobiology
Structure(s) of interest in the model
Skin layers
Spatial scales included in the model
Tissue scale
Time scales included in the model
Days
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) | Yes | Partial | ||
| in vivo pre-clinical (lower-level organism or small animal) | ||||
| in vivo pre-clinical (large animal) | Yes | Adequate | ||
| 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) | Yes | Partial | ||
| in vivo pre-clinical (lower-level organism or small animal) | ||||
| in vivo pre-clinical (large animal) | Yes | Adequate | ||
| 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 | Developers | Comparison against highly detailed models, mesh convergence, comparison against homogenized solution, comparison against published models | Partial | |
| Validation | ||||
| 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 |
|---|---|---|---|
| Available data is from animal studies but still not comprehensive. No human data available yet. | Users. | In the discussion of published papers limitations are clearly outlined. | Adequate |
5. Version control
| Current Conformance Level / Target Conformance Level |
|---|
| Partial |
| Naming Conventions? | Repository? | Code Review? | |
|---|---|---|---|
| individual modeler | none | Yes, Bitbucket repositories available through the PI Website, cited in the paper, and link also on the IMAG wiki | See verification above. |
| within the lab | none | Same as above | Same as above |
| collaborators |
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 | Publications | ||
| Models | Publications, Bitbucket repository | ||
| Software | Bitbucket repository | ||
| Results | Publications, Bitbucket repository | ||
| Implications of results | Publications |
8. Independent reviews
| Current Conformance Level / Target Conformance Level |
|---|
| Partial |
| Reviewer(s) name & affiliation: | Reviews have been through the peer-review process for journal paper publication, no independent software review has been performed |
|---|---|
| When was review performed? | When the paper was submitted for publication. Code is available with the paper. |
| How was review performed and outcomes of the review? | Paper was accepted and reviewers didn't raise concerns about the code |
9. Test competing implementations
| Current Conformance Level / Target Conformance Level |
|---|
| Insufficient |
| Yes or No (briefly summarize) | |
|---|---|
| Were competing implementations tested? | No. We verified the code as explained above, but we did not implement more than one solution, there was a single implementation of the code. |
| Did this lead to model refinement or improvement? | Model has been refined and improve based on the verification process, comparing against literature data, previous results of similar computational models, analytical or homogenized solutions, mesh convergence studies. |
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? | Yes, models of growth and remodel through the finite volume growth theory are well-established, at least a basic implementation. Our code and model follow this two decade history of model development and build upon it. |
| How do your modeling efforts conform? | Publications clearly outline the previous modeling efforts of growth and remodeling and state how our model resembles the literature and what are the differences |