Investigators
Thomas E. Yankeelov
Contact info (email)
thomas.yankeelov@utexas.edu
1. Define context(s)
reveal new biological insights
Current Conformance Level / Target Conformance Level
adequate
Primary goal of the model/tool/database
We have previously developed a novel image processing and computational modeling methods to characterize tumor-associated vessels to assist in the diagnosis of suspicious breast lesions. In this contribution, we provide a novel framework based on a dynamic digital phantom and virtual MRI simulation to systematically evaluate these image processing methods, and furthermore, rigorously determine an optimal acquisition-reconstruction protocol that balances acquisition demands with clinical reality.
Biological domain of the model
Kidney
Structure(s) of interest in the model
vasculature
Spatial scales included in the model
millimeter
Time scales included in the model
second
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 | Extensive | ||
| in vivo pre-clinical (lower-level organism or small animal) | ||||
| 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: ________________________ | No | User-specific simulation | adequate |
3. Validate within context(s)
| Who does it? | When does it happen? | How is it done? | Current Conformance Level / Target Conformance Level | |
|---|---|---|---|---|
| Verification | ||||
| Validation | ||||
| Uncertainty quantification | End user | After simulation | Monte-Carlo | adequate |
| 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 |
|---|---|---|---|
| User must be well-skilled in MRI acquisition. | User | In Methods sections of publications | adequate |
5. Version control
| Current Conformance Level / Target Conformance Level |
|---|
| insufficient (project still in progress) |
| Naming Conventions? | Repository? | Code Review? | |
|---|---|---|---|
| individual modeler | |||
| within the lab | |||
| collaborators |
6. Documentation
| Current Conformance Level / Target Conformance Level | |
|---|---|
| Code commented? | Partial (project still in progress) |
| Scope and intended use described? | Partial (project still in progress) |
| User’s guide? | Insufficient (project still in progress) |
| Developer’s guide? | Insufficient (project still in progress) |
7. Dissemination
| Current Conformance Level / Target Conformance Level |
|---|
| Adequate |
| Target Audience(s): | “Inner circle” | Scientific community | Public |
|---|---|---|---|
| Simulations | Publications | N/A | |
| Models | Publications | N/A | |
| Software | N/A | N/A | |
| Results | Publications | N/A | |
| Implications of results | Publications | N/A |
8. Independent reviews
| Current Conformance Level / Target Conformance Level |
|---|
| Insufficient; project still in progress and has not been submitted for peer review yet |
| 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 |
|---|
| Insufficient; it is not clear that there are competing implementations |
| 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 |
|---|
| adequate |
| 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? | N/A |