Investigators
C Darquenne, RA Corley, AP Kuprat, B Asgharian, O Price
Contact info (email)
cdarquenne@ucsd.edu
1. Define context(s)
aid in clinical trial design
other
Current Conformance Level / Target Conformance Level
Extensive
Primary goal of the model/tool/database
The primary goal of the model is to predict the deposition of inhaled aerosols in the respiratory system of humans and rats including those with chronic obstructive pulmonary diseases (COPD) that will improve assessments of risks for potentially susceptible individuals exposed to airborne aerosols of physical, chemical or biological origin as well as therapeutic interventions via respiratory drug delivery.
Biological domain of the model
lung
Structure(s) of interest in the model
respiratory tract including upper airway, conducting airways and alveolar region
Spatial scales included in the model
µm to cm
Time scales included in the model
msec to minutes
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) | ||||
| in vivo pre-clinical (lower-level organism or small animal) | y | y | cross-checked with other results | extensive |
| in vivo pre-clinical (large animal) | ||||
| Human subjects/clinical | y | y | cross-checked with other results | adequate |
| 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) | y | y | cross-checked with other results | adequate |
| in vivo pre-clinical (large animal) | ||||
| Human subjects/clinical | y | y | cross-checked with other results | adequate |
| Other: ________________________ |
3. Validate within context(s)
| Who does it? | When does it happen? | How is it done? | Current Conformance Level / Target Conformance Level | |
|---|---|---|---|---|
| Verification | students/postdocs and investigators | Throughout | By checking for 1) adequacy of equations used to simulate process, 2) mesh independency, 3) convergence of solution, 4) mass and flow balance, 5) fluid and particle properties | extensive |
| Validation | students/postdocs and investigators and third party | students/postdocs and investigators | Comparison with existing experimental database | adequate |
| Uncertainty quantification | students/postdocs and investigators | as different components of the models are validated | comparison against experimental data | adequate |
| Sensitivity analysis | students/postdocs and investigators | as different components of the models are validated | comparison against experimental data | 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 |
|---|---|---|---|
| Subject-specificity of anatomical models is limited by resolution of imaging datasets used to develop the models | relevant scientific community who intends to use/build/extend the mode | through dissemination in papers, abstracts, and public lectures | adequate |
5. Version control
| Current Conformance Level / Target Conformance Level |
|---|
| adequate |
| Naming Conventions? | Repository? | Code Review? | |
|---|---|---|---|
| individual modeler | yes | yes | peers |
| within the lab | yes | yes | project team |
| collaborators | yes | yes | through ZoomMeeting conference calls |
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 |
|---|
| partial |
| Target Audience(s): | “Inner circle” | Scientific community | Public |
|---|---|---|---|
| Simulations | Are shared directly within the project team, across institutions. | in progress as model/code are still under development | |
| Models | Are shared directly within the project team, across institutions. | in progress as model/code are still under development | |
| Software | Are shared directly within the project team, across institutions. | in progress as model/code are still under development | |
| Results | Are shared directly within the project team, across institutions. | in progress as model/code are still under development | |
| Implications of results | in progress as model/code are still under development |
8. Independent reviews
| Current Conformance Level / Target Conformance Level |
|---|
| partial |
| Reviewer(s) name & affiliation: | A/prof Mullins and Dr. Mead-Hunter, Curtin University, Perth, Australia |
|---|---|
| When was review performed? | first review planned for Year 3 of project |
| How was review performed and outcomes of the review? | Not yet available |
9. Test competing implementations
| Current Conformance Level / Target Conformance Level |
|---|
| partial |
| Yes or No (briefly summarize) | |
|---|---|
| Were competing implementations tested? | yes |
| Did this lead to model refinement or improvement? | yes |
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 |
| How do your modeling efforts conform? | Good |