Investigators
Reinhard Laubenbacher, Borna Mehrad, William Schroeder
Contact info (email)
Reinhard.laubenbacher@medicine.ufl.edu
1. Define context(s)
identify/explore new therapies
reveal new biological insights
Current Conformance Level / Target Conformance Level
Comprehensive
Primary goal of the model/tool/database
Provides a virtual laboratory for an immunologist to explore the early phases of the immune response to respiratory fungal infections and test possible new interventions.
Biological domain of the model
Immunology
Structure(s) of interest in the model
Alveolar structure/Lung tissue
Spatial scales included in the model
Intracellular; cellular; tissue; whole-body
Time scales included in the model
Minutes to 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.) | Yes | Flow cytometry | Extensive | |
| ex vivo (excised tissues) | ||||
| in vivo pre-clinical (lower-level organism or small animal) | Yes | Flow cytometry;staining | Extensive | |
| 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 | Both modelers and experimentalists | Continuously | Extensive | |
| Validation | Borna Mehrad | When data becomes available | Mouse models;histopathology | Extensive |
| Uncertainty quantification | ||||
| Sensitivity analysis | Reinhard Laubenbacher's lab | Continuously | 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 |
|---|---|---|---|
| No adaptive immunity | Everyone | Documentation | Extensive |
| Some innate immune cell types missing | Everyone | Documentation | Extensive |
| Limited to iron mediated mechanisms | Everyone | Documentation | Extensive |
| Simple models for epithelium/endothelium | Everyone | Documentation | Extensive |
5. Version control
| Current Conformance Level / Target Conformance Level |
|---|
| Extensive |
| Naming Conventions? | Repository? | Code Review? | |
|---|---|---|---|
| individual modeler | Diverse | Github | Unit testing/continuous integration |
| within the lab | Diverse | Github | Unit testing/continuous integration |
| collaborators | Diverse | Github | Unit testing/continuous integration |
6. Documentation
| Current Conformance Level / Target Conformance Level | |
|---|---|
| Code commented? | Adequate |
| 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 | nutritionallungimmunity.org;Github;Girder | Publications and presentations | |
| Models | nutritionallungimmunity.org;Github;Girder | Publications and presentations | |
| Software | nutritionallungimmunity.org;Github;Girder | Publications and presentations | |
| Results | |||
| Implications of results |
8. Independent reviews
| Current Conformance Level / Target Conformance Level |
|---|
| Extensive |
| Reviewer(s) name & affiliation: | Filippo Castiglione |
|---|---|
| When was review performed? | Fall 2020 |
| How was review performed and outcomes of the review? | In person site visit with whole project team. Overall satisfaction with |
9. Test competing implementations
| Current Conformance Level / Target Conformance Level |
|---|
| Extensive |
| 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 |
|---|
| Partial |
| 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? | Currently writing ODD Protocol |