Investigators
Charles Horn, PhD; Doug Weber, PhD; Matthew Schiefer, PhD; Murat Akcakaya, PhD; Ervin Sejdic, PhD
Contact info (email)
chorn@pitt.edu
1. Define context(s)
aid in clinical decision making
aid in clinical trial design
identify/explore new therapies
reveal new biological insights
Current Conformance Level / Target Conformance Level
Extensive
Primary goal of the model/tool/database
The goal of our model is to predict vagus nerve stimulation parameters which predict gastric emptying, and ultimately could be used to optimize treatment of obesity. The model is intended to be extensible to both male and female.
Biological domain of the model
Gastrointestinal tract
Structure(s) of interest in the model
Stomach
Spatial scales included in the model
1 mm to 0.5 m
Time scales included in the model
up to four hours
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) | yes & no | yes & no | SPARC curation team | partial |
| in vivo pre-clinical (large animal) | yes & no | yes & no | SPARC curation team | partial |
| 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) | does not currently exist | insufficient | ||
| 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 | planned | insufficient | |
| Validation | developers | planned | insufficient | |
| Uncertainty quantification | developers | planned | insufficient | |
| Sensitivity analysis | developers | planned | insufficient | |
| 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 will be primarily developed with preclinical data | Clinicians/translational scientists | Limitations will be provided with each model run and stated in the accompanying documentation. | insufficient |
| The model will focus on gastric emptying and early stage effects on weight control | Clinicians/translational scientists | Limitations will be provided with each model run and stated in the accompanying documentation. | insufficient |
5. Version control
| Current Conformance Level / Target Conformance Level |
|---|
| insufficient |
| Naming Conventions? | Repository? | Code Review? | |
|---|---|---|---|
| individual modeler | planned | planned (Github) | planned |
| within the lab | planned | planned | planned |
| collaborators | planned | planned | planned |
6. Documentation
| Current Conformance Level / Target Conformance Level | |
|---|---|
| Code commented? | insufficient (Python, PEP 8, and Matlab, Style Guidelines 2.0, planned) |
| Scope and intended use described? | insufficient (external documentation; https://readthedocs.org/, planned) |
| User’s guide? | insufficient (planned) |
| Developer’s guide? | insufficient (planned) |
7. Dissemination
| Current Conformance Level / Target Conformance Level |
|---|
| insufficient |
| Target Audience(s): | “Inner circle” | Scientific community | Public |
|---|---|---|---|
| Simulations | DOI (planned) | ||
| Models | DOI (planned) | ||
| Software | |||
| Results | |||
| Implications of results |
8. Independent reviews
| Current Conformance Level / Target Conformance Level |
|---|
| Insufficient |
| Reviewer(s) name & affiliation: | planned |
|---|---|
| When was review performed? | NA |
| How was review performed and outcomes of the review? | NA |
9. Test competing implementations
| Current Conformance Level / Target Conformance Level |
|---|
| insufficient |
| Yes or No (briefly summarize) | |
|---|---|
| Were competing implementations tested? | NA |
| Did this lead to model refinement or improvement? | NA |
10. Conform to standards
| Current Conformance Level / Target Conformance Level |
|---|
| insufficient |
| 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? | NA |