Investigators
Z Liu and LK Cheng
Contact info (email)
l.cheng@auckland.ac.nz
1. Define context(s)
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 model will be used to represent and predict stomach anatomy and function in response to external electrical stimuli. The model will anatomically and biophysical based and incorporate cell, tissue and organ level function.
Biological domain of the model
Gastric electrophysiology and motility
Structure(s) of interest in the model
Stomach, Vagas
Spatial scales included in the model
um to cms (ion channels to organ level)
Time scales included in the model
ms to minutes (ion channels to organ level)
Other uses for the model (optional)
The models have the ability to be adapted to other sections of the gastrointestinal tract that have similar function (in particular the small intestine and the colon). In addition, the modelling frameworks utilized are generic so can be updated to model the electrical function in other organs.
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 | Repeated studies | Extensive |
| in vivo pre-clinical (large animal) | Yes | No | Repeated studies | 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) | ||||
| in vivo pre-clinical (lower-level organism or small animal) | Yes | No | Repeated studies | Extensive |
| in vivo pre-clinical (large animal) | Yes | No | Repeated studies | 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 and users | During development cycle | Code review | Adequate |
| Validation | Developers and users | During development cycle | Reproduction of experimental data | Adequate |
| Uncertainty quantification | N/A | |||
| Sensitivity analysis | Developers and users | New model | Parameter sampling | 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 |
|---|---|---|---|
| Inter-species variability | All | Discussed with results | Extensive |
| Inter-subject variability | All | Discussed with results | Extensive |
5. Version control
| Current Conformance Level / Target Conformance Level |
|---|
| Extensive |
| Naming Conventions? | Repository? | Code Review? | |
|---|---|---|---|
| individual modeler | Yes | subversion | Yes |
| within the lab | Yes | subversion | Yes |
| collaborators | Yes | subversion | Yes |
6. Documentation
| Current Conformance Level / Target Conformance Level | |
|---|---|
| Code commented? | Yes, extensive |
| Scope and intended use described? | Yes, extensive |
| User’s guide? | Yes, extensive |
| Developer’s guide? | Yes, extensive |
7. Dissemination
| Current Conformance Level / Target Conformance Level |
|---|
| Adequate |
| Target Audience(s): | “Inner circle” | Scientific community | Public |
|---|---|---|---|
| Simulations | Yes | Yes, when possible | |
| Models | Yes | Yes, when possible | |
| Software | Yes | ||
| Results | Yes | Yes, when possible | |
| Implications of results | Yes | Yes, when possible |
8. Independent reviews
| Current Conformance Level / Target Conformance Level |
|---|
| Insufficient |
| 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 |
|---|
| Adequate |
| 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 |
|---|
| 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? |