Investigators
Rajanikanth Vadigepalli and Jan Hoek
Contact info (email)
rajanikanth.vadigepalli@jefferson.edu
1. Define context(s)
reveal new biological insights
Current Conformance Level / Target Conformance Level
Adequate
Primary goal of the model/tool/database
Modeling the molecular and cellular interaction network controlling regeneration response to liver injury. The present model of liver regeneration was designed to combine disparate data sets from multiple liver cell types towards an integrative, quantitative accounting of the overall liver regeneration process. Recent results from single cell gene and protein regulation studies are starting to uncover the previously under-appreciated fact that individual cells within a population exhibit high variability in the expression of mRNA and proteins (i.e., molecular variability). By combining cellular network modeling, and high-throughput gene expression measurements in single cells, we seek to reconcile the high molecular variability in single cells with the relatively low variability in tissue-scale gene and protein expression and the highly coordinated functional responses of tissues to physiological challenges.
Biological domain of the model
liver regeneration
Structure(s) of interest in the model
liver; hepatocytes; hepatic stellate cells; liver resident macrophages; liver sinusoidal cells
Spatial scales included in the model
molecular scale; cellular scale; liver lobule (tissue) scale;
Time scales included in the model
seconds; minutes; hours; 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 | Journal peer review | Adequate | |
| ex vivo (excised tissues) | Yes | Journal peer review | Adequate | |
| in vivo pre-clinical (lower-level organism or small animal) | Yes | Journal peer review | Adequate | |
| in vivo pre-clinical (large animal) | No | No | ||
| Human subjects/clinical | No | N0 | ||
| 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 | Journal peer review | Adequate | |
| in vivo pre-clinical (large animal) | No | No | ||
| Human subjects/clinical | No | No | ||
| Other: ________________________ |
3. Validate within context(s)
| Who does it? | When does it happen? | How is it done? | Current Conformance Level / Target Conformance Level | |
|---|---|---|---|---|
| Verification | Lab peers | Prior to manuscript submission | Independent cross-check starting with the manuscript | Adequate |
| Validation | Lab peers | Prior to manuscript submission | Independent cross-check starting with the manuscript | Adequate |
| Uncertainty quantification | Model developer | During modeling process | Established techniques | Adequate |
| Sensitivity analysis | Model developer | During modeling process | Established techniques | 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 |
|---|---|---|---|
| Model limited to resection injury response | Liver disease researchers | Description in the publications | Adequate |
5. Version control
| Current Conformance Level / Target Conformance Level |
|---|
| Inadequate |
| Naming Conventions? | Repository? | Code Review? | |
|---|---|---|---|
| individual modeler | Yes | No | Independent peer cross-check |
| within the lab | Yes | No | Independent peer cross-check |
| collaborators | Yes | No | No |
6. Documentation
| Current Conformance Level / Target Conformance Level | |
|---|---|
| Code commented? | Adequate |
| Scope and intended use described? | Adequate |
| User’s guide? | Indequate |
| Developer’s guide? | Inadequate |
7. Dissemination
| Current Conformance Level / Target Conformance Level |
|---|
| Adequate |
| Target Audience(s): | “Inner circle” | Scientific community | Public |
|---|---|---|---|
| Simulations | Shared folders; Lab presentations | Supplemental information in manuscripts | Manuscripts |
| Models | Shared folders; Lab presentations | Supplemental information in manuscripts | Manuscripts |
| Software | Shared folders; Lab presentations | NA | NA |
| Results | Shared folders; Lab presentations | Manuscripts | Manuscripts |
| Implications of results | Shared folders; Lab presentations | Manuscripts | Manuscripts; Institutional Newsletters |
8. Independent reviews
| Current Conformance Level / Target Conformance Level |
|---|
| Adequate |
| Reviewer(s) name & affiliation: | Lab peers |
|---|---|
| When was review performed? | Prior to manuscript submission |
| How was review performed and outcomes of the review? | Independent review was performed starting with the description in the manuscript to develop new code according to the equations, parameter values, and contextual information provided in the manuscript. |
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 |
|---|
| 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? | Yes |