Model: vanAsselt consumer phase model for transfer of Campylobacter during preparation of ready-to-eat chicken salad_V2

[schuelet]

Model Information

Model Name

vanAsselt consumer phase model for transfer of Campylobacter during preparation of ready-to-eat chicken salad_V2

References

To the model! Execute uncurated model!

Model Uploaded By admin41

Curation Pipeline

Model Status

• [x] in review (publication pending)
• [ ] ready for publication
• [ ] model has been uploaded and published in Zenodo KJ

Basic Quality Control

• By Chair of Curationboard: @Racem-br

General Check

• [x] Online Sanitation Check: validate

MIRARAM Check

• [x] Model Name
• [x] Model ID
• [x] Model Creator (different from author!)
• [x] Creation Date
• [x] License
• [x] Model Execution Metadata (script-language/tool/web-service API)
• [x] Reference Description (URI)
• [x] Scope (any)
• [x] Parameter Metadata (Input/Output)

Code Of Conduct

• [x] In case of re-implementations or re-use of digital objects without changes in the business logic of the model, the person who created the FSKX file is only listed as “Creator”. In cases where the business logic of the existing digital object was significantly modified or the Creator developed the business logic of the model himself the creator can be listed as Author as well.
• [x] The FSKX file Creator confirmed that in case of re-implementations or re-use of digital model objects the main author of the original work was contacted and did not express objections, unless the permissions given by the license of that digital model object already provides such clearance.
• [x] An “Author” of an FSKX model is the person who created the majority of the model code or, in cases where the model code was published in an online repository, the person who is listed there as primary contact person. Other persons who contributed to the model code would be referenced as an additional “Author” in the FSKX file. In those cases where Authors contributed to the FSKX file generation (e.g. by doing quality control), they would also be listed as one of the “Creators”.

Final Step

• [x] Curator assigned to this ticket

Advanced Quality Control

By Curator

• Technical Curation by: @schuelet
• Scientific Curation by: [name]

Technical Curation

• [x] Model does not contain malicious code
• [x] Model metadata validates against FSKX schema
• [x] Model can be executed with KNIME FSK-Lab
• [x] All provided simulation scenarios can be executed
• [x] Model can be executed on RAKIP Model Repository

Scientific Curation

• [ ] Default simulation results are in line with reference publication
• [ ] User defined simulation settings result in reasonable results
• [x] #516

Report

Changes Made

Changes made to the model in preparation for publication (Zenodo KJ)

Additional notes

Observations or remarks about the model or its curation

[OctavioMV]

It might not be relevant but Study identifier is mandatory (i.e. *). However, the model shows no one (Data Background/study/study identifier). Zenodo link provided (10.5281/zenodo.6645830) does not work.

[Racem-br]

from Octavio: I think there are values that differ significantly with the fskx (https://onlinelibrary.wiley.com/doi/10.1111/j.1539-6924.2010.01481.x) sigmacret I think it should be 1.2 instead of 0.2 and iterations should be 20000 instead of 10000. A minimal change is the value of std portion which should be 127 instead of 127. I haven't been able to run it locally. The error appears below.

I was unable to run the original code. I got the following error:"Visualization script failed WARN FSK Runner 0:24 There is no image created WARN FSK Runner 0:24 C:\Users\mesa\AppData\Local\Temp\1\FskxRunner-16692014226889967541.svg (Das System kann die angegebene Datei nicht finden) ERROR FSK Runner 0:24 Execute failed: Invalid result. Execution failed. Reason: Incorrect implementation; the execute method in "RunnerNodeModel" returned null or an incorrect number of output tables. "

On the other hand, I have runned it on the server. If no parameter is changed, the model works but the results are not consistent with the publication. that is, mean dose should be 64 instead of 1 (https://onlinelibrary.wiley.com/doi/10.1111/j.1539-6924.2010.01481.x). Further, the model generates a a plot of cumulative probability against logdose cfu. This plot is not in line with paper results.It might be because of the differences on the parameters. I have also verified that when modifying any parameter minimally, it stops working on the server. That is, I have changed the iterations from 10000 to 10001 or from 10000 to 9999 and it stops working. I believe that this model evaluates the risk of getting sick based on a dose of campylobacter consumed. Therefore, the name should perhaps be changed. The author of the risk quantification model is M. Nauta and B. Christensen instead of VanAsselt. Although the data and transfer modeling come from VanAsselt.

[Racem-br]

increasing/decreasing runs number seems to be working in the online executor. Library/ R subversion missing.