Our COMBINE Archive!!!

[ahodelin]

Hello,

hier is our COMBINE archive in testversion: id: 2e2f8798-aec7-40a1-b49b-62b3ec80fac2 Here the link again: https://cat.bio.informatik.uni-rostock.de/rest/share/6b507398-c103-4b92-9c90-d6b105ff1372

I need some info:

• What model(s) did you use in your group? SBML and Extra Files
  • bachmann.xml - JWS Online
  • BIOMD0000000347_url.xml - BioModels (Bachmann2011_JAK2-STAT5_FeedbackControl)
  • Bachmann2011.xml - BioModels (Bachmann2011 - Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range)
• Files for the experiment folder
  • please upload these files in Google Drive here experiment
• Files for the result folder
  • please upload these files in Google Drive here result

Name convention for files in eperiment/result: nameOfSBMLFromSource_yyyymmdd.some_extension

• yyyy = four digits for year. Example, 2021
• mm = two digits for month. Example, 06
• dd = two digits for day. Example, 08, 31

Some examples

• From JWS Online: bachmann_20210620.png
• From BioModels (Bachmann2011 - Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range): Bachmann2011_20210620.etc

Thanks

[jessvasseur]

initial SED-ML files and results were added to github yesterday - do we still need to upload them on GoogleDrive?

SED-ML files were generated using https://github.com/ahodelin/Bachmann_Archive/blob/main/model/Bachmann2011.xml. If this file is renamed we need to update the SED-ML files and the underlying tellurium scripts...

[jessvasseur]

do we really need the naming convention? I think our experiment and results files are clearly named.. maybe to discuss later today.

[ahodelin]

That is because wi have three different models in our repository and we need to know which were used for the experiments and results.

[jessvasseur]

all experiments and results were created using this model - the one chosen by Group 2. The SED-ML files contain a link to this model and I have included a txt file in each results folder with a short description regarding which model, which SED-ML file, which tool was used.

In my opinion all other model files could be deleted or put in a subfolder (other models) to avoid any confusion

[ahodelin]

Ok, thanks for the info

[jessvasseur]

the link to the COMBINE archive above is not working for me - any idea why?

[ahodelin]

Sorry, the COMBINE Web is not too intuitive, and I have posted the link without to share, here the shared link:

https://cat.bio.informatik.uni-rostock.de/rest/share/6b507398-c103-4b92-9c90-d6b105ff1372

There is a link with the name ::ba, this is our archive.

[fphans]

would recommend pushing all "unused" model files to a subfolder from "models". baybe itbecomes more clear on what code we simulate and what parts are only mentioned for integrity

[fphans]

respective conventions: there is a DCMI terminology in the sbml file (e.g. dcterms:W3CDTF describing the set of dates and times constructed according to the W3C Date and Time Formats Specification.) some details are already in the wiki

[jessvasseur]

@ahodelin could you update the COMBINE archive with the added / modified files for experiments and results? thank you :)