Changes to model names

A new year is approaching and with it also changes are coming to openCARP. Besides the

  • New naming scheme for the ionic models (Non backwards-compatible change planned for February 2022. Read below for information on how to update your experiments.)

this news post also covers

  • Further new features including tracing and sharing of experiments
  • Review of September 2021 user meeting
  • List of modeling resources

We want to further push the concept of standardization and reproducibility of in silico experiments. Thus, we would like to announce a new naming scheme for the ionic models, which will be named according to the publication's first author(s). If the author has published more than one ionic model, the year of the publication follows. For example: Land12.model and Land17.model. Use “bench --list-imps” to get a list of all available models. Plugin names are prefixed with their function, for example: INa_Bondarenko. A mapping from the old to the new names can be found in the README file of the models directory. The model files include extended metadata at the top now with a reference to the publication describing the model as well as comments describing potential adaptations to the initially published model. Use for example “bench --imp=Courtemanche --imp-info” to access the metadata and all variable names from the command line.

Additionally, we also want to improve consistency of variable names and updated the names of the variables in all ionic models according to the items below: Ion channel conductance: GIonnameGKr, GNa, GCaL, Gto Ionic currents: INameIKr, INa, ICaL, Ito

All of the provided examples, the carputils framework and the documentation were also adjusted according to the new naming scheme. Don't hesitate to ask any question in our Q&A system or report bugs in the GitLab project.

While we understand that this backwards-incompatible change will cause some effort for current users (.par files and scripts need to be adjusted to reflect the changed model and parameter names), we are convinced that this change will improve usability and will make it significantly easier for new users to get started with openCARP.

The change will become effective in a release version in February 2022. Until then, you can already check out the IMP_Variable_Renaming branches of openCARP, carputils and the experiments to adjust your simulation setups:

Further new features All features and improvements that were included in the latest openCARP releases can always be found in the CHANGELOG. One of the highlights is the trace feature that allows outputting arbitrary variables at selected nodes, which was requested by multiple users during the user meeting in September. Another highlight is the new bundle feature that allows easy sharing of experiments between openCARP users and even publishing your experiment on the RADAR4KIT repository with a DOI. Learn how to use it here.

User meeting Speaking of the user meeting, we want to thank all trainers and of course the enthusiastic crowd of more than 30 beginners and advanced openCARP users gathering in Karlsruhe. The advanced users worked on new carputils examples and we are looking forward to seeing them in one of the next releases! The recordings of selected sessions (meshalyzer, sharing experiments) are online.

List of modeling resources Another idea coming from the user meeting is this list of modeling resources including meshes, mesh generation tools and model augmentation tools. Check it out and of course send further items if you have something you want to share with the community.

Did you hear of the recent publication describing openCARP? Please cite this work for all studies that are based on a tool from the openCARP ecosystem

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