Sample models
Author: Andrea Vandin

Sample models that showcase the main features of ERODE.

Models
Speeding up stochastic and deterministic simulation by aggregation
Authors: Mirco Tribastone and Andrea Vandin

Accompanying files for the invited tutorial presented at the 21st Winter Simulation Conference (WSC'18).

Models Paper
A large-scale assessment of exact model reduction in the BioModels repository
Authors: Isabel Cristina Perez-Verona, Mirco Tribastone and Andrea Vandin

SBML and ERODE files of the models from the BioModels repository presented in the jouranl TCS extension of the paper originally presented at the 17th International Conference on Computational Methods in Systems Biology (CMSB'19).

Models of TCS extension Paper
Exact maximal reduction of stochastic reaction networks by species lumping
Authors: Luca Cardelli, Isabel Cristina Perez-Verona, Mirco Tribastone, Max Tschaikowski, Andrea Vandin, Tabea Waizmann

ERODE files of the models from BioNetGen and from the BioModels repository that have been used in the draft under review.

Models
Lumpability for Uncertain Continuous-Time Markov Chains
Authors: Luca Cardelli, Radu Grosu, Kim G. Larsen, Mirco Tribastone, Max Tschaikowski, Andrea Vandin

ERODE files of the models from PRISM/MRMC that have been used in the draft under review.

Models
A large-scale assessment of exact lumping of quantitative models in the BioModels repository
Authors: Isabel Cristina Perez-Verona, Mirco Tribastone and Andrea Vandin

SBML and ERODE files of the models from the BioModels repository that have been used in the paper submitted to the journal Theoretical Computer Science.

Models Paper

How to use the models
  1. Download the ERODE app for your platform
  2. Download and unzip the required collection of models, each being an ERODE project
  3. In ERODE, right click the Project Explorer, and select Import. Choose Existing Projects into Workspace and click Next
  4. Click Browse... and locate the Examples folder. Tick Copy projects into workspace and hit Finish
  5. Now you can use the loaded ERODE project containing the required models. Typically, you just have to
    1. Open the model of interest (double-click on the .ode file in the Project Explorer),
    2. Execute the commands present in the file by clicking on the ERODE-logo button in the menu bar