ERODE Benchmarks

This page provides the accompanying material of the following publication:

Quick Links

Download and Installation

ERODE can be installed following the instructions given here, while ERODE’s main page provides a manual and a collection of sample models.

Benchmarks

For reproducibility, we provide an ERODE project containing all models and experiments described in the draft.

To use it:

  1. Decompress the archive
  2. Right click on ERODE’s Project Explorer, and select Import. Choose Existing Projects into Workspace and click Next.
  3. Click Browse… and locate the Examples folder. Tick Copy projects into workspace and hit Finish.

In order to obtain reasonable file sizes:

  1. For each configuration, we provide only one out of the five randomly generated models from the draft;
  2. We provide the models in the compact .net format (described below). These are “imported on-the-fly” by the provided ERODE files.

Run the experiments

The project contains a folder per table in the draft, each containing the corresponding models and an ERODE file (.ode) to actually run the experiments.

In order to run an experiment just open the .ode file of interest, and click on the ERODE icon in the toolbar (top-left of ERODE’s GUI).

 


Notes on .net file format

Files in .net format are generated from a BNGL file using the well-established tool BioNetGen version 2.2.5-stable. The format is very compact, but not human readable. The following is a commented encoding of the running example used in our draft.

#Optional list of parameters. 
#Each parameter is given in a line of this form:
 # id
 # name
 # value
#For example, the first parameter has id 1, name "r1", and value 1.0
begin parameters
 1 r1 1.0
 2 r2 2.0
 3 r3 3.0
 4 r4 4.0
end parameters

#List of species. 
#Each species is given in a line of this form
 # species id
 # name
 # initialConcentration
#For example, the first species has id 1, name "Au", and initial concentration 1.0
begin species
 1 Au 1.0
 2 Ap 2.0
 3 B 3.0
 4 AuB 0.0
 5 ApB 0.0
end species

#List of reactions. 
#Each reaction is given in a line of this form
 # reaction id
 # comma separated list of reagents
 # comma separated list of products
 # rate
#For example, 
 # the first reaction is specified within ERODE as Au -> Ap , r1
 # the last reaction is specified within ERODE as ApB -> Ap + B , r3 
begin reactions
 1 1 2 r1
 2 2 1 r2
 3 1,3 4 r3
 4 4 1,3 r4
 5 2,3 5 r3
 6 5 2,3 r4 
end reactions