Instructions for Submission of Models to the JWS Online database

Submission information

The JWS Online system primarily focuses on systems of enzyme catalysed reactions, where we use ordinary differential equations (ODEs) to describe and model the system.

In principle a set of ODEs, parameter values and initial conditions is enough to completely describe any such system. However, since we are also interested in performing Metabolic Control Analysis on the models, the model description should also indicate the individual steps and the stoichiometry with respect to substrates and products. If such a description is not possible, we will also consider including models only consisting of ODE's (and parameter values, and initial conditions) on an individual basis, unfortunately these might take longer to convert to an online format.

In principle, we can translate into online form any complete model description, including models that are discontinuous in time (for example cell cycle models) or that in addition to ODEs also include algebraic functions. These models might take a bit longer to incorporate and often will involve a personal communication between us and the model author.

Submission procedure

Models are please to be submitted in an ascii (text) format by email to Jacky Snoep, standard compression (eg. zip, gz) formats may also be used. Any questions regarding the submission and formatting of model input files may also be addressed to .

Model description format

To enable the translation of the model into an JWS Online format, a model description should ideally be defined in the following categories:

  1. Model name
  2. Reaction stoichiometry containing the substrates on the left hand and products on the right hand of an equal sign (=)
  3. Rate equations
  4. Parameter values for all model parameters
  5. Initial conditions for all variables

A sample model that illustrates and expands on the above can be viewed here.