JWS Online collaborates with journals to promote the use and availability of scientific models. Authors submitting manuscripts to journals that contain models suitable to be added to the JWS database are invited to send a model description to us for conversion to an online format, full instructions for the submission of models are also available. During the reviewing stage of the manuscript. the models will be accessible only to the referees of the manuscript via a protected web interface. After the manuscript is accepted, models will be included in our database and be publicly available. With this collaboration we hope to make the reviewing of manuscripts that contain mathematical models more rigorous by:
The main web site is very easy to use, and experts and non-experts alike will be able to run and test the models. The advantage to the authors is that their model is publicly available and will not get lost in the literature.
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.
Models should be submitted in SBML (preferred) or text format (see below) 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 Jacky Snoep.
SBML models can be created directly on JWS Online, but existing SBML models created with other systems may also be submitted. Please submit models by email regardless of whether they were created on JWS Online or elsewhere.
To enable the translation of the model into an JWS Online format, a model description should ideally be defined in the following categories:
A sample model that illustrates and expands on the above can be viewed below:
S-->X2-->X3-->P
begin name
linear3
end name
begin reactions
v[1] {1}$s = {1}x2
v[2] {1}x2 = {1}x3
v[3] {1}x3 = {1}$p
end reactions
Note that the reactions have a label, e.g. v[1], which is also used to indicate which rate equation is associated with this reaction. Within curly brackets the stoichiometry of the reaction is given. This number is not necessarily an integer but can also be a rational. The dollar sign before s and p, e.g. $s indicates that these metabolites are clamped at their initial values. Thus these metabolites are parameters of the system, their values do not change during the simulation.
begin rate equations
v[1] = Vm1/K1s (s - x2[t]/Keq1) / (1 + s/K1s + x2[t]/K1x2)
v[2] = Vm2/K2x2 (x2[t] - x3[t]/Keq2) / (1 + x2[t]/K2x2 + x3[t]/K2x3)
v[3] = Vm3/K3x3 (x3[t] - p/Keq3) / (1 + x3[t]/K3x3 + p/K3p)
end rate equations
The description of the rate equation, this equation can have any form, it should have a label and make a clear distinction between parameters and variables. All variables are indicated to be functions of the independent variable time by the [t] addition, e.g. x2[t]. Note that s and p are parameters.
begin parameters
Vm1 = 1 (mM/s)
K1s = 1 (mM)
K1x2 = 1 (mM)
Keq1 = 1
Vm2 = 1 (mM/s)
K2x2 = 1 (mM)
K2x3 = 1 (mM)
Keq2 = 1
Vm3 = 1 (mM/s)
K3x3 = 1 (mM)
K3p = 1 (mM)
Keq3 = 1
s = 1 (mM)
p = 0 (mM)
end parameters
begin initial conditions
x2[0] = 0 (mM)
x3[0] = 0 (mM)
end initial conditions
Please contact Jacky Snoep if you need more information.