Variables

[Hossam ElQersh]

Hello there ,

I am new in modeling and simulation so my question might be silly . i want to know  wond how does copasi deal with dimensionless variables and range values ?

[Mendes,Pedro]

Hello Hossam,

COPASI is fine with dimensionless variables; you can either just ignore the units that are shown, or you can set all units to "1".

As for "range values" , these are not supported. (I assume you mean intervals with this term). COPASI does not do interval arithmetic.

Pedro

On 5/7/21 10:01 PM, Hossam ElQersh wrote:

Hello there ,

I am new in modeling and simulation so my question might be silly . i want to know  wond how does copasi deal with dimensionless variables and range values ?

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[Hossam ElQersh]

Hello Sir,

This might be out off-topic but I want to know how to deal with this as an inexperienced student who just started modeling Is there a way to use a value as a range with copasi(because i don't know another way to do this )
Thank you.

Pedro Mendes

[Mendes,Pedro]

I am not sure I understand your question. Are you asking if you can use a range like 2-4  for a variable or for a parameter?

A variable is what you have to calculate by simulation, a parameter is a value that you set in the model. An example of variable is the concentration of a chemical species along time. An example of a parameter is a rate constant (which is fixed throughout the simulation)

Parameter ranges can be used in two main contexts:
1- parameter scans: where you want to change the value of a parameter within that range and see the effect on variables by simulation; essentially the software runs a series of simulations where in each one the parameter of interest takes values within the range specified

2- in parameter estimation: you specfiy the range of values that the parameter is allowed to take (by giving a minimum and maximum)

I'm not sure this addresses your question, if not you will have to be more specific.

Pedro

To view this discussion on the web visit https://groups.google.com/d/msgid/copasi-user-forum/d7fae17b-e687-49fd-9332-22ab6e84299fn%40googlegroups.com.

[Hossam ElQersh]

Hi sir,
Thanks for the reply this was really helpful I want to ask something related to modeling and simulation and I don't know if I can reply the question here or make a new conversation
or somewhere else.
Let's say I have variable C that changes according to this differential equation.

now I don't know how to apply this equation to COPASI. 

should I use it in species and make the simulation type ODE  or as a reaction? (I know it seems silly but I am struggling with this any help would really save a life )

Thank you 

Hossam

[Frank Bergmann]

Hello  Hossam, 

in general, you can write ODE's for compartments, species or global quantities. For general ODE's that don;t fit the scheme, where species (which reside in compartments) and partake in reactions / processes, I would suggest to write the ODE on a global quantity. And for clarification if the simulation type of a species is reaction, that means it will be produced or consumed, as given by the stoichiometry and speed of the reaction it partakes in. In that case you would not be able to enter an ODE at all. 

That being said, your equation does require to differentiate with respect to space as well as time. This is not the kind of equation supported by COPASI. 

best

Frank