Access species concentration at an earlier time point?

[jsl...@iu.edu]

Is it possible to access a species concentration (or amount) at an earlier time point and use that information in a function? For example, get a species' concentration 10 minute prior to the current time. In the equation below, G(t-tau) could be species G at tau time units before the current time.

Thanks

Jim

[Pedro Mendes]

Hi Jim,

currently that is not possible in COPASI. The issue is not only access of a value in the past, but the actual equations are what is known as Delay Differential Equations, which require specific integration algorithms that we do not have presently. There have been plans to add them to COPASI, but so far we don't yet have a working version.

Sorry about that...
Pedro

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Pedro Mendes, PhD
Boehringer Ingelheim Professor in Cell Sciences
Director, Richard D. Berlin Center for Cell Analysis and Modeling
University of Connecticut School of Medicine
research group website: http://www.comp-sys-bio.org

[Sluka, James Patrick]

Thanks for the info Pedro.

 

As a work around, is it possible to access a particular time point in an external file loaded from the Parameter Estimation Task?

 

James P. Sluka, PhD
Biocomplexity Institute

Intelligent Systems Engineering

Luddy School of Informatics, Computing and Engineering

Indiana University

Bloomington, IN   USA

Cell: 317-331-7465

 

From: 'Pedro Mendes' via COPASI User Forum <copasi-u...@googlegroups.com>
Sent: Monday, June 29, 2026 1:27 PM
To: copasi-u...@googlegroups.com
Subject: Re: [copasi-user-forum] Access species concentration at an earlier time point?

 

Hi Jim,

currently that is not possible in COPASI. The issue is not only access of a value in the past, but the actual equations are what is known as Delay Differential Equations, which require specific integration algorithms that we do not have presently. There have been plans to add them to COPASI, but so far we don't yet have a working version.

Sorry about that...
Pedro

On 6/29/26 11:53, 'jsl...@iu.edu' via COPASI User Forum wrote:

Is it possible to access a species concentration (or amount) at an earlier time point and use that information in a function? For example, get a species' concentration 10 minute prior to the current time. In the equation below, G(t-tau) could be species G at tau time units before the current time.

 

 

Thanks

 

Jim

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--
Pedro Mendes, PhD
Boehringer Ingelheim Professor in Cell Sciences
Director, Richard D. Berlin Center for Cell Analysis and Modeling
University of Connecticut School of Medicine
research group website: http://www.comp-sys-bio.org

 

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[Pedro Mendes]

Jim,

if you can do with just some specific time points, then I suggest you set events at those times and store values in global quantities. That is something COPASI can do easily. It may get slow if you have too many of those time points (or tedious to define), but that should work without problems. The only issue is having a continuous variable that is some value earlier in time. For static variables of a concentration (or anything else) at specific time points that COPASI can do easily.  This approach works in any situation, not just parameter estimation.

Pedro

To view this discussion visit https://groups.google.com/d/msgid/copasi-user-forum/LV3PR08MB90463D061A6861AEAD69DDCEB6E82%40LV3PR08MB9046.namprd08.prod.outlook.com.

[Sluka, James Patrick]

That’s an interesting idea. Thanks for the help.

 

Jim

To view this discussion visit https://groups.google.com/d/msgid/copasi-user-forum/07ff879f-78fa-433d-afb1-c99db01957a5%40uchc.edu.