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artur....@posteo.de, … matteoeo17

Apr 15

Reaction Event Fluxes

Hi, I' m not sure I belong to this conversation any more, given the great time lapse. Anyway I am

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Reaction Event Fluxes

Hi, I' m not sure I belong to this conversation any more, given the great time lapse. Anyway I am

Apr 15

Evangelos Koutsouadis, … juergen6

Apr 15

Exact Simulation Steps in Stochastic Simulation

Hi Dante, Unfortunately, we haven't implemented it yet. I will bring this up in the next COPASI

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Exact Simulation Steps in Stochastic Simulation

Hi Dante, Unfortunately, we haven't implemented it yet. I will bring this up in the next COPASI

Apr 15

Marc Lefranc, Frank Bergmann2

Apr 8

Compute time course until an event is triggered

Hello Marc, You could try the following: - create an additional event assignment for your event, that

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Compute time course until an event is triggered

Hello Marc, You could try the following: - create an additional event assignment for your event, that

Apr 8

Harry Wilson, Pedro Mendes3

Mar 18

Insights on rate constants obtained via parameter estimation

*** Attention: This is an external email. Use caution responding, opening attachments or clicking on

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Insights on rate constants obtained via parameter estimation

*** Attention: This is an external email. Use caution responding, opening attachments or clicking on

Mar 18

sanjana kb, … Matthias König4

Mar 14

How to implement summation term with upper and lower limits in COPASI

Hi Sanjana, I have a similar use case, and I use sbmlutils to create models programmatically in

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How to implement summation term with upper and lower limits in COPASI

Hi Sanjana, I have a similar use case, and I use sbmlutils to create models programmatically in

Mar 14

Harry Wilson, … Pedro Mendes16

Mar 5

Automation of Copasi

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Automation of Copasi

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Mar 5

Stephane Ransac, … Hoops, Stefan (sh9cq)9

Mar 1

multicore processing ?

Hello Pedro, I found a Linux server on which I can run CopasiSE. So I should be able to test the

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multicore processing ?

Hello Pedro, I found a Linux server on which I can run CopasiSE. So I should be able to test the

Mar 1

Feb 27

Looking for COPASI Software experts for contracted work.

Hi Everyone, My company is looking for a COPASI expert to build a model of a multiplex (2 analytes)

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Looking for COPASI Software experts for contracted work.

Hi Everyone, My company is looking for a COPASI expert to build a model of a multiplex (2 analytes)

Feb 27

Feb 14

Attention Modeling Community

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Attention Modeling Community

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Feb 14

Nausheen Fatima

Feb 11

receptor recycling

Hi, I am building a model that involves a reaction of a receptor binding with the ligand and then

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receptor recycling

Hi, I am building a model that involves a reaction of a receptor binding with the ligand and then

Feb 11

Harry Wilson, Frank Bergmann5

Feb 5

Multiple concentration

Dear Frank, That helped me a lot to run the experiment in copasi. Like I said, the initial

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Multiple concentration

Dear Frank, That helped me a lot to run the experiment in copasi. Like I said, the initial

Feb 5

Andrew Weller, … Hoops, Stefan (sh9cq)6

Jan 25

Andrew Weller 06:53 (now) to COPASI User Forum Dear Frank and Stefan With immense thanks to you both.

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Andrew Weller 06:53 (now) to COPASI User Forum Dear Frank and Stefan With immense thanks to you both.

Jan 25

Ahmed Atta, Pedro Mendes2

Jan 22

How to Handle Species with Mixed Units in COPASI and Why It Divides by Compartment Volume

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How to Handle Species with Mixed Units in COPASI and Why It Divides by Compartment Volume

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Jan 22

Jan 10

CCB online workshop - build your computational model with COPASI and VCell – February 24-28, 2025

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CCB online workshop - build your computational model with COPASI and VCell – February 24-28, 2025

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Jan 10

Dante Kienigiel

12/7/24

Record when reactions happen

Hello! 1st time COPASI user here. I'm modeling virus replication right now and my particular

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Record when reactions happen

Hello! 1st time COPASI user here. I'm modeling virus replication right now and my particular

12/7/24

Sebastián, Hoops, Stefan (sh9cq)3

12/4/24

Integration step size used in parameter estimation task

Hello Sebastian, The step size is only used in COPASI to determine the output time points. It does

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Integration step size used in parameter estimation task

Hello Sebastian, The step size is only used in COPASI to determine the output time points. It does

12/4/24

Joshua Kaste, Frank Bergmann2

11/22/24

Defining a reaction as a fraction of another reaction's rate

Hello, what you can do is to create a global parameter with an assignment under "Global Quantity

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Defining a reaction as a fraction of another reaction's rate

Hello, what you can do is to create a global parameter with an assignment under "Global Quantity

11/22/24

manmath panigrahy, … frank.thom...@gmail.com11

11/21/24

LNA task execution in BASICO

Thank you, Professor. With regards, Manmath On Thu, Nov 21, 2024 at 4:11 PM <frank.thomas.bergmann

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LNA task execution in BASICO

Thank you, Professor. With regards, Manmath On Thu, Nov 21, 2024 at 4:11 PM <frank.thomas.bergmann

11/21/24

Sebastián, Pedro Mendes3

10/29/24

Simulating periodic input functions

Hi Pedro, Thanks for sharing this! I have been able to simulate the events as desired. The time

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Simulating periodic input functions

Hi Pedro, Thanks for sharing this! I have been able to simulate the events as desired. The time

10/29/24

Nausheen Fatima, Pedro Mendes3

10/15/24

molecular weight

I was thinking of incorporating the outcomes of different molecular weights for Hyaluronic acid in my

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molecular weight

I was thinking of incorporating the outcomes of different molecular weights for Hyaluronic acid in my

10/15/24

Hikmet Emre Kaya, Pedro Mendes3

10/15/24

An inhibitor acting on multiple enzymes

Dear Prof. Mendes, I appreciate the clarification! Many thanks. Emre On Monday, October 14, 2024 at 3

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An inhibitor acting on multiple enzymes

Dear Prof. Mendes, I appreciate the clarification! Many thanks. Emre On Monday, October 14, 2024 at 3

10/15/24

Severo III Balasbas

10/15/24

Fisher Information Matrix is Singular - Why?

Hello everyone, I am currently using COPASI but whenever I use particle swarm to estimate the

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Fisher Information Matrix is Singular - Why?

Hello everyone, I am currently using COPASI but whenever I use particle swarm to estimate the

10/15/24

Alice De Carli, Frank Bergmann2

8/23/24

Axes limits when plotting Time Courses

We don't have a setting to directly specify the axes limits. To control the x-axis for parameter

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Axes limits when plotting Time Courses

We don't have a setting to directly specify the axes limits. To control the x-axis for parameter

8/23/24

8/2/24

Biophysical Modeling of the Cell at Cell Bio 2024

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Biophysical Modeling of the Cell at Cell Bio 2024

*** Attention: This is an external email. Use caution responding, opening attachments or clicking on

8/2/24

Andrew Glanville, Frank Bergmann9

7/27/24

Merging Kinetic Models

Another question. I'm "assuming" if I poke one of my component models with a species

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Merging Kinetic Models

Another question. I'm "assuming" if I poke one of my component models with a species

7/27/24

Jerry Tanoury, Pedro Mendes4

7/19/24

Constraining a model to obey Principle of Detailed Balance

Thank you Pedro. On Thursday, July 18, 2024 at 2:53:36 PM UTC-4 Pedro Mendes wrote: *** Attention:

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Constraining a model to obey Principle of Detailed Balance

Thank you Pedro. On Thursday, July 18, 2024 at 2:53:36 PM UTC-4 Pedro Mendes wrote: *** Attention:

7/19/24

cel.c...@gmail.com, Frank Bergmann3

6/14/24

Parameter estimation for different reaction rates

Hello Frank, yes I chose AC_activity to be dependent and k_release to be independent and I would

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Parameter estimation for different reaction rates

Hello Frank, yes I chose AC_activity to be dependent and k_release to be independent and I would

6/14/24

5/31/24

Dear all, I have a question regarding the fit of the data when we have some induction time. How do we

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Dear all, I have a question regarding the fit of the data when we have some induction time. How do we

5/31/24

cel.c...@gmail.com, Frank Bergmann3

5/24/24

Events via Basico

Perfect! Thank you! Frank Bergmann schrieb am Mittwoch, 1. Mai 2024 um 14:28:36 UTC+2: Indeed, you

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Events via Basico

Perfect! Thank you! Frank Bergmann schrieb am Mittwoch, 1. Mai 2024 um 14:28:36 UTC+2: Indeed, you

5/24/24

Hikmet Emre Kaya, juergen3

5/13/24

Merging a deterministic and a stochastic model in COPASI

Dear Emre, There is no automatic way of merging the models, particularly if they are written with

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Merging a deterministic and a stochastic model in COPASI

Dear Emre, There is no automatic way of merging the models, particularly if they are written with

5/13/24

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