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Blinov,Michael
Feb 14
Attention Modeling Community
*** Attention: This is an external email. Use caution responding, opening attachments or clicking on
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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 Bergmann
5
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
Events set up
Andrew Weller 06:53 (now) to COPASI User Forum Dear Frank and Stefan With immense thanks to you both.
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Events set up
Andrew Weller 06:53 (now) to COPASI User Forum Dear Frank and Stefan With immense thanks to you both.
Jan 25
Ahmed Atta
,
Pedro Mendes
2
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
Blinov,Michael
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
*** Attention: This is an external email. Use caution responding, opening attachments or clicking on
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 Bergmann
2
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.com
11
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 Mendes
3
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 Mendes
3
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 Mendes
3
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 Bergmann
2
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
Blinov,Michael
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 Bergmann
9
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 Mendes
4
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 Bergmann
3
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
gemma aragay
5/31/24
induction time
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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induction time
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 Bergmann
3
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
,
juergen
3
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
Sebastián Espinel Ríos
,
juergen
4
5/13/24
Quantifying noise in stochastic simulations
Dear Sebastián, To the best of my knowledge, (1) there is no one minimum number of trajectories for
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Quantifying noise in stochastic simulations
Dear Sebastián, To the best of my knowledge, (1) there is no one minimum number of trajectories for
5/13/24
Breveruos Sh
,
Frank Bergmann
2
5/11/24
Automating Simulation and Scripting for reaction model
Hello Breveruos, Maybe you could have a look at: * CoRC: https://jpahle.github.io/CoRC/ for high
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Automating Simulation and Scripting for reaction model
Hello Breveruos, Maybe you could have a look at: * CoRC: https://jpahle.github.io/CoRC/ for high
5/11/24
Nausheen Fatima
,
Hoops, Stefan (sh9cq)
7
5/7/24
plots
Ok it is working now. Thank you. Nausheen. On Tue, May 7, 2024 at 8:18 PM 'Hoops, Stefan (sh9cq)
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plots
Ok it is working now. Thank you. Nausheen. On Tue, May 7, 2024 at 8:18 PM 'Hoops, Stefan (sh9cq)
5/7/24
Blinov,Michael
5/7/24
Computational Cell Biology Workshop Jul. 22-24, 2024
*** Attention: This is an external email. Use caution responding, opening attachments or clicking on
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Computational Cell Biology Workshop Jul. 22-24, 2024
*** Attention: This is an external email. Use caution responding, opening attachments or clicking on
5/7/24
Nausheen Fatima
, …
Pedro Mendes
5
5/6/24
syntax
Thank you for this clarification. It's making more sense now. On Sun, May 5, 2024 at 12:54 PM
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syntax
Thank you for this clarification. It's making more sense now. On Sun, May 5, 2024 at 12:54 PM
5/6/24
Frank Bergmann
4/19/24
Re: Help me in Copasi graph
You can change the displayed range with the mouse, to zoom into the area to narrow down the X / Y
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Re: Help me in Copasi graph
You can change the displayed range with the mouse, to zoom into the area to narrow down the X / Y
4/19/24
Tyler Nicholas Simmons
,
Frank Bergmann
4
3/14/24
Inconsistent Sensitivity Analysis
COPASI uses finite differences, to compute the sensitivities. For each cause a permutation is applied
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Inconsistent Sensitivity Analysis
COPASI uses finite differences, to compute the sensitivities. For each cause a permutation is applied
3/14/24
Stephen Sweeting
3/11/24
Sensitivity Analysis and Parameter Estimation
Hi everyone, I have generated a model (featuring 15 elementary steps) and using the parameter
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Sensitivity Analysis and Parameter Estimation
Hi everyone, I have generated a model (featuring 15 elementary steps) and using the parameter
3/11/24