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gemma aragay
May 31
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
May 31
cel.c...@gmail.com
,
Frank Bergmann
3
May 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
May 24
Hikmet Emre Kaya
,
juergen
3
May 13
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
May 13
Sebastián Espinel Ríos
,
juergen
4
May 13
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
May 13
Breveruos Sh
,
Frank Bergmann
2
May 11
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
May 11
Nausheen Fatima
,
Hoops, Stefan (sh9cq)
7
May 7
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)
May 7
Blinov,Michael
May 7
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
May 7
Nausheen Fatima
, …
Pedro Mendes
5
May 6
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
May 6
Frank Bergmann
Apr 19
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
Apr 19
Tyler Nicholas Simmons
,
Frank Bergmann
4
Mar 14
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
Mar 14
Stephen Sweeting
Mar 11
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
Mar 11
Sebastián Espinel Ríos
,
Pedro Mendes
2
Feb 20
Understanding stepsize in stochastic simulations
Hi Sebastián, your intuition is right. The "stepsize" is really only for output, ie it only
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Understanding stepsize in stochastic simulations
Hi Sebastián, your intuition is right. The "stepsize" is really only for output, ie it only
Feb 20
Victor Guo
,
Frank Bergmann
2
Feb 20
Event and Trigger Questions
One way to do something like that, is to ensure that your `k` parameter of your Reaction is a global
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Event and Trigger Questions
One way to do something like that, is to ensure that your `k` parameter of your Reaction is a global
Feb 20
Angelo Pisciotta
Feb 15
find k pseudo first order reaction
How i can find a K of pseudo first order reaction in copasi?
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find k pseudo first order reaction
How i can find a K of pseudo first order reaction in copasi?
Feb 15
juergen
2
Feb 14
Re: Help with stochastic simulation
Yes, that is exactly right (on average). On Wednesday, February 14, 2024 at 1:00:44 AM UTC+1
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Re: Help with stochastic simulation
Yes, that is exactly right (on average). On Wednesday, February 14, 2024 at 1:00:44 AM UTC+1
Feb 14
Hikmet Emre Kaya
,
Pedro Mendes
3
Feb 2
Using Metabolomics or Proteomics data as input in COPASI
Dear Pedro, Many thanks for your elaborate response. The bottleneck in my opinion (and what drove me
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Using Metabolomics or Proteomics data as input in COPASI
Dear Pedro, Many thanks for your elaborate response. The bottleneck in my opinion (and what drove me
Feb 2
gemma aragay
, …
Pedro Mendes
4
Feb 1
Fix thermodynamic association constant while iterating kon and koff
Thanks a lot for the response! Missatge de Pedro Mendes <men...@copasi.org> del dia dj., 1 de
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Fix thermodynamic association constant while iterating kon and koff
Thanks a lot for the response! Missatge de Pedro Mendes <men...@copasi.org> del dia dj., 1 de
Feb 1
cel.c...@gmail.com
,
sven....@gmail.com
3
Jan 30
Model results do not change on changed initial values
Hello Sven, thak you for your input. I would expect the amplitude to change with changing initial
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Model results do not change on changed initial values
Hello Sven, thak you for your input. I would expect the amplitude to change with changing initial
Jan 30
Angelo Pisciotta
Jan 29
Find k of scaravenger and NF
Hi From this article how i know the k of the scaravenger and which formula i have to insert in copasi
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Find k of scaravenger and NF
Hi From this article how i know the k of the scaravenger and which formula i have to insert in copasi
Jan 29
Angelo Pisciotta
,
Frank Bergmann
7
Jan 29
Graphs in Copasi
Here you are. I want see the effect in one graph of this combination of concentration of [Fe2+] and [
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Graphs in Copasi
Here you are. I want see the effect in one graph of this combination of concentration of [Fe2+] and [
Jan 29
Angelo Pisciotta
,
Matthias König
5
Jan 25
Help with Copasi
I want to know how i insert a scaravenger species in the model, because in the article there is TBA (
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Help with Copasi
I want to know how i insert a scaravenger species in the model, because in the article there is TBA (
Jan 25
cel.c...@gmail.com
,
Pedro Mendes
2
Jan 16
Boundary for Optimization function
Cel, you can put (linear) boundaries for any of the parameters that you are optimizing; these are
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Boundary for Optimization function
Cel, you can put (linear) boundaries for any of the parameters that you are optimizing; these are
Jan 16
Angelo Pisciotta
,
Frank Bergmann
5
Jan 15
Help for use copasi in fenton Reaction
Thanks, because is the first time for me and i'm not sure how put the radical. I add also the
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Help for use copasi in fenton Reaction
Thanks, because is the first time for me and i'm not sure how put the radical. I add also the
Jan 15
Torkel Loman
, …
Frank Bergmann
6
Jan 12
Create model (in GUI) without creating a compartment parameter
With the mentioned caveats in mind, here the script you asked for: https://gist.github.com/fbergmann/
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Create model (in GUI) without creating a compartment parameter
With the mentioned caveats in mind, here the script you asked for: https://gist.github.com/fbergmann/
Jan 12
Hideki Oka
, …
Frank Bergmann
19
Jan 12
stochastic parameter
Hello Oka, the easiest way to build the GUI, would probably to use our build scripts: https://github.
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stochastic parameter
Hello Oka, the easiest way to build the GUI, would probably to use our build scripts: https://github.
Jan 12
Pedro Mendes
Jan 4
Online Computational Cell Biology Workshop - February 26-28
25th Annual Computational Cell Biology Workshop ONLINE VERSION February 26-28 An intense online
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Online Computational Cell Biology Workshop - February 26-28
25th Annual Computational Cell Biology Workshop ONLINE VERSION February 26-28 An intense online
Jan 4
Hikmet Emre Kaya
12/21/23
CytoCopasi - Integrating COPASI functionality into Cytoscape
Hello Everyone, The Scientific Computing Research Unit (SCRU) at the University of Cape Town is
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CytoCopasi - Integrating COPASI functionality into Cytoscape
Hello Everyone, The Scientific Computing Research Unit (SCRU) at the University of Cape Town is
12/21/23
Yip Li
,
Pedro Mendes
2
12/8/23
Reaction involve henry's law constant
Hi, You can still model a reaction where you only have the equilibrium constant but not the explicit
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Reaction involve henry's law constant
Hi, You can still model a reaction where you only have the equilibrium constant but not the explicit
12/8/23
Pedro Mendes
11/30/23
Moderation on this list enabled
Apologies for the spam that you may have just seen. The messages have been deleted and the user
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Moderation on this list enabled
Apologies for the spam that you may have just seen. The messages have been deleted and the user
11/30/23
George Arnold
,
Frank Bergmann
2
11/15/23
Is anyone able to help me with my formula format in COPASI? Currently am trying to convert this formula below into a rate law for one of my models, however I can't wrap my head around it. Any help would be greatly appreciated
Hello, You could just enter this expression directly into COPASI as is. Where did you have problems
unread,
Is anyone able to help me with my formula format in COPASI? Currently am trying to convert this formula below into a rate law for one of my models, however I can't wrap my head around it. Any help would be greatly appreciated
Hello, You could just enter this expression directly into COPASI as is. Where did you have problems
11/15/23
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