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EDM
Jul 25
I'm finding it difficult to create plots
Hi everyone, I need help with some plots...unfortunately i can't share them on the group but only
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I'm finding it difficult to create plots
Hi everyone, I need help with some plots...unfortunately i can't share them on the group but only
Jul 25
Andrew Glanville
,
Frank Bergmann
8
Jul 22
Merging Kinetic Models
Thanks Frank, Yes, apologies for my noviceness, I thought what I was seeing was limited to one
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Merging Kinetic Models
Thanks Frank, Yes, apologies for my noviceness, I thought what I was seeing was limited to one
Jul 22
Jerry Tanoury
,
Pedro Mendes
4
Jul 19
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:
Jul 19
cel.c...@gmail.com
,
Frank Bergmann
3
Jun 14
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
Jun 14
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