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Yonatan Negash
, …
Frank Bergmann
6
3:59 AM
Steady state from parameter scan
Hello Yonatan, you need to set this setting once per model. So it will persist until you load another
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Steady state from parameter scan
Hello Yonatan, you need to set this setting once per model. So it will persist until you load another
3:59 AM
Ben G Small
Mar 24
Possible to upload sets of parameters from a *.csv file (or some such other flat format) to a COPASI model?
Hi. I just wanted to ask whether it's possible to upload a set of parameters into a COPASI model
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Possible to upload sets of parameters from a *.csv file (or some such other flat format) to a COPASI model?
Hi. I just wanted to ask whether it's possible to upload a set of parameters into a COPASI model
Mar 24
Hikmet Emre Kaya
,
Frank Bergmann
2
Mar 22
Java Bindings: Changing Metabolite Name
After the call to setObjectName, COPASI ensures that all elements referring to the metabolite will be
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Java Bindings: Changing Metabolite Name
After the call to setObjectName, COPASI ensures that all elements referring to the metabolite will be
Mar 22
Hideki Oka
,
Frank Bergmann
3
Mar 14
comment out
Dear Frank, Thank you quick reply. Your suggestion is not good for me because target species are used
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comment out
Dear Frank, Thank you quick reply. Your suggestion is not good for me because target species are used
Mar 14
Janek Kasper
, …
Sluka, James Patrick
3
Mar 13
Proton buffering
The best and easiest way would probably to set the hydronium concentration equal to a constant. That
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Proton buffering
The best and easiest way would probably to set the hydronium concentration equal to a constant. That
Mar 13
Hoops, Stefan (sh9cq)
Mar 8
Re: [copasi-user-forum] Enzyme inhibition
Hello Ken, You may want to have a look at the tutorials: https://copasi.org/Support/Video_Tutorials/
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Re: [copasi-user-forum] Enzyme inhibition
Hello Ken, You may want to have a look at the tutorials: https://copasi.org/Support/Video_Tutorials/
Mar 8
carlotta
, …
sven....@gmail.com
9
Mar 2
steady state fitting - set up
Thanks a lot Sven, it was very useful! Best Carlotta Il giorno venerdì 24 febbraio 2023 alle 09:56:36
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steady state fitting - set up
Thanks a lot Sven, it was very useful! Best Carlotta Il giorno venerdì 24 febbraio 2023 alle 09:56:36
Mar 2
josepantoni...@gmail.com
Mar 1
how to use the sliders?
Dear all, Sorry for this question, but I do not know how to move the slider and see the effect on the
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how to use the sliders?
Dear all, Sorry for this question, but I do not know how to move the slider and see the effect on the
Mar 1
rodrigo mora
,
Frank Bergmann
3
Feb 24
Problems with last version?
Thanks a lot Frank. Best regards, Rodrigo. On Fri, Feb 24, 2023 at 12:10 AM Frank Bergmann <frank.
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Problems with last version?
Thanks a lot Frank. Best regards, Rodrigo. On Fri, Feb 24, 2023 at 12:10 AM Frank Bergmann <frank.
Feb 24
Sara Kalvala
,
Frank Bergmann
3
Feb 14
Getting Gardner2000's toggle switch to toggle
Many thanks Frank, that is very helpful. I did play with volume and species quantities which makes
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Getting Gardner2000's toggle switch to toggle
Many thanks Frank, that is very helpful. I did play with volume and species quantities which makes
Feb 14
Hideki Oka
Feb 7
component multiply
Dear users, I saw two examples. First case, component V species belong is automatically multiplied.
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component multiply
Dear users, I saw two examples. First case, component V species belong is automatically multiplied.
Feb 7
Jikson P Mathew
, …
Deepa
5
Jan 9
Parameter Estimation
Hi Jikson, I'd like to add to Frank's reply. The error message in the first snapshot says the
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Parameter Estimation
Hi Jikson, I'd like to add to Frank's reply. The error message in the first snapshot says the
Jan 9
Hoops, Stefan (sh9cq)
12/9/22
Computational Cell Biology Workshop Online Feb. 13-15, 2023 - PLEASE SPREAD THE WORD
24 th CCB Workshop Feb. 13-15, 2023 The workshop is free. However, to be admitted please email the
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Computational Cell Biology Workshop Online Feb. 13-15, 2023 - PLEASE SPREAD THE WORD
24 th CCB Workshop Feb. 13-15, 2023 The workshop is free. However, to be admitted please email the
12/9/22
Daniel Koch
,
Frank Bergmann
4
12/6/22
Discrepancy parameter estimation task copasi GUI / basico
Hello Daniel, Thank you so much for the files, this turns out to be a documentation issue. That is,
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Discrepancy parameter estimation task copasi GUI / basico
Hello Daniel, Thank you so much for the files, this turns out to be a documentation issue. That is,
12/6/22
cel.c...@gmail.com
, …
Hoops, Stefan (sh9cq)
4
12/6/22
Trigger a reaction at some timepoint t
Hello Pedro, Thank you alot! This helped me big time. Best Celvic pedro.mendes schrieb am Freitag, 2.
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Trigger a reaction at some timepoint t
Hello Pedro, Thank you alot! This helped me big time. Best Celvic pedro.mendes schrieb am Freitag, 2.
12/6/22
Jikson P Mathew
,
Hoops, Stefan (sh9cq)
2
12/1/22
Rate constant
Hello Jikson, Please have look at the reactions. Since the second reaction has non- integer
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Rate constant
Hello Jikson, Please have look at the reactions. Since the second reaction has non- integer
12/1/22
Rahuman Sheriff
11/29/22
BioModels - Model of the year 2023 - Competition (Deadline 31st December 2022)
Dear Community members, Hope you are doing well and good. We recently launched the 'Model of the
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BioModels - Model of the year 2023 - Competition (Deadline 31st December 2022)
Dear Community members, Hope you are doing well and good. We recently launched the 'Model of the
11/29/22
Hikmet Emre Kaya
,
Frank Bergmann
2
11/28/22
Parameter Scan with the time course subtask: Custom Duration
Hello, the parameter scan task uses the time course task, so to adjust duration and all other
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Parameter Scan with the time course subtask: Custom Duration
Hello, the parameter scan task uses the time course task, so to adjust duration and all other
11/28/22
Hikmet Emre Kaya
,
Frank Bergmann
7
11/11/22
Java: Sensitivity Analysis
Hello, in your model you have many species that begin with an initial value of 0. The delta minimum
unread,
Java: Sensitivity Analysis
Hello, in your model you have many species that begin with an initial value of 0. The delta minimum
11/11/22
Deepa
11/1/22
Equilibrium steady-state and parameter estimation
Dear All, The following set of reactions are present in our model, I ran the steady-state analysis
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Equilibrium steady-state and parameter estimation
Dear All, The following set of reactions are present in our model, I ran the steady-state analysis
11/1/22
Deepa
,
Frank Bergmann
6
10/28/22
Setting up pre-simulation conditions for parameter estimation
Hello Deepa * for an event to fire at the initial time .. you have to click on the checkbox, Fire at
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Setting up pre-simulation conditions for parameter estimation
Hello Deepa * for an event to fire at the initial time .. you have to click on the checkbox, Fire at
10/28/22
Thomas Howard
,
Frank Bergmann
8
10/27/22
'Add New Rate Law' Difficulty/Bug?
Thanks Frank, I've just downloaded and have had a quick go - it looks good. Thanks for the quick
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'Add New Rate Law' Difficulty/Bug?
Thanks Frank, I've just downloaded and have had a quick go - it looks good. Thanks for the quick
10/27/22
cel.c...@gmail.com
, …
sven....@gmail.com
7
10/25/22
Simulation results do not comply with anticipated results
Hello Sven, thank you very much, this helped me now I have a clue on how to debug. Best! sven....@
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Simulation results do not comply with anticipated results
Hello Sven, thank you very much, this helped me now I have a clue on how to debug. Best! sven....@
10/25/22
Jikson P Mathew
, …
Sluka, James Patrick
5
10/24/22
Determining Chi square
Since these are correlations, you want numbers near zero. Near +1 means they are positively
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Determining Chi square
Since these are correlations, you want numbers near zero. Near +1 means they are positively
10/24/22
Matthias König
,
Hoops, Stefan (sh9cq)
5
10/20/22
Issue Tracker Database is Down & SBML model not read anymore in 4.37 (Build 264)
Hello Mathias, The check for appropriate units has been improved however an incorrect message was
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Issue Tracker Database is Down & SBML model not read anymore in 4.37 (Build 264)
Hello Mathias, The check for appropriate units has been improved however an incorrect message was
10/20/22
Roma Smirnov
,
Frank Bergmann
10
10/16/22
Combinatorial expansion functionality in COPASI
I figured out the problem: I have to paste 'writeSBML({})' command after the model generation
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Combinatorial expansion functionality in COPASI
I figured out the problem: I have to paste 'writeSBML({})' command after the model generation
10/16/22
Deepa
,
Hoops, Stefan (sh9cq)
5
10/14/22
Issue with the unit of a model parameter: SBML import
Hi Stefan, Thank you so much for the clarification. Best, Deepa On Fri, Oct 14, 2022 at 2:32 AM '
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Issue with the unit of a model parameter: SBML import
Hi Stefan, Thank you so much for the clarification. Best, Deepa On Fri, Oct 14, 2022 at 2:32 AM '
10/14/22
Hikmet Emre Kaya
2
10/13/22
Conversion between different Vmax units
Following up on this: I am actually struggling to reproduce the kinetic parameters of a study for my
unread,
Conversion between different Vmax units
Following up on this: I am actually struggling to reproduce the kinetic parameters of a study for my
10/13/22
Hikmet Emre Kaya
, …
Frank Bergmann
97
9/19/22
Linking COPASI and Cytoscape
Hi Frank, It does indeed work! I just noticed a syntax error in my code and fixed it. Thanks! On
unread,
Linking COPASI and Cytoscape
Hi Frank, It does indeed work! I just noticed a syntax error in my code and fixed it. Thanks! On
9/19/22
Deepa
,
Sluka, James Patrick
2
9/12/22
Finding optimal values from the results of parameter estimation repeats
As a starting point just look for correlations among the parameters. Often you get strong
unread,
Finding optimal values from the results of parameter estimation repeats
As a starting point just look for correlations among the parameters. Often you get strong
9/12/22