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carlotta
,
Frank Bergmann
4
Jan 9
steady state fitting - set up
Hello Carlotta, you might not have gotten the mail i sent to you privately before. Your parameter
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steady state fitting - set up
Hello Carlotta, you might not have gotten the mail i sent to you privately before. Your parameter
Jan 9
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
unread,
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
unread,
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
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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
Ricardo Soares
9/23/22
Experimental data - Independent variables
Dear all, I'm using COPASI to analyze the metabolism of one compound by two enzymes. I also use
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Experimental data - Independent variables
Dear all, I'm using COPASI to analyze the metabolism of one compound by two enzymes. I also use
9/23/22
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
Parvathy Sarma
, …
Matthias König
3
9/12/22
Problem in Adding events
Hello Parvathy, I would probably model this as two reactions: v1: A -> B v2: A -> C where you
unread,
Problem in Adding events
Hello Parvathy, I would probably model this as two reactions: v1: A -> B v2: A -> C where you
9/12/22
Hikmet Emre Kaya
,
Frank Bergmann
3
8/23/22
MCA Java bindings crashes
Hi Frank, I actually solved the issue, I forgot to run the process method for the MCA method before
unread,
MCA Java bindings crashes
Hi Frank, I actually solved the issue, I forgot to run the process method for the MCA method before
8/23/22
Melanie Stefan
, …
Hoops, Stefan (sh9cq)
4
8/16/22
Installing Copasi on Manjaro Linux: Problem and Solution
Hi Stefan and Frank, I can confirm that this works: I can start CopasiUI after removing that file.
unread,
Installing Copasi on Manjaro Linux: Problem and Solution
Hi Stefan and Frank, I can confirm that this works: I can start CopasiUI after removing that file.
8/16/22
Prof. Francisco Lopes
,
Hoops, Stefan (sh9cq)
5
8/9/22
Output Time Points
Hi Stefan, Thank you very much. I did not realize that I could have this option :-| Regards,
unread,
Output Time Points
Hi Stefan, Thank you very much. I did not realize that I could have this option :-| Regards,
8/9/22
Theo Redfern
, …
Mendes,Pedro
5
7/22/22
Unusually slow Parameter Estimation
Dear Dr Mendes, Excellent thank you, I will try this! Best, Theo On Friday, July 22, 2022 at 3:28:51
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Unusually slow Parameter Estimation
Dear Dr Mendes, Excellent thank you, I will try this! Best, Theo On Friday, July 22, 2022 at 3:28:51
7/22/22
Mohamed Chilmeran
,
Hoops, Stefan (sh9cq)
3
6/30/22
Parameter Estimation for different experiments
Hello Dr. Stefan, Many thanks for your reply. That makes sense. I will take a look at the video. Best
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Parameter Estimation for different experiments
Hello Dr. Stefan, Many thanks for your reply. That makes sense. I will take a look at the video. Best
6/30/22
Ritika Saxena
,
Frank Bergmann
4
6/24/22
regarding doubt
Hello, * the error in the `glucose transport` reaction comes from the fact, that the rate law uses a
unread,
regarding doubt
Hello, * the error in the `glucose transport` reaction comes from the fact, that the rate law uses a
6/24/22
Deepa
,
Hoops, Stefan (sh9cq)
5
6/16/22
Stability analysis
Thanks a lot, my mistake :) On Fri, Jun 17, 2022 at 7:26 AM 'Hoops, Stefan (sh9cq)' via
unread,
Stability analysis
Thanks a lot, my mistake :) On Fri, Jun 17, 2022 at 7:26 AM 'Hoops, Stefan (sh9cq)' via
6/16/22
Deepa
,
Mendes,Pedro
3
6/16/22
Transition time
Hi Prof., Thank you so much for the explanation. Would it be wrong to have a transition time in hours
unread,
Transition time
Hi Prof., Thank you so much for the explanation. Would it be wrong to have a transition time in hours
6/16/22