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Vijeth Ullal
, …
Pedro Mendes
3
Jun 6
Methodology to find Initial Concentration and Forward-Backward Reaction Kinetics of Molecular Species using Western Blot images
> I'm getting stuck at finding the concentration as the points on the > plot appear as a
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Methodology to find Initial Concentration and Forward-Backward Reaction Kinetics of Molecular Species using Western Blot images
> I'm getting stuck at finding the concentration as the points on the > plot appear as a
Jun 6
Hikmet Emre Kaya
,
Scampicchio Matteo Mario
4
May 30
Rate Law from Kd for a weak and transient PPI
I am afraid your question is more about experimental works in cancerous signaling rather than about
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Rate Law from Kd for a weak and transient PPI
I am afraid your question is more about experimental works in cancerous signaling rather than about
May 30
Zikra Bakhtawar Saeed
,
Scampicchio Matteo Mario
2
May 25
Query regarding unit conversion
You can express the concentration of your chemical species as mol/m^2 instead of mol/L. This can be
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Query regarding unit conversion
You can express the concentration of your chemical species as mol/m^2 instead of mol/L. This can be
May 25
carlotta
, …
sven....@gmail.com
12
May 12
steady state fitting - set up
Dear Sven, Thanks a lot for all your help! I was able to fit my steady-state data with Copasi as you
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steady state fitting - set up
Dear Sven, Thanks a lot for all your help! I was able to fit my steady-state data with Copasi as you
May 12
Pedro Mendes
May 10
CompCellBio workshop - modeling with COPASI and VCell – June 26-28, 2023
Dear Biologists interested in Modeling, The 24th Annual Workshop on Computational Cell Biology will
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CompCellBio workshop - modeling with COPASI and VCell – June 26-28, 2023
Dear Biologists interested in Modeling, The 24th Annual Workshop on Computational Cell Biology will
May 10
Anamul Haque
May 2
Boolean Logic Modeling in COPASI
Hi All, Say I have 5 species = A, B, C, D, E Reaction Rules - => A => B A => C B => D C
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Boolean Logic Modeling in COPASI
Hi All, Say I have 5 species = A, B, C, D, E Reaction Rules - => A => B A => C B => D C
May 2
Matteo Scampicchio
, …
sven....@gmail.com
4
May 2
Time course simulation, sliders and experimental data
Hello, I can think of another way (with a different set of drawbacks...): You could use the parameter
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Time course simulation, sliders and experimental data
Hello, I can think of another way (with a different set of drawbacks...): You could use the parameter
May 2
Janek Kasper
,
Matteo Scampicchio
2
May 2
Drawing graphs
I guess that the graphical features of Copasi are quite limited as the main purpose of Copasi is not
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Drawing graphs
I guess that the graphical features of Copasi are quite limited as the main purpose of Copasi is not
May 2
Janek Kasper
,
Frank Bergmann
3
Apr 19
Is it possible to convert cellml file to SBML ?
Thanks a lot, Frank! Best, Janek Frank Bergmann kirjutas kolmapäev, 12. aprill 2023 kl 09:20:31 UTC+3
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Is it possible to convert cellml file to SBML ?
Thanks a lot, Frank! Best, Janek Frank Bergmann kirjutas kolmapäev, 12. aprill 2023 kl 09:20:31 UTC+3
Apr 19
Jikson P Mathew
,
Pedro Mendes
2
Apr 18
Pseudo first order reaction for an organic reaction
Hi Jikson, A pseudo-first order reaction is written the same way as a true first-order reaction,
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Pseudo first order reaction for an organic reaction
Hi Jikson, A pseudo-first order reaction is written the same way as a true first-order reaction,
Apr 18
Alexandre de Assis Bento Lima
,
Frank Bergmann
7
Apr 12
Multiline INI file issue
Thanks a lot, Frank! I'll give it a try. Best, Alexandre A 12 de abril de 2023 03:51:39, Frank
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Multiline INI file issue
Thanks a lot, Frank! I'll give it a try. Best, Alexandre A 12 de abril de 2023 03:51:39, Frank
Apr 12
Ben G Small
,
Frank Bergmann
3
Mar 31
Possible to upload sets of parameters from a *.csv file (or some such other flat format) to a COPASI model?
Dear Frank Thanks for your reply, as an R user - I'll try CoRC. Thanks! Ben On Wed, 29 Mar 2023
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Possible to upload sets of parameters from a *.csv file (or some such other flat format) to a COPASI model?
Dear Frank Thanks for your reply, as an R user - I'll try CoRC. Thanks! Ben On Wed, 29 Mar 2023
Mar 31
Blinov,Michael
Mar 29
CompCellBio workshop - modeling with COPASI and VCell – June 26-28, 2023
Dear Biologists interested in Modeling, The 24th Annual Workshop on Computational Cell Biology will
unread,
CompCellBio workshop - modeling with COPASI and VCell – June 26-28, 2023
Dear Biologists interested in Modeling, The 24th Annual Workshop on Computational Cell Biology will
Mar 29
Yonatan Negash
, …
Frank Bergmann
6
Mar 28
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
Mar 28
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
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
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
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