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Hideki Oka
, …
Pedro Mendes
5
7:58 AM
stochastic parameter
Oka, the best way to think about this is that the event generation and the data output are two
unread,
stochastic parameter
Oka, the best way to think about this is that the event generation and the data output are two
7:58 AM
Pedro Mendes
Nov 30
Moderation on this list enabled
Apologies for the spam that you may have just seen. The messages have been deleted and the user
unread,
Moderation on this list enabled
Apologies for the spam that you may have just seen. The messages have been deleted and the user
Nov 30
George Arnold
,
Frank Bergmann
2
Nov 15
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
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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
Nov 15
Hideki Oka
,
Frank Bergmann
2
Nov 15
reaction order
Hello, The reaction order has no influence on the simulation results. Reactions are converted into
unread,
reaction order
Hello, The reaction order has no influence on the simulation results. Reactions are converted into
Nov 15
Hikmet Emre Kaya
,
Frank Bergmann
3
Oct 4
Segmentation Fault while customizing output plot specification
Hello Frank, OH I cannot believe I skipped it (lack of morning coffee). That should work fine, then.
unread,
Segmentation Fault while customizing output plot specification
Hello Frank, OH I cannot believe I skipped it (lack of morning coffee). That should work fine, then.
Oct 4
Stephen Sweeting
,
Sluka, James Patrick
2
Sep 29
Setting up parameter estimation using experiments with different initial conditions
I'm sure there are COPASI expert that can help more, but quickly: Your experimental data gets
unread,
Setting up parameter estimation using experiments with different initial conditions
I'm sure there are COPASI expert that can help more, but quickly: Your experimental data gets
Sep 29
jsl...@iu.edu
,
Frank Bergmann
3
Sep 15
Can't remove Time Course Sentivities time range
Yep, that was the problem. On the main tab the start time have been changed. The 'Time Course
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Can't remove Time Course Sentivities time range
Yep, that was the problem. On the main tab the start time have been changed. The 'Time Course
Sep 15
Blinov,Michael
Sep 12
COMBINE 2023 update
Hello, fellow SBMLers, SBGNers, BioPAXers, BNGLers, and other modelers and developers, COMBINE in
unread,
COMBINE 2023 update
Hello, fellow SBMLers, SBGNers, BioPAXers, BNGLers, and other modelers and developers, COMBINE in
Sep 12
Hikmet Emre Kaya
,
Frank Bergmann
3
Sep 5
Global Parameter Expression
Ah, that makes sense; I tried it but did not verify the existence of some of the expressions, which
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Global Parameter Expression
Ah, that makes sense; I tried it but did not verify the existence of some of the expressions, which
Sep 5
Theo Redfern
,
Frank Bergmann
2
Sep 5
Event error after updating model with BasiCO
Hello Theo, do you think you could (perhaps privately share the model code creating the model, or
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Event error after updating model with BasiCO
Hello Theo, do you think you could (perhaps privately share the model code creating the model, or
Sep 5
Hikmet Emre Kaya
,
Frank Bergmann
3
Sep 5
Java Bindings for MacOS Ventura
Dear Frank, Apologies for my delayed response, and thank you for the clarification. I used the two
unread,
Java Bindings for MacOS Ventura
Dear Frank, Apologies for my delayed response, and thank you for the clarification. I used the two
Sep 5
Blinov,Michael
Aug 29
COMBINE/ICSB tutorials and workshops, COMBINE financial aid
Dear colleagues, Time is running out for tutorials/workshop proposals and financial aid applications!
unread,
COMBINE/ICSB tutorials and workshops, COMBINE financial aid
Dear colleagues, Time is running out for tutorials/workshop proposals and financial aid applications!
Aug 29
Hideki Oka
,
Hoops, Stefan (sh9cq)
3
Aug 28
IF statement
Dear Stefan, Thank you, it is sll right. Yes, IF() is a function, best regards, Oka 2023年8月25日金曜日 19:
unread,
IF statement
Dear Stefan, Thank you, it is sll right. Yes, IF() is a function, best regards, Oka 2023年8月25日金曜日 19:
Aug 28
Vincenzo Rosso
,
Hoops, Stefan (sh9cq)
3
Aug 24
Streamlining COPASI Workflow: Efficient Experiment Updates after Parameter Estimation
Dear Hoops, Thank you for your swift and precise response to my previous email. Your help allowed me
unread,
Streamlining COPASI Workflow: Efficient Experiment Updates after Parameter Estimation
Dear Hoops, Thank you for your swift and precise response to my previous email. Your help allowed me
Aug 24
Hoops, Stefan (sh9cq)
,
Montano, Nieves M - (nievesmontano)
2
Aug 14
Re: [copasi-user-forum] Time course simulation error
please unsubscribe from this list. From: 'Hoops, Stefan (sh9cq)' via COPASI User Forum <
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Re: [copasi-user-forum] Time course simulation error
please unsubscribe from this list. From: 'Hoops, Stefan (sh9cq)' via COPASI User Forum <
Aug 14
Blinov,Michael
Aug 14
COMBINE 2023: October 5-8th, Farmington, CT
Dear Computational Biologists, The "Computational Modeling in Biology" Network (COMBINE,
unread,
COMBINE 2023: October 5-8th, Farmington, CT
Dear Computational Biologists, The "Computational Modeling in Biology" Network (COMBINE,
Aug 14
Jikson P Mathew
,
Pedro Mendes
2
Aug 9
Parameter estimation for detemining the rate constant for the formation of E
Hi Jikson, I am not going to comment on whether this makes sense from a chemical point of view, I am
unread,
Parameter estimation for detemining the rate constant for the formation of E
Hi Jikson, I am not going to comment on whether this makes sense from a chemical point of view, I am
Aug 9
Ricardo Soares
,
Frank Bergmann
2
Jul 7
Parameter Estimation - Time Sens
Hello Ricardo, this was an experimental feature that got accidentally enabled for the release. I don
unread,
Parameter Estimation - Time Sens
Hello Ricardo, this was an experimental feature that got accidentally enabled for the release. I don
Jul 7
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
unread,
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
unread,
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
unread,
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
unread,
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
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
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
unread,
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
unread,
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
unread,
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
unread,
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,
unread,
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
unread,
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
unread,
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