libsbml-development

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Welcome to libsbml-development, a mailing list and Google Group for technical discussions specifically about libSBML and its development.

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9/6/22

Not able to squeeze the rate equation in cell designer using SBML squeezer as a plugin

Dear all I am Angitha Melvin pursuing an M.Tech in Biotechnology from Dr BR Ambedkar National

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Not able to squeeze the rate equation in cell designer using SBML squeezer as a plugin

Dear all I am Angitha Melvin pursuing an M.Tech in Biotechnology from Dr BR Ambedkar National

9/6/22

Gui GuiGui, … Herbert M Sauro8

7/4/22

Sounds like good advice. Herbert On Sun, Jul 3, 2022 at 11:33 PM 'Matthias König' via libsbml

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Sounds like good advice. Herbert On Sun, Jul 3, 2022 at 11:33 PM 'Matthias König' via libsbml

7/4/22

Matthias König, Frank T. Bergmann3

7/13/21

Relax validation rule 10503

Hi Frank, thanks for the answer. I just tried to create some examples for the issue on sbml-discuss

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Relax validation rule 10503

Hi Frank, thanks for the answer. I just tried to create some examples for the issue on sbml-discuss

7/13/21

11/27/20

[sbml-discuss] Release of libSBML-5.19.0

--------------------------------------- libSBML-5.19.0 ---------------------------------------- This

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[sbml-discuss] Release of libSBML-5.19.0

--------------------------------------- libSBML-5.19.0 ---------------------------------------- This

11/27/20

Zbigniew Jędrzejewski-Szmek, Frank T. Bergmann4

11/18/20

build failure with python3.10

IIRC, we didn't use the cmake system because it had some shortcomings with the final installation

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build failure with python3.10

IIRC, we didn't use the cmake system because it had some shortcomings with the final installation

11/18/20

3/3/20

Re: To discuss about the format in which libSBML store model's and its component's annotations

Hi, Thanks for your interest. There are some explanations at http://sbml.org/Community/Wiki/

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Re: To discuss about the format in which libSBML store model's and its component's annotations

Hi, Thanks for your interest. There are some explanations at http://sbml.org/Community/Wiki/

3/3/20

Michiel Karrenbelt, … Frank T. Bergmann4

5/13/19

adding package plugins

Hello, it is difficult to work out what precisely you would want to achieve.So perhaps you could let

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adding package plugins

Hello, it is difficult to work out what precisely you would want to achieve.So perhaps you could let

5/13/19

David Hagen, … Brett5

5/8/19

Python 3.7 wheels on PyPI

Just as a follow up. Python 3.7 binaries are available as part of the recent 5.18 release. Brett On

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Python 3.7 wheels on PyPI

Just as a follow up. Python 3.7 binaries are available as part of the recent 5.18 release. Brett On

5/8/19

Keating, Sarah M.

4/22/19

Release of libSBML-5.18.0

--------------------------------------- libSBML-5.18.0 ---------------------------------------- We

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Release of libSBML-5.18.0

--------------------------------------- libSBML-5.18.0 ---------------------------------------- We

4/22/19

Michiel Karrenbelt, Frank T. Bergmann2

4/10/19

valid model incorrect after reading / writing

Hello Michiel, this comes about from the fact that you do declare the SBML namespace twice (and in

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valid model incorrect after reading / writing

Hello Michiel, this comes about from the fact that you do declare the SBML namespace twice (and in

4/10/19

Alex Enersen, Lucian Smith2

4/9/19

Outputting an SBMLDocument

The functions 'writeSBMLToString' and 'writeSBMLToFile' are what you want. You can

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Outputting an SBMLDocument

The functions 'writeSBMLToString' and 'writeSBMLToFile' are what you want. You can

4/9/19

Matthias König, … Hoops, Stefan (sh9cq)4

4/8/19

How to trigger an event repeatedly at constant intervals?

Hi Frank and Stefan, thanks a lot for the help. This solves my issue, both solutions work. The sinus

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How to trigger an event repeatedly at constant intervals?

Hi Frank and Stefan, thanks a lot for the help. This solves my issue, both solutions work. The sinus

4/8/19

Athénaïs Vaginay, … Michael Hucka3

3/19/19

a little mistake in the libSBML Python API online documentation

Thanks for reporting that. Indeed that's a mistake. MH On 18 Mar 2019, at 8:53, Athénaïs Vaginay

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a little mistake in the libSBML Python API online documentation

Thanks for reporting that. Indeed that's a mistake. MH On 18 Mar 2019, at 8:53, Athénaïs Vaginay

3/19/19

Matthias König, Keating, Sarah M.4

3/14/19

How to create an SBML document with empty listOfs ?

Hi all, this is solved. Thanks for all the help. Best Matthias On Friday, February 8, 2019 at 11:05:

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How to create an SBML document with empty listOfs ?

Hi all, this is solved. Thanks for all the help. Best Matthias On Friday, February 8, 2019 at 11:05:

3/14/19

Matthias König, … Brett4

3/14/19

How to build libsbml with distrib python package?

Hi Brett & Frank, thanks so much for the bug fix. Everything works. Best Matthias On Thursday,

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How to build libsbml with distrib python package?

Hi Brett & Frank, thanks so much for the bug fix. Everything works. Best Matthias On Thursday,

3/14/19

Matthias König, Frank T. Bergmann3

3/13/19

How to retrieve SBase object via id or metaid in O(1)?

Hi Frank, thanks, this solves my problem. Best Matthias On Wednesday, March 13, 2019 at 1:55:54 PM

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How to retrieve SBase object via id or metaid in O(1)?

Hi Frank, thanks, this solves my problem. Best Matthias On Wednesday, March 13, 2019 at 1:55:54 PM

3/13/19

3/2/19

Obtaining stoichiometry from speciesReference

getStoichiometry () works. Thanks! On Sun, Mar 3, 2019 at 8:44 AM Deepa <deepama...@gmail.com

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Obtaining stoichiometry from speciesReference

getStoichiometry () works. Thanks! On Sun, Mar 3, 2019 at 8:44 AM Deepa <deepama...@gmail.com

3/2/19

Michiel Karrenbelt, Matthias König4

2/11/19

obtaining math level

You should look at the API documentation for ASTNode class. Things you want are probably: def

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obtaining math level

You should look at the API documentation for ASTNode class. Things you want are probably: def

2/11/19

Alex Enersen, Frank T. Bergmann2

1/16/19

Standard time units in SBML File

Hello, the UnitKind in SBML will always be in SI units, so 'seconds' is indeed the only time

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Standard time units in SBML File

Hello, the UnitKind in SBML will always be in SI units, so 'seconds' is indeed the only time

1/16/19

Alex Enersen, … Matthias König5

1/15/19

Returning Denominator of Units

Hi Alex, if there is a self-defined unit it should give the id of the unit (which is the

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Returning Denominator of Units

Hi Alex, if there is a self-defined unit it should give the id of the unit (which is the

1/15/19

Matthias König, Keating, Sarah M.5

1/2/19

Unit checking warnings on log(2 dimensionless)

Hi Sarah, thanks a lot for the fix. I wanted to check the next few days if the issue with the various

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Unit checking warnings on log(2 dimensionless)

Hi Sarah, thanks a lot for the fix. I wanted to check the next few days if the issue with the various

1/2/19

Keating, Sarah M.

12/7/18

Release of libSBML-5.17.2-experimental

--------------------------------------- libSBML-5.17.2-experimental ---------------------------------

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Release of libSBML-5.17.2-experimental

--------------------------------------- libSBML-5.17.2-experimental ---------------------------------

12/7/18

Andreas Tille, … Michael Hucka5

12/5/18

Issue when trying to create Python3 bindings when using Python 3.7

Whoops, sorry about that! Thanks for catching my error. MH On 5 Dec 2018, at 2:10, Keating, Sarah M.

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Issue when trying to create Python3 bindings when using Python 3.7

Whoops, sorry about that! Thanks for catching my error. MH On 5 Dec 2018, at 2:10, Keating, Sarah M.

12/5/18

Michiel Karrenbelt, … Matthias König3

12/3/18

libsbml set fbc model / reaction / species extension

Hi Michiel, You have to enable the package on the SBMLDocument instance. In addition you have to set

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libsbml set fbc model / reaction / species extension

Hi Michiel, You have to enable the package on the SBMLDocument instance. In addition you have to set

12/3/18

Alexander Tille, Frank T. Bergmann5

11/8/18

unexpected results after manual installation

I build a minimal program that just reads and prints the model, that I wanted to upload here to show

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unexpected results after manual installation

I build a minimal program that just reads and prints the model, that I wanted to upload here to show

11/8/18

Herbert M Sauro, … Michael Hucka6

11/4/18

Are XMLError_t and SBMLError_t the same thing?

The class relationship is, thankfully, more clear in the docs for the other languages. Owing to how

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Are XMLError_t and SBMLError_t the same thing?

The class relationship is, thankfully, more clear in the docs for the other languages. Owing to how

11/4/18

Alex Enersen, Frank Bergmann2

11/3/18

Cloning an SBML file with changes

from the snippet you were posting, there seems actually, to be no reason to create a new document at

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Cloning an SBML file with changes

from the snippet you were posting, there seems actually, to be no reason to create a new document at

11/3/18

Herbert M Sauro

10/31/18

How to get the error message using the C API

I'm trying to figure out how to get the error message from libSBML using the C API. I can get the

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How to get the error message using the C API

I'm trying to figure out how to get the error message from libSBML using the C API. I can get the

10/31/18

Herbert M Sauro, … Frank T. Bergmann7

10/30/18

libSBML method to automatically add modifiers to a model

ok, I'll look again to reconfigure VS. Herbert On Tue, Oct 30, 2018 at 2:40 PM Frank T. Bergmann

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libSBML method to automatically add modifiers to a model

ok, I'll look again to reconfigure VS. Herbert On Tue, Oct 30, 2018 at 2:40 PM Frank T. Bergmann

10/30/18

10/16/18

Updated math code in libSBML

Hi LibSBML-users **FEEDBACK REQUEST** Previously libSBML had included an implementation of the

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Updated math code in libSBML

Hi LibSBML-users **FEEDBACK REQUEST** Previously libSBML had included an implementation of the

10/16/18

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