sbml-interoperability

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As of January 2021, this group is no longer active. Please use sbml-discuss instead. The previous contents of sbml-interoperability are being left here as an archive.

This group was originally based on both the sbml-interoperability and libsbml-discuss mailing lists; the latter was started in 2004 and renamed sbml-interoperability in 2008.

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2/3/21

This list is being closed & merged into sbml-discuss

Dear members of sbml-interoperability, Following discussions on sbml-discuss last December [1], the

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This list is being closed & merged into sbml-discuss

Dear members of sbml-interoperability, Following discussions on sbml-discuss last December [1], the

2/3/21

Иван Борисов, … Lucian Smith4

8/5/20

sbml-test-suite tolerance setup

Hemil, Lucian, thanks for clarification! To summarize, if I understood correctly SBML suite doesn

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sbml-test-suite tolerance setup

Hemil, Lucian, thanks for clarification! To summarize, if I understood correctly SBML suite doesn

8/5/20

Mikołaj Dziurzynski, … Matthias König5

7/30/20

libsbml - python: best way to work with annotation

Hi Matthias, That is exactly what I was looking for! Thank you! Best, Mikolaj czw., 30 lip 2020 o 02:

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libsbml - python: best way to work with annotation

Hi Matthias, That is exactly what I was looking for! Thank you! Best, Mikolaj czw., 30 lip 2020 o 02:

7/30/20

Hannes Baukmann, … Lucian Smith7

6/19/20

python-libsbml: qual plugin error when using SBML 3.2

Just wanted to chime in here and say that if you want to assign a value to a 'qual' element,

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python-libsbml: qual plugin error when using SBML 3.2

Just wanted to chime in here and say that if you want to assign a value to a 'qual' element,

6/19/20

fabien chambodut, … Andrei Kramer5

6/8/20

Create SBML file with R

Hello Frank, thanks, that did work as you said, very nice. Best, Andrei On Friday, 5 June 2020 15:04:

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Create SBML file with R

Hello Frank, thanks, that did work as you said, very nice. Best, Andrei On Friday, 5 June 2020 15:04:

6/8/20

Иван Борисов, Frank T. Bergmann5

3/26/20

Executing SBML Runner tests from CMD

Frank, I see, thank you! Ivan

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Executing SBML Runner tests from CMD

Frank, I see, thank you! Ivan

3/26/20

srikiran chandrasekaran, … Frank T. Bergmann5

12/6/19

Stochastic solvers that pass tests?

Thank you so much! On Tuesday, 3 December 2019 08:05:39 UTC-8, Frank T. Bergmann wrote: Hello, To

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Stochastic solvers that pass tests?

Thank you so much! On Tuesday, 3 December 2019 08:05:39 UTC-8, Frank T. Bergmann wrote: Hello, To

12/6/19

Andrew Briand, Lucian Smith2

9/16/19

Building libRoadRunner with libSBML experimental branch produces error

The Distributions package has been updated to no longer have a DistribFunctionDefinitionPlugin: it

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Building libRoadRunner with libSBML experimental branch produces error

The Distributions package has been updated to no longer have a DistribFunctionDefinitionPlugin: it

9/16/19

David Hoksza, … Zhang, Fengkai (NIH/NIAID) [E]8

9/9/19

working with multi package from Python

Hi David, I also played your example model and tried to import it Simmune. It passed the validation

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working with multi package from Python

Hi David, I also played your example model and tried to import it Simmune. It passed the validation

9/9/19

Randy Heiland, … Michael Hucka6

7/12/19

namespace and undefined symbols on OSX

On 12 Jul 2019, at 4:29, Frank T. Bergmann wrote: > Reading your initial email again, if you

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namespace and undefined symbols on OSX

On 12 Jul 2019, at 4:29, Frank T. Bergmann wrote: > Reading your initial email again, if you

7/12/19

Ahmad, Michiel Karrenbelt4

6/21/19

SBML-qual export error

Good News I have a contact with their developer and they fixed the error Thanks Michiel for the reply

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SBML-qual export error

Good News I have a contact with their developer and they fixed the error Thanks Michiel for the reply

6/21/19

Sai Teja, … Matthias König9

4/8/19

Convert Recon3DModel from L3V1 to L2V4

Hi Matthais, No, I couldn't run "full" iMAT on Recon3D using COBRA. I am able to use

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Convert Recon3DModel from L3V1 to L2V4

Hi Matthais, No, I couldn't run "full" iMAT on Recon3D using COBRA. I am able to use

4/8/19

Athénaïs Vaginay

3/19/19

automatic conversion from ode sbml model to qualitative sbml model

Hello, I hope you will be able to provide me some clues on this question : I am wondering whether or

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automatic conversion from ode sbml model to qualitative sbml model

Hello, I hope you will be able to provide me some clues on this question : I am wondering whether or

3/19/19

ver...@uw.edu, … Herbert Sauro5

1/18/19

Function in libSBML to return parameter/species names specified by an assignment rule from XML string?

Thank you, Lucian and Herbert. Taking your responses, I find this solves the problem and returns a

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Function in libSBML to return parameter/species names specified by an assignment rule from XML string?

Thank you, Lucian and Herbert. Taking your responses, I find this solves the problem and returns a

1/18/19

Andreas Dräger

12/21/18

Fwd: [sbml-discuss] Poll for the development of an user-friendly graphical editor for SBML

Dear all, Please find below a request to submit your opinion about the requirements for an SBML-

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Fwd: [sbml-discuss] Poll for the development of an user-friendly graphical editor for SBML

Dear all, Please find below a request to submit your opinion about the requirements for an SBML-

12/21/18

Marek Havlík, Frank Bergmann2

11/15/18

building PHP bindings

Hello, you can add additional include directories via the CMake variable EXTRA_INCLUDE_DIRS that

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building PHP bindings

Hello, you can add additional include directories via the CMake variable EXTRA_INCLUDE_DIRS that

11/15/18

11/12/18

How can you take strings imported with TranslateSBML and turn them as functions?

Hello, I am currently working on a project for school where I will take a .xml file created in

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How can you take strings imported with TranslateSBML and turn them as functions?

Hello, I am currently working on a project for school where I will take a .xml file created in

11/12/18

Michiel Karrenbelt, … Frank T. Bergmann4

11/9/18

parameter units FBA model for valid SBML

Hello Michiel, The error indicates, that while you have correctly copied the parameters, the new

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parameter units FBA model for valid SBML

Hello Michiel, The error indicates, that while you have correctly copied the parameters, the new

11/9/18

Alex Lubbock, Brett Olivier2

10/31/18

python-libsbml anaconda binaries for Python 3.7

Dear Alex Thanks for your question. We are planning on adding support for Python 3.7 in our next

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python-libsbml anaconda binaries for Python 3.7

Dear Alex Thanks for your question. We are planning on adding support for Python 3.7 in our next

10/31/18

Michiel Karrenbelt, … Michael Hucka6

10/23/18

model not properly returned

Hi, Yeah, this is a frustrating side-effect of using SWIG to create language bindings for Python and

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model not properly returned

Hi, Yeah, this is a frustrating side-effect of using SWIG to create language bindings for Python and

10/23/18

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

9/18/18

Re: [sbml-discuss] Manuscript describing SBML

Sorry I was perhaps not completely clear. Nicolas Le Novere has withdrawn from the paper and has

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Re: [sbml-discuss] Manuscript describing SBML

Sorry I was perhaps not completely clear. Nicolas Le Novere has withdrawn from the paper and has

9/18/18

9/10/18

Converting the differential equations in XML file to matrix differential equations.

Hello Everyone, I'm trying to use the matrix differential equation solver, in MATLAB, for a

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Converting the differential equations in XML file to matrix differential equations.

Hello Everyone, I'm trying to use the matrix differential equation solver, in MATLAB, for a

9/10/18

8/6/18

[sbml-discuss] Manuscript describing SBML

Dear Colleagues, We are in the process of submitting a manuscript describing SBML Level 3 for

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[sbml-discuss] Manuscript describing SBML

Dear Colleagues, We are in the process of submitting a manuscript describing SBML Level 3 for

8/6/18

yosh...@uw.edu, … Sarah Keating5

7/17/18

Changing Model Names with Antimony or libSBML

Hi Sarah, You are totally right. Tellurium has a function te.sbmlToAntimony() that converts SBML

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Changing Model Names with Antimony or libSBML

Hi Sarah, You are totally right. Tellurium has a function te.sbmlToAntimony() that converts SBML

7/17/18

s.mo...@campus.unimib.it, … Isabella Casini6

7/12/18

Groups in libSBML

Hi Frank, All of your suggestions worked! Thank you so much! Best, Isabella On Thursday, 12 July 2018

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Groups in libSBML

Hi Frank, All of your suggestions worked! Thank you so much! Best, Isabella On Thursday, 12 July 2018

7/12/18

7/10/18

SBML Online validator supports COMBINE Archive

Dear SBML users We are pleased to announce that the SBML Online validator will now accept a COMBINE

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SBML Online validator supports COMBINE Archive

Dear SBML users We are pleased to announce that the SBML Online validator will now accept a COMBINE

7/10/18

bur...@miamioh.edu, Frank Bergmann2

6/20/18

Spatial Package Use Clarification

Hello, I'm not sure I am absolutely certain what you are after. Let us take for example the

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Spatial Package Use Clarification

Hello, I'm not sure I am absolutely certain what you are after. Let us take for example the

6/20/18

darrenjwilkinson, Frank T. Bergmann3

5/8/18

libsbml R bindings

That works (both ways) - many thanks! Darren On Tuesday, May 8, 2018 at 2:44:33 PM UTC+1, Frank T.

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libsbml R bindings

That works (both ways) - many thanks! Darren On Tuesday, May 8, 2018 at 2:44:33 PM UTC+1, Frank T.

5/8/18

12/13/17

SBML Test Suite version 3.3.0 released

The SBML Team is pleased to announce the full release of version 3.3.0 of the SBML Test Suite. You

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SBML Test Suite version 3.3.0 released

The SBML Team is pleased to announce the full release of version 3.3.0 of the SBML Test Suite. You

12/13/17

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