jsbml-development

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Welcome to jsbml-development, a mailing list and Google Group for technical discussions specifically about JSBML (a pure Java SBML library) and its development.

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Andreas Dräger, … Bill Yang9

1/16/22

Re: [sbml-discuss] Extracting fbc logical expressions

Hi Andreas, Yes, that's what I did to make codes work. I was testing the converter with the yeast

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Re: [sbml-discuss] Extracting fbc logical expressions

Hi Andreas, Yes, that's what I did to make codes work. I was testing the converter with the yeast

1/16/22

jsbml-development

1/10/22

Stable release of JSBML version 1.6.1 available from GitHub and Maven Central

Dear users of JSBML, With this, we are announcing the stable release of JSBML version 1.6.1, which is

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Stable release of JSBML version 1.6.1 available from GitHub and Maven Central

Dear users of JSBML, With this, we are announcing the stable release of JSBML version 1.6.1, which is

1/10/22

jsbml-development

1/5/22

New version of JSBML available

Dear JSBML users, We are pleased to announce the release of JSBML-1.6.1, which is now available for

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New version of JSBML available

Dear JSBML users, We are pleased to announce the release of JSBML-1.6.1, which is now available for

1/5/22

Nicolas Rodriguez

1/29/21

Re: [Biomodels-net-support] SBML conversion - FBC package converter to SBML Level 2

Hi, So the SBML to SBML conversions should be working again, could you give it a try ? I did put

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Re: [Biomodels-net-support] SBML conversion - FBC package converter to SBML Level 2

Hi, So the SBML to SBML conversions should be working again, could you give it a try ? I did put

1/29/21

Matthias König

7/21/20

JSBML functions: renameSIdRefs, renameMetaIdRefs, renameUnitSIdRefs

Hi all, I am working on the comp flattening in JSBML. As part of the flattening algorithm I have to

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JSBML functions: renameSIdRefs, renameMetaIdRefs, renameUnitSIdRefs

Hi all, I am working on the comp flattening in JSBML. As part of the flattening algorithm I have to

7/21/20

HEMIL PANCHIWALA

7/12/20

Regarding the status of FBC Version 3

Hi all, I am currently working on the Systems Biology Simulation Core Library (SBSCL) as a GSoC 2020

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Regarding the status of FBC Version 3

Hi all, I am currently working on the Systems Biology Simulation Core Library (SBSCL) as a GSoC 2020

7/12/20

HEMIL PANCHIWALA, Miguel de Alba3

5/18/20

GSoC 2020: Simulation of systems biology models in Java

Hi, Thanks for the greetings! SBSCL currently overlaps with SED-ML and its backend for SED-ML depends

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GSoC 2020: Simulation of systems biology models in Java

Hi, Thanks for the greetings! SBSCL currently overlaps with SED-ML and its backend for SED-ML depends

5/18/20

MEDHA BHATTACHARYA, Andreas Dräger2

5/15/20

Participation in GSoC 2020

> Am 15.05.2020 um 16:30 schrieb MEDHA BHATTACHARYA <me19...@gmail.com>: > > Hello

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Participation in GSoC 2020

> Am 15.05.2020 um 16:30 schrieb MEDHA BHATTACHARYA <me19...@gmail.com>: > > Hello

5/15/20

Nicolas Rodriguez

4/22/20

Release of JSBML 1.5

We are pleased to announce the release of JSBML-1.5, which is now available for download from GitHub

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Release of JSBML 1.5

We are pleased to announce the release of JSBML-1.5, which is now available for download from GitHub

4/22/20

jsbml-development

4/1/20

release 1.5 preparation

Hello all, We are preparing the next release, the current plan is to make it Monday-Wednesday next

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release 1.5 preparation

Hello all, We are preparing the next release, the current plan is to make it Monday-Wednesday next

4/1/20

Nicolas Rodriguez, Matthias König7

7/2/19

Re: [sbml-distrib] Another new version (0.23) of distrib!

Hi Nico, thanks so much. Best Matthias On Mon, Jul 1, 2019 at 5:46 PM Nicolas Rodriguez <rodrigue@

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Re: [sbml-distrib] Another new version (0.23) of distrib!

Hi Nico, thanks so much. Best Matthias On Mon, Jul 1, 2019 at 5:46 PM Nicolas Rodriguez <rodrigue@

7/2/19

5/27/19

GoSC 2019: New Build System for Plugin Framework Insilico

Hello everyone, My name is Nikhil Ghodke. I am happy to share that I recently got selected for Google

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GoSC 2019: New Build System for Plugin Framework Insilico

Hello everyone, My name is Nikhil Ghodke. I am happy to share that I recently got selected for Google

5/27/19

5/27/19

GoSC 2019: New Build System for Plugin Framework Insilico

Hello everyone, My name is Nikhil Ghodke. I am happy to share that I recently got selected for Google

unread,

GoSC 2019: New Build System for Plugin Framework Insilico

Hello everyone, My name is Nikhil Ghodke. I am happy to share that I recently got selected for Google

5/27/19

5/20/19

GSoC 2019 : Validation of Spatial Systems Biology Models in Java

Dear All, I am Bhavye Jain, an undergraduate computer science student at the Indian Institute of

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GSoC 2019 : Validation of Spatial Systems Biology Models in Java

Dear All, I am Bhavye Jain, an undergraduate computer science student at the Indian Institute of

5/20/19

Andreas Dräger, Michael Hucka2

9/30/18

Cleanup of JSBML's history completed

Thank you for doing this great cleanup effort! MH On 17 Sep 2018, at 6:28, Andreas Dräger wrote: >

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Cleanup of JSBML's history completed

Thank you for doing this great cleanup effort! MH On 17 Sep 2018, at 6:28, Andreas Dräger wrote: >

9/30/18

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

Andreas Dräger

9/4/18

Cleanup of the project history

Dear all, When migrating from the previous SVN-based repository on SourceForge to GitHub, the project

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Cleanup of the project history

Dear all, When migrating from the previous SVN-based repository on SourceForge to GitHub, the project

9/4/18

Nicolas Rodriguez

8/20/18

Release of JSBML-1.4

We are pleased to announce the release of JSBML-1.4, which is now available for download from GitHub

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Release of JSBML-1.4

We are pleased to announce the release of JSBML-1.4, which is now available for download from GitHub

8/20/18

Nicolas Rodriguez

8/9/18

release preparation and distrib package problem

Hello all, We are preparing the next release, the current plan is to make it Monday-Wednesday next

unread,

release preparation and distrib package problem

Hello all, We are preparing the next release, the current plan is to make it Monday-Wednesday next

8/9/18

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

Matthias König, … Nicolas Rodriguez5

3/5/18

DerivedUnits on KineticLaws are not calculated correctly (invalid units)

Hi Nico, thanks for the fix. Works. Best Matthias On Monday, March 5, 2018 at 4:31:13 PM UTC+1,

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DerivedUnits on KineticLaws are not calculated correctly (invalid units)

Hi Nico, thanks for the fix. Works. Best Matthias On Monday, March 5, 2018 at 4:31:13 PM UTC+1,

3/5/18

Matthias König, Nicolas Rodriguez4

3/2/18

JSBML lacks support for inline units

Hi Nicolas, thanks. Sounds good. Best Matthias On Fri, Mar 2, 2018 at 4:45 PM, Nicolas Rodriguez <

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JSBML lacks support for inline units

Hi Nicolas, thanks. Sounds good. Best Matthias On Fri, Mar 2, 2018 at 4:45 PM, Nicolas Rodriguez <

3/2/18

1/4/18

Unifying behaviour

Hi Users of libSBML/JSBML - particularly users of both We need to resolve an issue and would like

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Unifying behaviour

Hi Users of libSBML/JSBML - particularly users of both We need to resolve an issue and would like

1/4/18

Nicolas Rodriguez

12/19/17

Release of JSBML-1.3.1

We are pleased to announce the release of JSBML-1.3.1, which is now available for download from

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Release of JSBML-1.3.1

We are pleased to announce the release of JSBML-1.3.1, which is now available for download from

12/19/17

Matthias König, Nicolas Rodriguez7

12/18/17

NullPointerException in reaction.getDerivedUnits with JSBML-v1.3

Thanks a lot. Issue is fixed. Best Matthias On Mon, Dec 18, 2017 at 11:48 AM, Nicolas Rodriguez <

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NullPointerException in reaction.getDerivedUnits with JSBML-v1.3

Thanks a lot. Issue is fixed. Best Matthias On Mon, Dec 18, 2017 at 11:48 AM, Nicolas Rodriguez <

12/18/17

Andreas Tille, Nicolas Rodriguez2

12/5/17

How to get Python3 bindings?

Hi Andreas, You need to ask your question in the libsbml-development mailing list: https://groups.

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How to get Python3 bindings?

Hi Andreas, You need to ask your question in the libsbml-development mailing list: https://groups.

12/5/17

Matthias König, … niko.rodrigue5

10/4/17

Simple assignments are not converted to correct formulas

Hi Nico, thanks for the help and input. Brought me on the right track. The problem was on my side.

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Simple assignments are not converted to correct formulas

Hi Nico, thanks for the help and input. Brought me on the right track. The problem was on my side.

10/4/17

Nicolas Rodriguez

9/18/17

Re: [jsbml-team] rewrite ASTNode in another format

Hi Isabel, Into what form do you want to write them exactly ? http://sbml.org/Special/Software/JSBML/

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Re: [jsbml-team] rewrite ASTNode in another format

Hi Isabel, Into what form do you want to write them exactly ? http://sbml.org/Special/Software/JSBML/

9/18/17

7/27/17

Feedback on Mapping for "SBML core"<->"SBGN PD", "SBML layout"<->"SBGN PD", and "SBML qual"<->"SBGN AF"

I'm also going to attach the mapping diagram for converter (4) "SBML core"<->

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Feedback on Mapping for "SBML core"<->"SBGN PD", "SBML layout"<->"SBGN PD", and "SBML qual"<->"SBGN AF"

I'm also going to attach the mapping diagram for converter (4) "SBML core"<->

7/27/17

Andreas Dräger, Nicolas Rodriguez3

7/24/17

Re: [sbml-interoperability] JSBML Installation

Hi Deepa, You can find a ready to use eclipse project at https://github.com/sbmlteam/jsbml/raw/master

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Re: [sbml-interoperability] JSBML Installation

Hi Deepa, You can find a ready to use eclipse project at https://github.com/sbmlteam/jsbml/raw/master

7/24/17

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