sbml-discuss

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Welcome to sbml-discuss, the primary mailing list and Google Group for discussions of SBML. Appropriate topics for this list include discussions of SBML features and its design, questions about SBML, problems using SBML software, and similar SBML-focused topics. Announcements directly related to SBML and SBML-compatible software are also accepted, but no other advertisements are permitted.

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Feiin Lou, Matthias König2

Sep 27

PlantReactome SBML model Download

Hi Felin, this seems due to an issue in the SBML export on plantreactome. I would report the issue

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PlantReactome SBML model Download

Hi Felin, this seems due to an issue in the SBML export on plantreactome. I would report the issue

Sep 27

Ayesha Abubakr, Rahuman Sheriff2

Sep 24

SBML Model Download

Hi Ayesha, Feel free to explore BioModels [1] https://www.ebi.ac.uk/biomodels/search?query=

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SBML Model Download

Hi Ayesha, Feel free to explore BioModels [1] https://www.ebi.ac.uk/biomodels/search?query=

Sep 24

Eliott Tixier, Frank Bergmann2

Aug 20

Converting MathML ASTNode to XML XMLNode

I'm afraid we are not directly creating XMLNodes when constructing the MathML, but instead we use

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Converting MathML ASTNode to XML XMLNode

I'm afraid we are not directly creating XMLNodes when constructing the MathML, but instead we use

Aug 20

Jun 17

Dear Colleagues, The “Computational Modeling in Biology” Network (COMBINE) is an initiative to

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Dear Colleagues, The “Computational Modeling in Biology” Network (COMBINE) is an initiative to

Jun 17

May 7

Computational Cell Biology Workshop Jul. 22-24, 2024

*** Attention: This is an external email. Use caution responding, opening attachments or clicking on

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Computational Cell Biology Workshop Jul. 22-24, 2024

*** Attention: This is an external email. Use caution responding, opening attachments or clicking on

May 7

Mar 25

Harmony Deadlines extended- 29 March

We are extending the deadlines for lightning talks/posters/breakouts until March 29. Sarah &

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Harmony Deadlines extended- 29 March

We are extending the deadlines for lightning talks/posters/breakouts until March 29. Sarah &

Mar 25

Mar 11

First Announcement: ISGSB 2024 conference in Stellenbosch, ZA (Sept 2024)

Dear SBML community, I've also posted this to combine-discuss but this conference may also be of

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First Announcement: ISGSB 2024 conference in Stellenbosch, ZA (Sept 2024)

Dear SBML community, I've also posted this to combine-discuss but this conference may also be of

Mar 11

Samuel Pastva, … Sarah Keating4

Mar 6

Questions regarding the test suite

Thank you very much for the answers! This is indeed very helpful! Now I understand how we should

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Questions regarding the test suite

Thank you very much for the answers! This is indeed very helpful! Now I understand how we should

Mar 6

Rahuman Sheriff

Feb 27

BioModels Model of the year 2024 competition

Dear Colleagues, I hope you are doing well. I am reaching out to highlight the BioModels' Model

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BioModels Model of the year 2024 competition

Dear Colleagues, I hope you are doing well. I am reaching out to highlight the BioModels' Model

Feb 27

Feb 22

HARMONY REGISTRATION

Don't forget to register for Harmony. https://docs.google.com/forms/d/e/1FAIpQLScCdF8eUNiryV-roU-

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HARMONY REGISTRATION

Don't forget to register for Harmony. https://docs.google.com/forms/d/e/1FAIpQLScCdF8eUNiryV-roU-

Feb 22

Feb 9

Release Candidate for review: FBC version 3

The SBML editors are happy to announce that a release candidate specification for FBC version 3 is

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Release Candidate for review: FBC version 3

The SBML editors are happy to announce that a release candidate specification for FBC version 3 is

Feb 9

Lucian Smith, Herbert M Sauro2

Feb 7

New SBML Editor: Michael Blinov

Congrats to Michael. Herbert On Tue, Feb 6, 2024 at 4:01 PM Lucian Smith <lucianoelsmitho@gmail.

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New SBML Editor: Michael Blinov

Congrats to Michael. Herbert On Tue, Feb 6, 2024 at 4:01 PM Lucian Smith <lucianoelsmitho@gmail.

Feb 7

Feb 5

HARMONY DEADLINE FOR TRAVEL SUPPORT REQUEST:15 February

Note the deadline for travel support requests is next week:15 February https://co.mbine.org/events/

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HARMONY DEADLINE FOR TRAVEL SUPPORT REQUEST:15 February

Note the deadline for travel support requests is next week:15 February https://co.mbine.org/events/

Feb 5

Jan 19

Call for votes: SBML Editor for 2021-2023

Dear SBML community, This is a call for votes for electing an SBML Editor for 2024-2026. Every

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Call for votes: SBML Editor for 2021-2023

Dear SBML community, This is a call for votes for electing an SBML Editor for 2024-2026. Every

Jan 19

Jan 17

Registration for HARMONY 2024 NOW OPEN

https://co.mbine.org/events/ Travel Awards are available please register early to apply(see the main

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Registration for HARMONY 2024 NOW OPEN

https://co.mbine.org/events/ Travel Awards are available please register early to apply(see the main

Jan 17

Jan 11

DEADLINE APPROACHING: Computational Cell Biology Workshop

ONLY 5 DAYS TILL THE APPLICATION DEADLINE. Details on how to apply are below. Apply to blinov@uchc.

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DEADLINE APPROACHING: Computational Cell Biology Workshop

ONLY 5 DAYS TILL THE APPLICATION DEADLINE. Details on how to apply are below. Apply to blinov@uchc.

Jan 11

12/30/23

Sharing Cancer Research Software? NIH Wants to Hear from You!

Some of you may be working on cancer topics, so this seemed potentially relevant: https://datascience

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Sharing Cancer Research Software? NIH Wants to Hear from You!

Some of you may be working on cancer topics, so this seemed potentially relevant: https://datascience

12/30/23

12/20/23

Announce: new versions of Tellurium, Roadrunner, and Antimony

The Sauro lab is happy to announce new versions of three of our software packages: * Tellurium v2.2.9

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Announce: new versions of Tellurium, Roadrunner, and Antimony

The Sauro lab is happy to announce new versions of three of our software packages: * Tellurium v2.2.9

12/20/23

Andreas Dräger

12/18/23

Postdoc/Research Assistant Position in Computer Modeling of Human Respiratory Microbiota

Dear colleagues, There is an exciting opportunity to join my research group that might interest you

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Postdoc/Research Assistant Position in Computer Modeling of Human Respiratory Microbiota

Dear colleagues, There is an exciting opportunity to join my research group that might interest you

12/18/23

Matthias König, Paul Lang2

12/13/23

JIB "COMBINE issue" 2024: Call for specifications and papers

Thanks for sharing this, Matthias. A while back, I wanted to make SBMLToolkit.jl (an importer for

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JIB "COMBINE issue" 2024: Call for specifications and papers

Thanks for sharing this, Matthias. A while back, I wanted to make SBMLToolkit.jl (an importer for

12/13/23

12/9/23

Call for SBML Editor Nominations

Dear SBML community, This is a call for nominations for a new SBML Editor to replace the outgoing

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Call for SBML Editor Nominations

Dear SBML community, This is a call for nominations for a new SBML Editor to replace the outgoing

12/9/23

12/7/23

HARMONY 2024 April 8-11

HARMONY 2024 will be hosted by UCL from Monday April 8th until Thursday April 11th. As part of our

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HARMONY 2024 April 8-11

HARMONY 2024 will be hosted by UCL from Monday April 8th until Thursday April 11th. As part of our

12/7/23

12/5/23

Computational Cell Biology Workshop Online Feb. 26-28, 2024 - PLEASE SPREAD THE WORD

The workshop is free. However, to be admitted please email the following information to l...@uchc.edu

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Computational Cell Biology Workshop Online Feb. 26-28, 2024 - PLEASE SPREAD THE WORD

The workshop is free. However, to be admitted please email the following information to l...@uchc.edu

12/5/23

Rahuman Sheriff

11/21/23

EMBL-EBI training course: Mathematics of Life 2024 & Model of the Year 2024 competition !!!

Dear Colleagues, Hope you are doing well and good. I would be grateful if you could circulate this

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EMBL-EBI training course: Mathematics of Life 2024 & Model of the Year 2024 competition !!!

Dear Colleagues, Hope you are doing well and good. I would be grateful if you could circulate this

11/21/23

Randy Heiland, Frank Bergmann3

11/4/23

Thanks for the prompt reply, Frank! I'll try the copasi deps and see how it goes. On Sat, Nov 4,

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Thanks for the prompt reply, Frank! I'll try the copasi deps and see how it goes. On Sat, Nov 4,

11/4/23

9/27/23

Release of libSBML 5.20.2

We are pleased to announce the release of libSBML-5.20.2. available at https://github.com/sbmlteam/

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Release of libSBML 5.20.2

We are pleased to announce the release of libSBML-5.20.2. available at https://github.com/sbmlteam/

9/27/23

9/25/23

Release of BioUML 2023.3

Dear all! We are glad to announce that new 2023.3 version of BioUML was released and can be

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Release of BioUML 2023.3

Dear all! We are glad to announce that new 2023.3 version of BioUML was released and can be

9/25/23

9/12/23

COMBINE 2023 update

Hello, fellow SBMLers, SBGNers, BioPAXers, BNGLers, and other modelers and developers, COMBINE in

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COMBINE 2023 update

Hello, fellow SBMLers, SBGNers, BioPAXers, BNGLers, and other modelers and developers, COMBINE in

9/12/23

8/29/23

COMBINE/ICSB tutorials and workshops, COMBINE financial aid

Dear colleagues, Time is running out for tutorials/workshop proposals and financial aid applications!

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COMBINE/ICSB tutorials and workshops, COMBINE financial aid

Dear colleagues, Time is running out for tutorials/workshop proposals and financial aid applications!

8/29/23

8/14/23

COMBINE workshop October 5-8th, 2023

Dear Computational Biologists, The "Computational Modeling in Biology" Network (COMBINE,

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COMBINE workshop October 5-8th, 2023

Dear Computational Biologists, The "Computational Modeling in Biology" Network (COMBINE,

8/14/23

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