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Simulation Experiment Description Markup Language
This is the official forum to discuss all things related to SED-ML.
official homepage
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http://www.sed-ml.org/
github repository:
https://github.com/SED-ML
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Lucian Smith
2
Feb 1
SED2 at HARMONY
OK, now that I'm here at HARMONY (yay!) it turns out that neither of those times quite work. We
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SED2 at HARMONY
OK, now that I'm here at HARMONY (yay!) it turns out that neither of those times quite work. We
Feb 1
David Nickerson
Feb 1
Call for votes: SED-ML Editors for 2026-2028
Dear all, This is a call for votes in the election of two SED-ML editors to replace David Nickerson
unread,
Call for votes: SED-ML Editors for 2026-2028
Dear all, This is a call for votes in the election of two SED-ML editors to replace David Nickerson
Feb 1
Rahuman Sheriff
Jan 30
BioModels Update
Dear BioModels users and community members, We would like to remind you that BioModels has now fully
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BioModels Update
Dear BioModels users and community members, We would like to remind you that BioModels has now fully
Jan 30
David Nickerson
Jan 30
HARMONY starts Monday (NZ time)
Hi all, HARMONY 2026 is happening next week in Auckland, New Zealand. The current schedule overview
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HARMONY starts Monday (NZ time)
Hi all, HARMONY 2026 is happening next week in Auckland, New Zealand. The current schedule overview
Jan 30
Lucian Smith
Jan 29
Reminder: one more day to nominate SED-ML Editors for 2026
It's the final day for nominations for SED-ML Editors! https://forms.gle/w9XkrfTPN4VkCEs88 If you
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Reminder: one more day to nominate SED-ML Editors for 2026
It's the final day for nominations for SED-ML Editors! https://forms.gle/w9XkrfTPN4VkCEs88 If you
Jan 29
Lucian Smith
Jan 23
Reminder: Nominate SED-ML editors for 2026-2028
This is a reminder that nominations are open for two new SED-ML editors for the 2026-2028 term: https
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Reminder: Nominate SED-ML editors for 2026-2028
This is a reminder that nominations are open for two new SED-ML editors for the 2026-2028 term: https
Jan 23
Lucian Smith
Jan 16
Call for Nominations for SED-ML Editor, 2026-2028
Dear SED-ML community, Please nominate SED-ML editors using the form at https://forms.gle/
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Call for Nominations for SED-ML Editor, 2026-2028
Dear SED-ML community, Please nominate SED-ML editors using the form at https://forms.gle/
Jan 16
David Nickerson
2
Jan 5
Re: HARMONY 2026 - Registration now open
Hi all, Just a quick reminder that in-person registration for HARMONY 2026 closes on 12 January at 23
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Re: HARMONY 2026 - Registration now open
Hi all, Just a quick reminder that in-person registration for HARMONY 2026 closes on 12 January at 23
Jan 5
David Nickerson
12/9/25
JIB Special issue - submission deadline 31 January 2026
Hi all, Thanks to Falk, there will be another special issue of the Journal of Integrative
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JIB Special issue - submission deadline 31 January 2026
Hi all, Thanks to Falk, there will be another special issue of the Journal of Integrative
12/9/25
Agmon,Eran
, …
Weiwei Ai
5
11/2/25
SED2 / Multisim composition Working Group
I'm interested. Best regards, Weiwei On Sat, 1 Nov 2025 at 07:58, 'Blinov,Michael' via
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SED2 / Multisim composition Working Group
I'm interested. Best regards, Weiwei On Sat, 1 Nov 2025 at 07:58, 'Blinov,Michael' via
11/2/25
Lucian Smith
10/22/25
COMBINE discussion of SED2 tomorrow
Hey, everyone! Eran's going to be leading a breakout discussion of a possible 'SED2'
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COMBINE discussion of SED2 tomorrow
Hey, everyone! Eran's going to be leading a breakout discussion of a possible 'SED2'
10/22/25
David Nickerson
3
10/10/25
COMBINE 2025 - registration updates, confirmed speakers, and travel funding
Hi all, There is still time to register for COMBINE 2025 (https://co.mbine.org/events/) - local
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COMBINE 2025 - registration updates, confirmed speakers, and travel funding
Hi all, There is still time to register for COMBINE 2025 (https://co.mbine.org/events/) - local
10/10/25
David Nickerson
6/17/25
COMBINE 2025 - registration now open
Hi all, The “Computational Modeling in Biology” Network (COMBINE) is an initiative to coordinate the
unread,
COMBINE 2025 - registration now open
Hi all, The “Computational Modeling in Biology” Network (COMBINE) is an initiative to coordinate the
6/17/25
Lucian Smith
5/19/25
Reminder: SED-ML Editor's Meeting in an hour
Just a reminder that there's a SED-ML Editor's meeting at noon Pacific today! https://
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Reminder: SED-ML Editor's Meeting in an hour
Just a reminder that there's a SED-ML Editor's meeting at noon Pacific today! https://
5/19/25
Lucian Smith
4/17/25
Proposal: add 'timePoints' to UniformTimeCourse
As initially proposed by Ion at today's HARMONY meeting: https://github.com/SED-ML/sed-ml/issues/
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Proposal: add 'timePoints' to UniformTimeCourse
As initially proposed by Ion at today's HARMONY meeting: https://github.com/SED-ML/sed-ml/issues/
4/17/25
Lucian Smith
4/17/25
Proposal: add 'timeInterval' attribute to UniformTimeCourse
As proposed by Alan Garny at HARMONY today: https://github.com/SED-ML/sed-ml/issues/223 "Add a
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Proposal: add 'timeInterval' attribute to UniformTimeCourse
As proposed by Alan Garny at HARMONY today: https://github.com/SED-ML/sed-ml/issues/223 "Add a
4/17/25
Rahuman Sheriff
4/8/25
Last chance to apply: BioModels Model of the Year 2025 – £1000 Prize! - Deadline 18th April
Dear Colleague, We're excited to announce the final call for entries for the BioModels Model of
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Last chance to apply: BioModels Model of the Year 2025 – £1000 Prize! - Deadline 18th April
Dear Colleague, We're excited to announce the final call for entries for the BioModels Model of
4/8/25
Lucian Smith
, …
David Nickerson
5
4/7/25
SED-ML meeting at HARMONY
Hi all, I've started an agenda / notes document here: https://docs.google.com/document/d/
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SED-ML meeting at HARMONY
Hi all, I've started an agenda / notes document here: https://docs.google.com/document/d/
4/7/25
Lucian Smith
3/31/25
Election Result: Herbert Sauro joins as SED-ML editor!
With 14 unique votes, Herbert Sauro has been elected to be a SED-ML editor for the 2025-2027 term. I
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Election Result: Herbert Sauro joins as SED-ML editor!
With 14 unique votes, Herbert Sauro has been elected to be a SED-ML editor for the 2025-2027 term. I
3/31/25
Lucian Smith
3
3/24/25
Call for Votes: SED-ML Editors for 2024-2026
As a reminder: there is one more week left to vote for the next SED-ML editor! Also, apologies: the
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Call for Votes: SED-ML Editors for 2024-2026
As a reminder: there is one more week left to vote for the next SED-ML editor! Also, apologies: the
3/24/25
Lucian Smith
,
Matthias König
4
1/27/25
Call for Nominations for SED-ML editors
Dear SED-ML community, Please nominate SED-ML editors using the form at:https://forms.gle/
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Call for Nominations for SED-ML editors
Dear SED-ML community, Please nominate SED-ML editors using the form at:https://forms.gle/
1/27/25
David Nickerson
12/19/24
Fwd: Join us at HARMONY 2025: Advancing Computational Biology Standards | April 15-18, KU Leuven
Dear colleagues, We are pleased to invite you to HARMONY 2025 a codefest-type meeting with a focus on
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Fwd: Join us at HARMONY 2025: Advancing Computational Biology Standards | April 15-18, KU Leuven
Dear colleagues, We are pleased to invite you to HARMONY 2025 a codefest-type meeting with a focus on
12/19/24
David Nickerson
6/11/24
COMBINE 2024 - Save the date
Dear Colleagues, The “Computational Modeling in Biology” Network (COMBINE) is an initiative to
unread,
COMBINE 2024 - Save the date
Dear Colleagues, The “Computational Modeling in Biology” Network (COMBINE) is an initiative to
6/11/24
Rahuman Sheriff
2/27/24
BioModels Model of the year 2024 competition
Dear Colleagues, I hope you are doing well. I am reaching out to highlight the BioModels' Model
unread,
BioModels Model of the year 2024 competition
Dear Colleagues, I hope you are doing well. I am reaching out to highlight the BioModels' Model
2/27/24
Lucian Smith
2/6/24
One new editor and one run-off election
Matthias König has been elected to be one of our two new SED-ML editors for 2024-2026.
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One new editor and one run-off election
Matthias König has been elected to be one of our two new SED-ML editors for 2024-2026.
2/6/24
Lucian Smith
1/2/24
SED-ML Level 1 Version 5
Happy New Year, everyone! This is an open call for comments on our draft specification for SED-ML
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SED-ML Level 1 Version 5
Happy New Year, everyone! This is an open call for comments on our draft specification for SED-ML
1/2/24
Lucian Smith
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
Matthias König
12/13/23
JIB "COMBINE issue" 2024: Call for specifications and papers
Hi all There will be another special issue of the Journal of Integrative Bioinformatics covering
unread,
JIB "COMBINE issue" 2024: Call for specifications and papers
Hi all There will be another special issue of the Journal of Integrative Bioinformatics covering
12/13/23
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
David Nickerson
8/14/23
Fwd: COMBINE 2023: October 5-8th, Farmington, CT
---------- Forwarded message --------- From: Blinov,Michael <bli...@uchc.edu> Date: Tue, 15 Aug
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Fwd: COMBINE 2023: October 5-8th, Farmington, CT
---------- Forwarded message --------- From: Blinov,Michael <bli...@uchc.edu> Date: Tue, 15 Aug
8/14/23