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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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David Nickerson
2
Sep 17
COMBINE 2025 - registration updates, confirmed speakers, and travel funding
Hi all, Please note that further information has now been added to the COMBINE 2025 website (https://
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COMBINE 2025 - registration updates, confirmed speakers, and travel funding
Hi all, Please note that further information has now been added to the COMBINE 2025 website (https://
Sep 17
David Nickerson
Jun 17
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
Jun 17
Lucian Smith
May 19
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://
May 19
Lucian Smith
Apr 17
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/
Apr 17
Lucian Smith
Apr 17
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
Apr 17
Rahuman Sheriff
Apr 8
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
Apr 8
Lucian Smith
, …
David Nickerson
5
Apr 7
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/
Apr 7
Lucian Smith
Mar 31
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
Mar 31
Lucian Smith
3
Mar 24
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
Mar 24
Lucian Smith
,
Matthias König
4
Jan 27
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/
Jan 27
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
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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
unread,
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
Lucian Smith
2
5/24/23
HARMONY proposal #1: new KiSAO terms for multiple algorithms in one SED-ML file
These are now implemented in KiSAO, as 694 for 'ODE Solver' (with 'CVODE-like method'
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HARMONY proposal #1: new KiSAO terms for multiple algorithms in one SED-ML file
These are now implemented in KiSAO, as 694 for 'ODE Solver' (with 'CVODE-like method'
5/24/23
Lucian Smith
5/2/23
HARMONY proposal #3: 'quick' L1v5 with generic Tasks and Changes.
One final suggestion, this from Frank. It would require an L1v5 release of SED-ML, but is fairly
unread,
HARMONY proposal #3: 'quick' L1v5 with generic Tasks and Changes.
One final suggestion, this from Frank. It would require an L1v5 release of SED-ML, but is fairly
5/2/23
Lucian Smith
5/2/23
HARMONY proposal #2: figure out KiSAO term for deriving absolute tolerances
I recently discovered that COPASI does not actually use the value it calls 'absolute tolerance
unread,
HARMONY proposal #2: figure out KiSAO term for deriving absolute tolerances
I recently discovered that COPASI does not actually use the value it calls 'absolute tolerance
5/2/23
Rahuman Sheriff
4/28/23
Fwd: Invitation: Global Alliance for Immune Prediction and Intervention
Dear COMBINE/SBML/SED-ML community members, This could be an interesting initiative and it will be
unread,
Fwd: Invitation: Global Alliance for Immune Prediction and Intervention
Dear COMBINE/SBML/SED-ML community members, This could be an interesting initiative and it will be
4/28/23
David Nickerson
2
3/29/23
HARMONY 2023 - registration now open!
Hi all, Just a reminder of the upcoming deadlines to submit abstracts and breakouts for HARMONY 2023
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HARMONY 2023 - registration now open!
Hi all, Just a reminder of the upcoming deadlines to submit abstracts and breakouts for HARMONY 2023
3/29/23
David Nickerson
2/15/23
Invitation to hackathons on FAIR model indicators (Feb 17-Mar 3)
Dear all, Some of you might remember the Workshop on FAIR indicators that we ran in Berlin 2022
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Invitation to hackathons on FAIR model indicators (Feb 17-Mar 3)
Dear all, Some of you might remember the Workshop on FAIR indicators that we ran in Berlin 2022
2/15/23
Lucian Smith
2/13/23
SED-ML Editor results: Eran Agmon and David Nickerson
Congratulations to Eran Agmon and David Nickerson, who received the most votes for the election of
unread,
SED-ML Editor results: Eran Agmon and David Nickerson
Congratulations to Eran Agmon and David Nickerson, who received the most votes for the election of
2/13/23
Lucian Smith
3
2/6/23
Call for Votes: SED-ML Editors for 2023-2025
This is the final reminder for the call for votes in the election of two SED-ML editors to replace
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Call for Votes: SED-ML Editors for 2023-2025
This is the final reminder for the call for votes in the election of two SED-ML editors to replace
2/6/23
Frank Bergmann
2
12/22/22
Call for Nominations for SED-ML editors
Dear SED-ML community, this is a reminder, that we are currently looking for nominations for two new
unread,
Call for Nominations for SED-ML editors
Dear SED-ML community, this is a reminder, that we are currently looking for nominations for two new
12/22/22
David Nickerson
12/14/22
Fwd: [sbml-discuss] Survey about research software
---------- Forwarded message --------- From: Michael Hucka <mhu...@library.caltech.edu> Date:
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Fwd: [sbml-discuss] Survey about research software
---------- Forwarded message --------- From: Michael Hucka <mhu...@library.caltech.edu> Date:
12/14/22
Rahuman Sheriff
11/21/22
BioModels - Model of the Year Competition 2023
Dear community members, We launched 'Model of the year' competition 2023 at ICSB2022 Berlin
unread,
BioModels - Model of the Year Competition 2023
Dear community members, We launched 'Model of the year' competition 2023 at ICSB2022 Berlin
11/21/22