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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
Jun 11
COMBINE 2024 - Save the date
Dear Colleagues, The “Computational Modeling in Biology” Network (COMBINE) is an initiative to
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COMBINE 2024 - Save the date
Dear Colleagues, The “Computational Modeling in Biology” Network (COMBINE) is an initiative to
Jun 11
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
Lucian Smith
Feb 6
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.
Feb 6
Lucian Smith
Jan 16
Call for Votes: SED-ML Editors for 2024-2026
Dear all, This is a call for votes in the election of two SED-ML editors to replace Jonathan Karr and
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Call for Votes: SED-ML Editors for 2024-2026
Dear all, This is a call for votes in the election of two SED-ML editors to replace Jonathan Karr and
Jan 16
Lucian Smith
Jan 2
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
Jan 2
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
Lucian Smith
,
Matthias König
3
12/10/23
Call for Nominations for SED-ML editors
Whoops! Re-activated. Nominate away! -Lucian On Sun, Dec 10, 2023 at 8:16 AM 'Matthias König'
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Call for Nominations for SED-ML editors
Whoops! Re-activated. Nominate away! -Lucian On Sun, Dec 10, 2023 at 8:16 AM 'Matthias König'
12/10/23
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
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
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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
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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
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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
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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
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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
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BioModels - Model of the Year Competition 2023
Dear community members, We launched 'Model of the year' competition 2023 at ICSB2022 Berlin
11/21/22
Lucian Smith
10/28/22
My SED-ML Level 2 Proposal
(Note: I'm posting this both here and on the SED-ML Issue Tracker at https://github.com/SED-ML/
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My SED-ML Level 2 Proposal
(Note: I'm posting this both here and on the SED-ML Issue Tracker at https://github.com/SED-ML/
10/28/22
Lucian Smith
9/30/22
SED-ML L2 Discussion
Hello, everyone! We're having a breakout session at COMBINE next week on Thursday at 9:00 AM
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SED-ML L2 Discussion
Hello, everyone! We're having a breakout session at COMBINE next week on Thursday at 9:00 AM
9/30/22
David Nickerson
9/14/22
Fwd: COMBINE 2022 registration reminder and abstract submission for posters still open
Hi all, COMBINE 2022 is being held Oct 6-8 at Humboldt University of Berlin, Philippstraße 13, Haus
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Fwd: COMBINE 2022 registration reminder and abstract submission for posters still open
Hi all, COMBINE 2022 is being held Oct 6-8 at Humboldt University of Berlin, Philippstraße 13, Haus
9/14/22
David Nickerson
8/26/22
Fwd: COMBINE 2022 and ICSB - abstract submission deadline extended, preliminary program available
Hi all, To bring COMBINE 2022 (https://combine-org.github.io/events/) into alignment with the
unread,
Fwd: COMBINE 2022 and ICSB - abstract submission deadline extended, preliminary program available
Hi all, To bring COMBINE 2022 (https://combine-org.github.io/events/) into alignment with the
8/26/22
David Nickerson
7/26/22
COMBINE 2022 in Berlin this October
Hi all, The plans for COMBINE 2022 are coming together. You can find details here: https://combine-
unread,
COMBINE 2022 in Berlin this October
Hi all, The plans for COMBINE 2022 are coming together. You can find details here: https://combine-
7/26/22
Matthias König
5/31/22
COMBINE 2022 - Save the date: 6-8 Oct, Berlin
Join us in October for our annual COMBINE Meeting! Save the Date: October, 6-8 (THU-SAT) Co-located
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COMBINE 2022 - Save the date: 6-8 Oct, Berlin
Join us in October for our annual COMBINE Meeting! Save the Date: October, 6-8 (THU-SAT) Co-located
5/31/22
Lucian Smith
4/25/22
Breakout at HARMONY
Hey, everyone! There's a breakout on SED-ML during HARMONY at 9:45 Eastern. Come discuss the
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Breakout at HARMONY
Hey, everyone! There's a breakout on SED-ML during HARMONY at 9:45 Eastern. Come discuss the
4/25/22
Matthias König
3/31/22
HARMONY 2022 - lightning talks submission deadline extended until Monday, April 4
Hi all, The deadline to submit lightning talks for HARMONY 2022 has been extended until Monday.
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HARMONY 2022 - lightning talks submission deadline extended until Monday, April 4
Hi all, The deadline to submit lightning talks for HARMONY 2022 has been extended until Monday.
3/31/22
Matthias König
2/28/22
HARMONY 2022 (26-30 April)
Dear all, Save the date for HARMONY 2022! Date: 26-30 April 2022 Place: Washington, DC (USA) - Hybrid
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HARMONY 2022 (26-30 April)
Dear all, Save the date for HARMONY 2022! Date: 26-30 April 2022 Place: Washington, DC (USA) - Hybrid
2/28/22