The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats in systems biology, synthetic biology, and related fields.
HARMONY is a codefest-type meeting, with a focus on the development of standards, interoperability, and infrastructure. There are generally not many general discussions or oral presentations during HARMONY; instead, the time is devoted to allowing hands-on hacking and interaction between people focused on the practical development of software and standards.
HARMONY 2023 was hosted by Herbert Sauro and the Center for Reproducible Biomedical Modeling at the University of Washington, Seattle, WA. It was organized primarily as an in-person meeting but included individual breakout sessions responsible for enabling remote participation as needed.
Most of each day was scheduled by the communities as breakouts, with lightning talks scheduled on the first day. Posters were displayed for the duration of the meeting. In addition, each day included time for community discussion and wrap-ups of breakouts and advertisements for following breakouts
Please see the full event schedule and videos below.
Monday – April 24
| Monday | |||
| (PDT // UTC-7) | Track A: Room 130 | Track B: Room 230 | Track C: Room 303 |
| 08:30 – 9:00 |
Welcome
Invited presentation & lightning talks |
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| 9:00 – 9:30 | |||
| 9:30 – 10:00 | |||
| 10:00-10:30 | |||
| 10:30-11:00 | Morning tea | ||
| 11:00-11:30 |
SBOL Ontology Terms
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* FROG based curation of constraint-based models and manuscript preparation
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| 11:30-12:00 | |||
| 12:00-12:30 | |||
| 12:30-1:00 (13:00) |
Lunch
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| 1:00-1:30 (13:00-13:30) | |||
| 1:30-2:00 (13:30-14:00) | |||
| 2:00-2:30 (14:00-14:30) | |||
| 2:30-3:00 (14:30-15:00) |
Layout and render breakout
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SEED Tutorial Prepation
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libOmexMeta support for CellML 2.0
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| 3:00-3:30 (15:00-15:30) | |||
| 3:30-4:00 (15:30-16:00) | |||
| 4:00-4:30 (16:00-16:30) | Afternoon tea | ||
| 4:30-5:00 (16:30-17:00) | Wrapups (Room 130) |
SBOL Hackathons
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| 5:00-5:30 (17:00-17:30) | |||
| 5:30-6:00 (17:30-18:00) | |||
| 6:00-6:30 (18:00-18:30) | |||
Tuesday – April 25
| Tuesday | |||
| (PDT // UTC-7) | Track A: Room 130 | Track B: Room 230 | Track C: Room 403 |
| 08:30 – 9:00 |
Welcome and Breakout Introductions (Room 130)
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| 9:00 – 9:30 |
Human-friendly JSON for RDF Objects
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* FAIRSPACE – a community infrastructure for validation, execution and FAIR sharing of multiscale multicellular virtual tissue simulation
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| 9:30 – 10:00 | |||
| 10:00-10:30 | |||
| 10:30-11:00 | Morning tea | ||
| 11:00-11:30 |
Choosing annotation resources: Kegg, CheBI, UniProt, BioCyc… ?
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SBOL tools and best practices
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Rule-based modeling and SBML Multi Package
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| 11:30-12:00 | |||
| 12:00-12:30 | |||
| 12:30-1:00 (13:00) |
Lunch
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| 1:00-1:30 (13:00-13:30) | |||
| 1:30-2:00 (13:30-14:00) | |||
| 2:00-2:30 (14:00-14:30) | |||
| 2:30-3:00 (14:30-15:00) |
SED-ML Workshop
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Identity aliases for SBOL
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| 3:00-3:30 (15:00-15:30) | |||
| 3:30-4:00 (15:30-16:00) | |||
| 4:00-4:30 (16:00-16:30) | Afternoon tea | ||
| 4:30-5:00 (16:30-17:00) | Wrapups (Room 130) | ||
| 5:00-5:30 (17:00-17:30) |
SED-ML Workshop
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SBOL Hackathons
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| 5:30-6:00 (17:30-18:00) | |||
| 6:00-6:30 (18:00-18:30) | |||
Wednesday – April 26
| Wednesday | |||
| (PDT // UTC-7) | Track A: Room 130 | Track B: Room 230 | Track C: Room 403 |
| 08:30 – 9:00 |
Welcome and Breakout Introductions (Room 130)
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| 9:00 – 9:30 |
FAIR indicators and evaluation tool of COMBINE archives
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Community outreach & SBOL industrial engagement
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* FAIRSPACE – a community infrastructure for validation, execution and FAIR sharing of multiscale multicellular virtual tissue simulation
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| 9:30 – 10:00 | |||
| 10:00-10:30 | |||
| 10:30-11:00 | Morning tea | ||
| 11:00-11:30 |
FAIR indicators and evaluation tool of COMBINE archives
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SBOL Community Media and Developer Documentation
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Rule-based modeling and SBML Multi Package
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| 11:30-12:00 | |||
| 12:00-12:30 | |||
| 12:30-1:00 (13:00) | |||
| 1:00-1:30 (13:00-13:30) |
Lunch
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| 1:30-2:00 (13:30-14:00) | |||
| 2:00-2:30 (14:00-14:30) | |||
| 2:30-3:00 (14:30-15:00) |
Biosimulations Workshop
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SBOL Hackathons
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Updating / fixing the biomodels.net qualifiers web pages
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| 3:00-3:30 (15:00-15:30) | |||
| 3:30-4:00 (15:30-16:00) | |||
| 4:00-4:30 (16:00-16:30) | Afternoon tea | ||
| 4:30-5:00 (16:30-17:00) | Wrapups (Room 1) | ||
| 5:00-5:30 (17:00-17:30) |
Spatial Visualization Workshop
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SBOL Hackathons
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libCellML 1.0
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| 5:30-6:00 (17:30-18:00) | |||
| 6:00-6:30 (18:00-18:30) | |||
Thursday – April 27
| Thursday | |||
| (PDT // UTC-7) | Track A: Room 130/303 | Track B: Room 230 | Track C: 403 |
| 08:30 – 9:00 |
Welcome and Breakout Introductions (Room 130)
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| 9:00 – 9:30 |
Python Tools for the COMBINE community
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Integration of experimental data and data management with SBOL
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* FAIRSPACE – a community infrastructure for validation, execution and FAIR sharing of multiscale multicellular virtual tissue simulation
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| 9:30 – 10:00 | |||
| 10:00-10:30 | |||
| 10:30-11:00 | Morning tea | ||
| 11:00-11:30 |
Python Tools for the COMBINE community
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Migration issues from SBOL2 to SBOL3
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| 11:30-12:00 | |||
| 12:00-12:30 | |||
| 12:30-1:00 (13:00) |
Lunch
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| 1:00-1:30 (13:00-13:30) | |||
| 1:30-2:00 (13:30-14:00) | |||
| 2:00-2:30 (14:00-14:30) | |||
| 2:30-3:00 (14:30-15:00) |
SBOL Hackathons
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| 3:00-3:30 (15:00-15:30) | |||
| 3:30-4:00 (15:30-16:00) | |||
| 4:00-4:30 (16:00-16:30) | Afternoon tea | ||
| 4:30-5:00 (16:30-17:00) | Wrapups (Room 1) | ||
| 5:00-5:30 (17:00-17:30) |
SBOL Hackathons
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| 5:30-6:00 (17:30-18:00) | |||
| 6:00-6:30 (18:00-18:30) | |||