Harmony 2023

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 development of the 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 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, with individual breakout sessions responsible for enabling remote participation as needed.

Most of each day was scheduled by the communities as breakouts. In addition, we had some time each day for community discussion and wrap-ups of breakouts and advertisements for following breakouts.

Schedule

Here’s the full (editable) schedule. Note that many events are scheduled somewhat spontaneously at these events; keep an eye out here or on the COMBINE discord for last-minute changes and additions.

Workshop Location Details

HARMONY 2023 takes place at the University of Washington (UW, and commonly called “U-Dub”) in Seattle, Washington. HARMONY 2023 will take place in the William H. Foege Bioengineering building, at 3720 15th Ave NE, Seattle, WA 98195. The building is locked during the day, but will be open the half-hour before the meeting begins. If you arrive later than that, call the department reception at 206-685-2000, or email any of the organizers, or ping us on the COMBINE slack channel.

Foege building and map

The doors will be locked, so please knock (there’s lots of glass), call the Department front desk at (206) 685-2000 or email lpsmith@uw or bioeasst@uw.edu or ping us on the COMBINE Slack!

Arrival and Transportation

From the Seatac Airport, take the Link Light Rail north from the airport, and exit at the University of Washington station (NOT Univeristy Street Station; that’s a downtown stop). It’s a relatively short walk from there to the Bioengineering building. The nearest hotel is slightly further; a little over one mile, so you might want to bus/taxi depending on how much luggage you have. If you get an ORCA card, you can use that on any of the buses or other light rail trips you might take during your stay. There’s also a ‘Transit GO Ticket’ app you should be able to use from your phone (untested by me, but it seems reasonable?).

Hotels

The closest hotel to the Bioengineering department is the Univeristy Inn at 4140 Roosevelt Way NE, Seattle, WA 98105; it’s about a half mile walk between there and the venue. About a block further (and inexplicably slightly more expensive) is the Watertown Hotel, at 4242 Roosevelt Way NE, Seattle, WA 98105. Any hotel anywhere along the Link Light Rail line will be easy to get to/from as well, as the Univeristy of Washington station is just a half mile away from the venue.

Attendees

The following is the list of known attendees as of 24/04/2023 23:58:54 UTC (72 total registered, 63 listed below)

NameAffiliationAttendance
Eran AgmonUConn HealthIn person
Multicellular modeling, SBML, SED-ML
BioSimulators: https://biosimulators.org, Vivarium: https://vivarium-collective.github.io
Azka AhmedUW MadisonRemotely (virtually)
BioPAX, CellML, COMBINE Archive, Multicellular modeling
Daniel AjuzieWisconsin Institute for DiscoveryRemotely (virtually)
BioPAX, CellML, COMBINE Archive, Multicellular modeling, SBML, SED-ML
Our lab develops models at multiple scales ranging from gene network, metabolic network, signal transduction to multicellular models. We model individual cells (bacteria and mammalian) and interactions between cells (microbial and host-microbe).
Steve AndrewsUWIn person

Spatial modeling, including particularly with the Smoldyn package.
Mihail AntonNBIS, SciLifeLab, Chalmers University of TechnologyRemotely (virtually)
COMBINE Archive, OMEX Metadata, SBGN, SBML
standard-GEM
Bryan BartleyRaytheon BBNIn person
SBOL and SBOL Visual
Jacob BealRaytheon BBNIn person
SBOL and SBOL Visual
Frank BergmannHeidelberg UniversityIn person
COMBINE Archive, SBGN, SBML, SED-ML
COPASI (copasi.org), basico (basico.rtfd.io), libsbml, libsedml, libcombine
Lutz BruschTechnische Universität Dresden, GermanyRemotely (virtually)
Multicellular modeling, SBML
COMBINE Archive and OMEX, PEtab, MorpheusML, SBML-Spatial, FAIRSPACE, https://www.MultiCellML.org
Lukas BuecherlUniversity of Colorado BoulderIn person
COMBINE Archive, SBML, SBOL and SBOL Visual, SED-ML
Genetic Design Automation
Kevin ChenUniversity of WashingtonIn person
BioPAX, CellML, COMBINE Archive, NeuroML, OMEX Metadata, SBML, SED-ML
Rafael CostaFCT-NOVA, NOVA School of Science and TechnologyRemotely (virtually)
COMBINE Archive, SBML
Alan GarnyUniversity of AucklandIn person
CellML, COMBINE Archive, Multicellular modeling, OMEX Metadata, SED-ML
libOpenCOR and OpenCOR
Tom GebhardtUniversity of GreifswaldRemotely (virtually)
CellML, COMBINE Archive, SBGN, SBML
John GennariU of WashingtonIn person
BioPAX, CellML, OMEX Metadata, SBML, SBOL and SBOL Visual, SED-ML
James GlazierIndiana UniversityRemotely (virtually)
COMBINE Archive, Multicellular modeling, SBML
Replication and annotation of multicellular models
Issa GnassePasteur Institute of DakarIn person
Multicellular modeling, OMEX Metadata
Application of Machine learning to find early biomarker in cervical cancer.
Misirli GokselKeele UniversityRemotely (virtually)
COMBINE Archive, OMEX Metadata, SBML, SBOL and SBOL Visual
Jenn HadlockInsitute for Systems BiologyRemotely (virtually)
BioPAX, OMEX Metadata, SBML
NCATS Biomedical Translator
Joseph HellersteineScience Institute, University of WashingtonIn person
COMBINE Archive, SBML
VSCode-Antimony smart editor, AMAS (Automated Model Annotation System)
Ron HenkelMedical Informatics Laboratory, Institute for Community Medicine, University Medicine GreifswaldIn person
CellML, COMBINE Archive, SBGN, SBML
FAIR
Adel HeydarabadipourUniversity of WashingtonIn person
Multicellular modeling, SBGN, SBML, SBOL and SBOL Visual
Yan-kay HoUniversity of CambridgeRemotely (virtually)
SBML, SBOL and SBOL Visual
https://openbioeconomy.org/research_categories/toolkits/ https://github.com/openplant/openplant_automation_protocols
Diego JahnCenter for Information Services and High Performance Computing (ZIH), TU Dresden, GermanyRemotely (virtually)
Multicellular modeling, MultiCellML, MorpheusML
Morpheus (https://morpheus.gitlab.io/), MorpheusML Model Repository (https://morpheus.gitlab.io/model/)
Bart JardineUniversity of WashingtonIn person
COMBINE Archive, Multicellular modeling, OMEX Metadata, SBML, SED-ML
Chemical network modeling software and support for SBML
Paul jonas JostUniversity of BonnRemotely (virtually)
COMBINE Archive, SBGN, SBML
pyPESTO, petab
Jonathan KarrFormic LabsRemotely (virtually)
COMBINE Archive, OMEX Metadata, SBML, SED-ML
BioSimulators, BioSimulations
Sarah KeatingUCLRemotely (virtually)
SBML
Carlos LopezAltos LaboratoriesRemotely (virtually)
Multicellular modeling, SBML, models as computer programs
PySB, PyDREAM, PyViPR, all things multiscale modeling
Augustin LunaHarvard Medical SchoolRemotely (virtually)
BioPAX, OMEX Metadata, SBGN, SBOL and SBOL Visual
Pathway Commons (pathwaycommons.org); SBGN (sbgn.org); libsbgn (github.com/sbgn/libsbgn); stonpy (github.com/adrienrougny/stonpy)
Karin LundengårdAuckland Bioengineering InstituteRemotely (virtually)
Harvey ManneringUCLIn person
NeuroML, SBML, SED-ML
Tools and standards for single-cell modeling in neuroscience. Currently involved in the ongoing development of libSBML
Elebeoba MayUniversity of Wisconsin-MadisonRemotely (virtually)
BioPAX, CellML, COMBINE Archive, Multicellular modeling, SBML, SED-ML
My lab develops models at multiple scales ranging from gene network, metabolic network, signal transduction to multicellular models. We model individual cells (bacteria and mammalian) and interactions between cells (microbial and host-microbe).
Gerhard MayerHITS gGmbHRemotely (virtually)
BioPAX, CellML, COMBINE Archive, Multicellular modeling, NeuroML, OMEX Metadata, SBGN, SBML, SBOL and SBOL Visual, SED-ML, identifiers.org
EDITH (European Virtual Human Twin project)
Pedro MendesUConn HealthRemotely (virtually)
OMEX Metadata, SBML, SED-ML
COPASI
Blinov MichaelUConn HealthRemotely (virtually)
BioPAX, COMBINE Archive, Multicellular modeling, OMEX Metadata, SBGN, SBML, SED-ML
VCell, BioNetGen, SBML
Tom MitchellRaytheon BBN TechnologiesRemotely (virtually)
SBOL and SBOL Visual
pySBOL3, SBOL-utilities
Ion MoraruUConn HealthIn person
COMBINE Archive, Multicellular modeling, SBML, SED-ML
http://vcell.org/, http://biosimulations.org/
Sébastien MorettiSIB Swiss Institute of BioinformaticsRemotely (virtually)
SBML
https://www.metanetx.org/
Robert MuellerTU DresdenRemotely (virtually)
Multicellular modeling, Morpheus
Chris MyersUniversity of Colorado BoulderIn person
COMBINE Archive, SBML, SBOL and SBOL Visual, SED-ML
SynBioHub, SynBioSuite, iBioSim
David NickersonAuckland Bioengineering Institute, University of AucklandIn person
CellML, COMBINE Archive, OMEX Metadata, SED-ML
Physiome Model Repository; Center for Reproducible Biomedical Modeling; Physiome journal
Alexander PatrieUconn HealthRemotely (virtually)
COMBINE Archive, OMEX Metadata, SBML, SED-ML
Biosimulators: https://www.biosimulators.org
Tim Rudgenewcastle universityRemotely (virtually)
Multicellular modeling, SBML, SBOL and SBOL Visual, SED-ML
Flapjack, LOICA
Sai SamineniUniversity of Colorado BoulderRemotely (virtually)
SBOL and SBOL Visual, LabOp
LabOp, Army Data Standards
Jim SchaffUConn HealthRemotely (virtually)
COMBINE Archive, Multicellular modeling, OMEX Metadata, SBML, SED-ML
SBML Spatial
T.j. SegoUniversity of FloridaIn person
CellML, COMBINE Archive, Multicellular modeling, SBGN, SBML, SED-ML
CompuCell3D, Tellurium, Tissue Forge
Bilal ShaikhDeepOriginRemotely (virtually)
CellML, COMBINE Archive, Multicellular modeling, OMEX Metadata, SBML, SED-ML
Biosimulations
Rahuman SheriffEMBL-EBIRemotely (virtually)
CellML, COMBINE Archive, Multicellular modeling, OMEX Metadata, SBGN, SBML, SED-ML, FROG
SBML, BioModels, FROG, FAIRSPACE
Woosub ShinUniversity of AucklandRemotely (virtually)
COMBINE Archive, OMEX Metadata, SBML
Lucian SmithUniversity of WashingtonIn person
CellML, COMBINE Archive, Multicellular modeling, OMEX Metadata, SBML, SED-ML
Antimony, Tellurium
Hugh SorbyAuckland Bioengineering InstituteIn person
CellML, COMBINE Archive, SED-ML
Ryan SpanglerAltos LabsIn person
Multicellular modeling
Vivarium
Jörn StarrußTechnische Universität DresdenRemotely (virtually)
COMBINE Archive, Multicellular modeling, SBML, SED-ML
Nguyen TungEMBL-EBIRemotely (virtually)
BioPAX, COMBINE Archive, Multicellular modeling, OMEX Metadata, SBGN, SBML, SED-ML
BioModels, COMBINE Archive 2.0
Lorenzo VeschiniKing’s Collge LondonRemotely (virtually)
Multicellular modeling, OMEX Metadata, SBML
Gonzalo andrés Vidal peñaNewcastle UniversityRemotely (virtually)
SBOL and SBOL Visual
https://github.com/RudgeLab/PUDU https://github.com/RudgeLab/LOICA
Carolus VitalisUniversity of Colorado BoulderRemotely (virtually)
SBOL and SBOL Visual
Khoi VoUniversity of California, RiversideIn person
BioPAX, CellML, COMBINE Archive, Multicellular modeling, NeuroML, OMEX Metadata, SBGN, SBML, SBOL and SBOL Visual, SED-ML
Multiscale modeling of blood clot
Daniel WeindlHelmholtz MunichRemotely (virtually)
SBML, SED-ML, PEtab
https://github.com/AMICI-dev/AMICI/ https://github.com/ICB-DCM/pyPESTO/ https://petab.readthedocs.io/en/latest/
Felipe Xavier busonCambridge UniversityRemotely (virtually)
SBOL and SBOL Visual
Guillermo Yanez feliuNewcastle UniversityRemotely (virtually)
Multicellular modeling, Flapjack
Multicellular pattern formation, computational synthetic biology, microscopy, microfluidics and image analysis.
Fengkai ZhangNIAID/NIHIn person
COMBINE Archive, Multicellular modeling, SBGN, SBML, SED-ML
Simmune