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 2025 was held at KU Leuven, Leuven, Belgium, 15-18 April 2025.
The local organizers were Liesbet Geris, Luiz Ladeira, and Bernard Staumont.
Sister Meetings
9th Disease Maps Community Meeting - DMCM2025
Simultaneously from 15th to 17th April 2025 at the same venue.
The 2025 edition of the Disease Maps Community Meeting took take place in Leuven, Belgium. This annual gathering brings together the researchers, clinicians, and domain experts involved in mapping and modelling disease mechanisms. The meeting provides a forum for exchanging best practices, sharing information, and developing tools to advance the use of systems medicine in translational medicine projects and decision making support. Building on the success of previous editions in locations like Belval, Maastricht, Sevilla, and Paris, the 2025 meeting in Leuven is attracted a diverse group of participants dedicated to furthering the understanding and application of disease maps in research and healthcare.
The DMCM2025 was held simultaneously with HARMONY 2025, in the same venue. This enhanced interaction between the COMBINE and the Disease Maps communities, fostering collaboration opportunities and networking. Coffee breaks and meals were shared between both meetings.
More information can be found here: DMCM2025.
byteMAL'25
Monday 14th April 2025
ByteMAL is a conference created by and for early-career researchers in the fields of bioinformatics and systems biomedicine and aims to provide a networking platform for knowledge and expertise exchange across borders. Aiming to vitalize communication amongst researchers from The Netherlands, Belgium, and Germany, ByteMAL has been hosted alternately by the Universities of Maastricht, Aachen, and Liege and for the first time it comes to Leuven! More information will be announced soon.
Schedule
The schedule is available below. People who have attended HARMONY in the past will know that this is inclined to change as participants make their own arrangements for conversations/discussions. A link to the editable version will be sent to the mailing list.
Schedule
Abstract book
Break out booklet
Registration for the meeting is free. Please register at the link above as soon as possible. This will help us plan the schedule and match your interests to the timing of the breakouts, etc. Note, only registered attendees will be sent information related to the meeting.
Register here. Registrations for in person participation are closed. Please use the link to register for online participation.
All attendees can suggest breakout sessions for hacking and/or detailed discussions of certain aspects of one or several of the COMBINE standard(s), metadata and semantic annotations (format-specific or overarching), application and implementations of the COMBINE standards, or any other topic relevant for the COMBINE community. The topics for those breakout sessions, and the time slots which would suit their communities can be submitted via the link above. Note, breakout session organizers will be responsible for creating and hosting their own online sessions, if required.
Submit your breakout session and tutorial proposal here.
Requests for a lightning talk (5 min max.) and/or poster can be submitted via the link above. Please use several forms if you want to submit abstracts on different topics. The submission deadline is outlined above. Talks will take place during the community session and posters will be displayed throughout the meeting.
Submit your lightning talks and posters here
Topics of Interest
- Data exchange, pipelines and model standards for systems and synthetic biology
- Visualization and graphical notation standards for systems and synthetic biology
- Standards for sharing and analyzing biological pathway data
- Standards for computational biological models and modelling support
- Metadata description and model annotation in COMBINE standard formats
- Implementation of COMBINE standards in tools, databases and other resources
- Integrated model and data management for systems and synthetic biology
- Standardization of Artificial Intelligence approaches in biological modelling
- Emerging standardization needs and multicellular modeling
- Community aspects of COMBINE
Workshop Location
HARMONY 2025 will be held at KU Leuven - Katholieke Universiteit Leuven
Ghb - Onderwijs en Navorsing 2
ON2 Herestraat 49
3000 Leuven - Belgium
Building number: 402-18
Arrival and Transportation
From Brussels-Zaventem Airport (BRU) you can take a train at the airport station to Leuven Central Station and then a bus at the bus station in front of the train station. The R90 should take around 14min to arrive at the Leuven Gasthuisberg Campus stop, just in front of the venue.
From Brussels South-Charleroi Airport (CRL) you can take a bus, taxi or shuttle to Charleroi Central train station and take a train to Leuven from there. Shuttles to Midi (Zuid) station in Brussels and then a train to Leuven from there is also an option.
Leuven is a very cyclable city. If you come by train or car you can bring your bike and enjoy the beautiful city!
Accommodations and meals
Hotel Mille Colonnes
Martelarenplein 5, 3000 Leuven, Belgium
In front of the train station, easy access to the bus station.
Distance to the conference venue: 14 min by bus, 14 min by bike, 45 min walking.
ibis Leuven Centrum
Brusselsestraat 52, 3000 Leuven, Belgium
At the core of the city center, easy access to bus stops.
Distance to the conference venue: 13 min by bus. 9 min by bike. 28 min walking.
Other accommodations options can be found on Booking.com and Airbnb (specially if you want to stay closer to the venue).
Tea and coffee will be freely available throughout the meeting. In view of the number of people using the building, it may be advisable to bring your own mug!
A sandwich lunch will also be provided - please make sure you give us the correct information as to which days you will be in attendance and any dietary requirements when you fill in the registration form.
Power outlet
E-type plugs are used in Belgium.
Support
Interested in sponsoring our meeting? Please contact Luiz Ladeira for details.
Attendees - in person
| Name | Organization | Interests |
|---|
| Lorenzo Veschini | King’s College London, Indiana University Bloomington | COMBINE Archive, Multicellular modeling; Building Immune Digital Twins |
| Anna Niarakis | University of Toulouse, MCD-CBI, CNRS | COMBINE Archive, Multicellular modeling, SBML, SED-ML, SBML QUAL; Building Immune Digital Twins; CoLoMoTo |
| Matthias König | Humboldt-University Berlin, Systems Medicine of the Liver | COMBINE Archive, Multicellular modeling, OMEX Metadata, SBGN, SBML, SED-ML, PE-TAB, FROG; SBML4Humans, libroadrunner |
| Carissa Bleker | National Institute of Biology | COMBINE Archive, SBGN, SBML, SED-ML, SBML-qual; https://nib-si.github.io/BoolDog/ |
| Alan Garny | University of Auckland | CellML, COMBINE Archive, Multicellular modeling, OMEX Metadata, SED-ML; libCellML, libOpenCOR, and OpenCOR |
| Frank T. Bergmann | BioQUANT / Heidelberg University | COMBINE Archive, SBML, SED-ML, PE-TAB, FROG; COPASI (https://copasi.org), basico (http://basico.readthedocs.io/), libsbml |
| Te Chen | Novo Nordisk Foundation Center for Biosustainability | CellML, SBML |
| Rahuman Sheriff | European Bioinformatics Institute (EMBL-EBI) | CellML, COMBINE Archive, Multicellular modeling, OMEX Metadata, SBGN, SBML, SED-ML, PE-TAB, FROG; EFECT stocastic simulation reproducibility |
| T.J. Sego | University of Florida | Multicellular modeling, SBML, SED-ML, PE-TAB |
| Charl Linssen | Jülich Supercomputing Centre; RWTH Aachen | CellML, NeuroML, SBML, SED-ML; NESTML domain-specific modeling language and code generator - https://nestml.readthedocs.org/ ; Automatic analysis and solver generation for dynamical systems simulation - https://ode-toolbox.readthedocs.org/ |
| Brett Olivier | Vrije Universiteit Amsterdam | COMBINE Archive, SBML, SED-ML, FROG |
| Alessio Gamba | University of Liege | BioPAX, CellML, SBGN, SBML; ONTOX project. Information about the project available at https://ontox-project.eu/project/ |
| Hugh Sorby | Auckland Bioengineering Institute | CellML, COMBINE Archive, SBML, SED-ML |
| David Nickerson | Auckland Bioengineering Institute, University of Auckland | CellML, COMBINE Archive, Multicellular modeling, OMEX Metadata, SED-ML, PE-TAB, Repositories, publishing; Center for Reproducible Biomedical Modeling; Physiome / Virtual Physiological Human; Physiome Model Repository; SPARC |
| Nguyen Tung | EMBL-EBI | COMBINE Archive, Multicellular modeling, OMEX Metadata, SBGN, SBML, SED-ML, FROG; BioModels is a repository of mathematical models of biological and biomedical systems. It hosts a vast selection of existing literature-based physiologically and pharmaceutically relevant mechanistic models in standard formats. http://biomodels.org |
| Tomas Kulhanek | VITO | CellML, SBML; Physiolibrary, Pharmacolibrary, https://www.physiolibrary.org |
| Crawley Francis P. | Committee on Data (CODATA), International Science Council (ISC) | CellML, NeuroML, OMEX Metadata; Engaged with the EU-funded ‘Developing an advanced and secure environment for data visitation across the RDA (DV4RDA) as part of the EOSC-Future/RDA Artificial Intelligence and Data Visitation Working Group. |
| Chris Myers | University of Colorado Boulder | SBML, SBOL and SBOL Visual, SED-ML; iBioSim, SynBioHub, and SynBioSuite |
| Jacob Barhak | Jacob Barhak Analytics | SBML; The Reference Model for Disease Progression: https://simtk.org/projects/therefmodel and ClinicalUnitMapping.com: https://clinicalunitmapping.com/about |
| Thomas Schueler | German Federal Institute for Risk Assessment | COMBINE Archive, OMEX Metadata, SBML, SED-ML; FSKX - FAIR Scientific Knowledge Exchange Format: standardized file format designed to facilitate the efficient sharing of scientific models and datasets (https://foodrisklabs.bfr.bund.de/fskx-food-safety-knowledge-exchange-format/); RAKIP-Initiative |
| Martin Golebiewski | HITS gGmbH | COMBINE Archive, Multicellular modeling, OMEX Metadata, SBML, ISO standards, health metadata standards; ISO/TC 276 Biotechnology; European Virtual Human Twin (EDITH); National Research Data Infrastructure for Personal Health Data (NFDI4Health) |
| Loïc Comeliau | University of Liège | Multicellular modeling, SBML |
Attendees - remote
| Name | Organization | Interests |
|---|
| Lutz Brusch | Technische Universität Dresden | OpenVT, MorpheusML, MultiCellML, SBML-spatial, PEtab-MS; Multicellular modeling, https://MultiCellML.org, MorpheusML, https://morpheus.gitlab.io, PEtab-MS, https://gitlab.com/fitmulticell/fit |
| Ilya Kiselev | Biosoft.RU | COMBINE Archive, Multicellular modeling, SBGN, SBML, SBOL and SBOL Visual, SED-ML; BioUML platform (www.biouml.rog) |
| Luna Li | University of Washington | COMBINE Archive, Multicellular modeling, OMEX Metadata, SBML, SED-ML, FROG; Working at the Center for Reproducible Biomedical Modeling on standardizing and annotating models |
| Adel Heydarabadipour | University of Washington | SBGN, SBML; Model Visualization |
| Lucian Smith | University of Washington | COMBINE Archive, Multicellular modeling, OMEX Metadata, SBML, SED-ML, FROG; I work with the Center for Reproducible Biomomedical Modeling (https://reproduciblebiomodels.org/), particularly working on Tellurium, Roadrunner, and Antimony |
| Arnau Montagud | Institute for Integrative Systems Biology (I2SysBio), CSIC-UV | CellML, COMBINE Archive, Multicellular modeling, SBML, SED-ML; EDITH, PerMedCoE |
| Rupert Overall | Humboldt University of Berlin | SBGN |
| Prashant Vaidyanathan | Oxford Biomedica | SBOL and SBOL Visual |
| Loïc Paulevé | CNRS/LaBRI, Bordeaux, France | COMBINE Archive, SED-ML; CoLoMoTo software distribution - https://colomoto.github.io/colomoto-docker/ |
| Claudine Chaouiya | I2M, Aix Marseille University | SBML, SED-ML; CoLoMoTo, GINsim |
| Sylvain Soliman | Inria | SBML, SED-ML |
| Michael Blinov | UConn Health | BioPAX, COMBINE Archive, Multicellular modeling, OMEX Metadata, SBGN, SBML, SED-ML; http://vcell.org; http://vcelldb.org; http://bnglviz.github.io; http://MolClustpy.github.io; http://SpringSaLaDpy.github.io |
| Goksel Misirli | Keele University | Multicellular modeling, OMEX Metadata, SBML, SBOL and SBOL Visual |
| Metehan Unal | Keele University | SBOL and SBOL Visual; I am a postdoctoral research associate at the School of Computer Science and Mathematics of Keele University. I am working on a BBSRC-funded project to create, visualise and validate biological designs. |
| Felipe Xavier Buson | University of Bristol | SBOL and SBOL Visual |
| Fengkai Zhang | NIH, US | COMBINE Archive, Multicellular modeling, OMEX Metadata, SBGN, SBML, SED-ML, PE-TAB |
| May Elebeoba | University of Wisconsin-Madison | Multicellular modeling, SBML, SBOL and SBOL Visual, SED-ML |
| Charalampos Katselis | None | BioPAX, CellML, COMBINE Archive, Multicellular modeling, SBML, SED-ML |
| John Gennari | University of Washington | BioPAX, CellML, COMBINE Archive, OMEX Metadata, SBML, SED-ML |
| Bhavyahshree Navaneetha Krishnan | University of Washington | BioPAX, CellML, Multicellular modeling, SBML, SED-ML |
