HARMONY 2024
Conference Date
8-11 April, 2024Conference Location
UCL, London, UKImportant Dates
Breakouts and tutorials submission deadline
NOW CLOSEDNotification of acceptance for breakout and tutorials
3 Apr, 2024Lightning talk and poster submission deadline
NOW CLOSEDNotification of acceptance for lightning talks and posters
3 Apr, 2024Travel support applications NOW CLOSED
Notification of travel support awards
21 February, 2024Important Links
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 2024 will be held at University College London
Local organizers are Sarah Keating (s.keating@ucl.ac.uk) and Padraig Gleeson, (p.gleeson@ucl.ac.uk).
Workshop Location
HARMONY 2024 will be held at Centre For Medical Image Computing, University College London, 90 High Holborn, London, WC1V 6LJ.
On entering the building turn left to find the reception desk which is hidden away in the left hand corner. The receptionist will let you through to the lifts to the first floor, where somebody will be waiting to let you in.
You should have received an invitation to the meeting mailing list harmony_2024 @ googlegroups.com which will be used for communications.
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.
Arrival and Transportation
London is served by six international airports and twelve major stations including St. Pancras International, which is the Eurostar hub, with multiple direct connections to Europe.
Travel within London can be done by Tube, Bicycle, Bus, Taxi and more. More information can be found here.
Accommodations and meals
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 when you fill in the registration form.
Visa
Given that the UK is no longer part of the EU, visa requirements may have changed for you. Please check here. If you need a letter to support your application, please contact one of the organizers.
Additionally, if you need confirmation that a talk/poster/breakout session will be accepted before the confirmation deadline, please get in contact.
Power outlet
G-type plugs are used in the UK.
Support
This meeting has been generously supported by the Kavli Foundation.
Attendees - in person
| Name | Organization | Interests |
|---|---|---|
| Alex Fedorec | UCL | COMBINE Archive, Multicellular modeling, SBML, SBOL and SBOL Visual, SED-ML |
| Ankur Sinha | UCL | CellML, COMBINE Archive, Multicellular modeling, NeuroML, OMEX Metadata, SBML, SED-ML, Open Source Brain: https://opensourcebrain.org |
| Augustin Luna | National Library of Medicine | BioPAX, SBGN, SBML, sbgn.org; pathwaycommons.org |
| Carolus Vitalis | University of Colorado Boulder | SBOL and SBOL Visual |
| Casey Chen | UCL | Multicellular modeling, SBML, SBOL and SBOL Visual |
| Chris Barnes | UCL | Multicellular modeling, SBML, SBOL and SBOL Visual |
| Chris Myers | CU Boulder | COMBINE Archive, SBML, SBOL and SBOL Visual, SED-ML, iBioSim, SynBioHub, SBOLCanvas |
| Dilan Pathirana | University of Bonn | CellML, SBML, SED-ML, PE-TAB, PEtab extensions (timecourses, model selection, NLME) |
| Eleonora Bernasconi | University of Herfordshire, Hatfield, Hertfordshire, AL10 9AB, UK | NeuroML, I am a PhD student working on a large scale, biologically realistic model of the cerebellar cortex. |
| Fabian Fröhlich | The Francis Crick Institute | BioPAX, SBML, PE-TAB |
| Felipe Xavier Buson | Universit of Cambridge | SBOL and SBOL Visual |
| Fengkai Zhang | NIH | COMBINE Archive, Multicellular modeling, OMEX Metadata, SBGN, SBML, SED-ML, Simmune. SBML-Multi and rule-based model |
| Frank Bergmann | BioQUANT, Heidelberg University, INF 267 | COMBINE Archive, SBML, SED-ML, PE-TAB, FROG, COPASI - modeling, simulation and analysis environment for biochemical networks, https://copasi.org. basico - a convenient python interface to COPASI, https://basico.rtfd.io/ |
| Georgie Sorensen | University of Bristol | SBOL and SBOL Visual |
| Goksel Misirli | Keele University, School of Computer Science and Mathematics | Multicellular modeling, OMEX Metadata, SBML, SBOL and SBOL Visual, SBOL3 Java Library |
| Gonzalo Vidal | University of Colorado Boulder, Boulder, Colorado, US | SBML, SBOL and SBOL Visual, https://gonza10v.github.io/ |
| Hugh Sorby | Auckland Bioengineering Institute | CellML, SED-ML |
| Ion Moraru | UConn Health, Farmington, CT, USA | COMBINE Archive, NeuroML, OMEX Metadata, SBML, SED-ML, BioSimulations, VCell |
| Jörn Starruß | Technische Universität Dresden | CellML, Multicellular modeling, SBML, SED-ML, PE-TAB, MorpheusML, Morpheus, |
| Jona Leka | UCL | NeuroML |
| Kathleen Zhang | UCL | BioPAX, CellML, COMBINE Archive, Multicellular modeling, NeuroML, OMEX Metadata, SBGN, SBML, SBOL and SBOL Visual, SED-ML, PE-TAB, FROG |
| Louie Destouches | UCL | Multicellular modeling, SBML, SBOL and SBOL Visual |
| Lucian Smith | University of Washington, Seattle, WA | COMBINE Archive, Multicellular modeling, OMEX Metadata, SBML, SED-ML, FROG, Tellurium, Roadrunner, and Antimony (https://tellurium.readthedocs.io/) |
| Lukas Buecherl | University of Colorado Boulder | COMBINE Archive, SBML, SBOL and SBOL Visual, SED-ML |
| Manuel Lera Ramirez | UCL | SBOL and SBOL Visual, https://genestorian.org/ |
| Maren Philipps | University of Bonn; LIMES Institute | COMBINE Archive, Multicellular modeling, SBML, PE-TAB, PEtab, pyPESTO |
| Michael Blinov | Center for Cell Analysis and Modeling, UConn Health, Farmington, CT, USA | BioPAX, COMBINE Archive, Multicellular modeling, OMEX Metadata, SBGN, SBML, SED-ML, http://vcell.org; http://MolClustPy.github.io; http://www.ModelBricks.org/ |
| Natasa Miskov-Zivanov | University of Pittsburgh | BioPAX, COMBINE Archive, NeuroML, OMEX Metadata, SBGN, SBML, SBOL and SBOL Visual, SED-ML, BioRECIPE (melody-biorecipe.readthedocs.io); ACCORDION (melody-accordion.readthedocs.io); CLARINET (melody-clarinet.readthedocs.io) |
| Padraig Gleeson | UCL, London | CellML, Multicellular modeling, NeuroML, OMEX Metadata, SBML, SED-ML, Open Source Brain |
| Pedro Fontanarrosa | UCL | SBOL and SBOL Visual |
| Prashant Vaidyanathan | Oxford Biomedica | SBOL and SBOL Visual, SBOL focuses on standardizing biological data to support FAIR principles, enhancing data sharing and reuse in biology. If you’re interested in learning more or contributing, let’s connect! |
| Rahuman Sheriff | EMBL-EBI | COMBINE Archive, Multicellular modeling, NeuroML, OMEX Metadata, SBML, SED-ML, PE-TAB, FROG, Stochastic Reproducibility, BioModels |
| Robert Vickerstaff | UCL | NeuroML, SBML, SED-ML |
| Sarah Keating | UCL, London | NeuroML, SBML, SED-ML, FROG, CHIMERA |
| Sebastian Persson | University of Gothenburg | SBML, PE-TAB |
| Sotirios Panagiotou | Erasmus Medical Center, Rotterdam, NL | CellML, COMBINE Archive, Multicellular modeling, NeuroML, OMEX Metadata, SED-ML, VCell, EDEN neural simulator for NeuroML https://eden-simulator.org , BrainFrame for HPC in simulations https://neurocomputinglab.com/research-themes/brainframe/ |
| Stela Prins | UCL | Multicellular modeling, NeuroML, SBML, SED-ML, Metabolic modeling, COBRA |
| Subhasis Ray | Plaksha University, Alpha, Sector 101, IT City Rd, Sahibzada Ajit Singh Nagar, Punjab 140306 | CellML, NeuroML, SBML, SED-ML, Multiscale Object Oriented Simulation Environment (https://moose.ncbs.res.in) |
| Swathi Anil | Imperial College London, Bernstein Centre Freiburg | NeuroML, Large scale network modeling to study perturbation-induced connectivity changes in the brain: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011027 |
| T.J. Sego | University of Florida | Multicellular modeling, SBML, CompuCell3D, Tissue Forge |
| Xiaoming Hu | HITS gGmbH, Schloss-Wolfsbrunnenweg 35 69118 Heidelberg Germany | CellML, SBML, SED-ML, Fairdom (https://fair-dom.org/) and NFDI4Health (https://www.nfdi4health.de/en/) |
| Yan-Kay Ho | University of Cambridge | SBOL and SBOL Visual |
| Zainab Ashimiyu-Abdusalam | EMBL-EBI, CB10, 1SD, Hinxton near Cambridge | NeuroML, SBML |
Attendees - remote
| Name | Organization | Interests |
|---|---|---|
| Bart Jardine | University of Washington | CellML, COMBINE Archive, Multicellular modeling, SBML, SED-ML, OpenVT (multicell AB modeling), SBML web related tools |
| Carissa Bleker | National Institute of Biology, Slovenia | COMBINE Archive, Multicellular modeling, SBGN, SBML, SED-ML, FROG, ELIXIR Systems Biology community |
| Chris Evelo | Maastricht University, The Netherlands | BioPAX, SBGN, SBML, WikiPathways, ELIXIR’s task on PBPK modelling and SBML conversions for that |
| Francis Chemorion | University of Pompeu Fabra, InSilicoTrials Technologies | BioPAX, CellML, COMBINE Archive, Multicellular modeling, NeuroML, OMEX Metadata, SBGN, SBML, SBOL and SBOL Visual, SED-ML, PE-TAB, FROG, I am a phd student researching the management of clinical, biological and simulated data for uniform simulation workflows in the Disc4All project https://disc4all.upf.edu |
| Gaoxiang(Gavin) Zhou | University of Pittsburgh, 4200 Fifth Ave, Pittsburgh PA 15260 | BioPAX, CellML, COMBINE Archive, SBML, SBOL and SBOL Visual, PE-TAB, Dish2.0 https://github.com/pitt-miskov-zivanov-lab/DiSH BioRECIPE https://github.com/pitt-miskov-zivanov-lab/BioRECIPE Model analysis in sensitivity etc |
| Haomiao Luo | University of Pittsburgh | BioRECIPE, CAR T cell, DiSH, BioRECIPE, http://www.nmzlab.pitt.edu |
| Herbert Sauro | University of Washington, Seattle, USA | COMBINE Archive, Multicellular modeling, OMEX Metadata, SBML, SED-ML |
| Ilya Kiselev | Biosoft.ru | CellML, COMBINE Archive, Multicellular modeling, SBGN, SBML, SED-ML, BioUML platform |
| Jacob Beal | BBN | SBOL and SBOL Visual |
| James Glazier | Indiana University, Bloomington, IN 47408 USA | COMBINE Archive, Multicellular modeling, SBML, SED-ML, OpenVT (Building communities for multicell modeling), CompuCell3D multicell modeling framework (www.compucell3d.org) |
| John Hancock | University of Ljubljana | COMBINE Archive, SBML, SED-ML, FROG, ELIXIR Systems Biology Community |
| Leonie Lorenz | EMBL-EBI | SBML, SED-ML, PE-TAB, Pathogen transmission and evolution models |
| Lokesh V | Indian Institute of Technology, Bombay | SBML, FROG, I generate high quality genome scale metabolic models for industrial microorganisms. I understand the basic science of the metabolism using models and provide insilico predictions for engineering applications. |
| Luisa Zapata Saldarriaga | Universidad de Antioquia | BioPAX, CellML, COMBINE Archive, Multicellular modeling, NeuroML, OMEX Metadata, SBGN, SBML, SBOL and SBOL Visual, SED-ML, PE-TAB, FROG |
| Lutz Brusch | Technische Universität Dresden, Dresden, Germany | COMBINE Archive, Multicellular modeling, SBML, PE-TAB, MorpheusML (https://morpheus.gitlab.io/model/published-models/), SBML-Spatial, FAIRSPACE, https://www.MultiCellML.org |
| Matthias König | Humboldt-University Berlin, Faculty of Life Science, Institute for Theoretical Biology, Berlin, Germany | COMBINE Archive, Multicellular modeling, OMEX Metadata, SBGN, SBML, SED-ML, PE-TAB, FROG |
| Nguyen Tung | EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK | BioPAX, CellML, COMBINE Archive, OMEX Metadata, SBGN, SBML, SED-ML, PE-TAB, FROG, BioModels: https://www.ebi.ac.uk/biomodels/ |
| Nicholas Owen | UCL | Multicellular modeling, SBML, SBOL and SBOL Visual, Data Stewardship at UCL |
| Paola Dr Di Maio | IGDORE | BioPAX, CellML, COMBINE Archive, Multicellular modeling, NeuroML, SED-ML, Model Cards ML, Neuroscience Model Cards |
| Qi Wu | HITS | |
| Randy Heiland | Indiana University, Bloomington, IN USA | CellML, Multicellular modeling, SED-ML, PhysiCell, CompuCell3D |
| Thomas Gorochowski | University of Bristol | SBOL and SBOL Visual |
| Veronica Henao | Universidad de Antioquia | COMBINE Archive, NeuroML, https://www.canva.com/design/DAFmX5dbOQA/5y0xNdtqzE7RmHXdCERZ3w/view?website#4 |
Last updated 4 April 2024
Registration
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.Call for Breakout Sessions and Tutorials
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 organisers will be responsible for creating and hosting their own online sessions, if required.Call for Lightning Talks and Posters
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.Application for travel funding
We have limited funding for travel bursaries or contributions towards accommodation. These will be given out to those who have a significant contribution to make to the HARMONY meeting.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 analysing 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