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).
HARMONY 2024 will be held at Centre For Medical Image Computing, University College London, 90 High Holborn, London, WC1V 6LJ.
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.
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.
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.
G-type plugs are used in the UK.
More details to follow…
Name | Title | Organization |
---|---|---|
Paola Di Maio | Neuroscience Model Card ML (NMCML | IGDORE |
Manuel Lera-Ramirez | ShareYourCloning: towards a FAIR standard for sequence provenance | University College London |
Name | Title | Organization |
---|---|---|
Paola Di Maio | Neuroscience Model Card ML (NMCML | IGDORE |
Manuel Lera-Ramirez | ShareYourCloning: towards a FAIR standard for sequence provenance | University College London |
Chair | Title | Outline of the session | Time | Location |
---|---|---|---|---|
Fengkai Zhang | Demo of Simmune Modeler and Analyzer | We will demonstrate how to create rule-based models using Simmune Modeler and how to explore the parameter space of biological pathways using Simmune Analyzer. We will do our demo on ubuntu 22.04. Virtualbox on windows or intel Mac OS will also be ok for participants to do hand-on practice. Virtualbox file with ubuntu installation will be provided. | TBC | TBC |
Padraig Gleeson | NeuroML hackathon: convert your neuron and network models to open, standardised, reusable formats | This will be an opportunity for developers of models in computational neuroscience to get an introduction to the aims and structure of NeuroML, a guide to the tools available for building/converting your models to NeuroML, and to receive hands on help with expressing their models (or other published models they are interested in) in NeuroML format, making them more open, accessible and reusable. | Tuesday 9 April | TBC |
Name | Organization | Interests | Attendance |
---|---|---|---|
Alex Fedorec | UCL | COMBINE Archive, Multicellular modeling, SBML, SBOL and SBOL Visual, SED-ML | In person |
Ankur Sinha | UCL | CellML, COMBINE Archive, Multicellular modeling, NeuroML, OMEX Metadata, SBML, SED-ML, Open Source Brain: https://opensourcebrain.org | In person |
Casey Chen | UCL | Multicellular modeling, SBML, SBOL and SBOL Visual | In person |
Chris Barnes | UCL | Multicellular modeling, SBML, SBOL and SBOL Visual | In person |
Fabian Fröhlich | The Francis Crick Institute | BioPAX, SBML, PE-TAB | In person |
Felipe Xavier Buson | University of Cambridge | SBOL and SBOL Visual | In person |
Fengkai Zhang | NIH | COMBINE Archive, Multicellular modeling, OMEX Metadata, SBGN, SBML, SED-ML, Simmune. SBML-Multi and rule-based model | In person |
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/ | In person |
Georgie Sorensen | University of Bristol | SBOL and SBOL Visual | In person |
Gonzalo Vidal | University of Colorado Boulder, Boulder, Colorado, US | SBML, SBOL and SBOL Visual, https://gonza10v.github.io/ | In person |
Ilya Kiselev | Biosoft.ru | CellML, COMBINE Archive, Multicellular modeling, SBGN, SBML, SED-ML, BioUML platform | Remotely (virtually) |
Jacob Beal | BBN | SBOL and SBOL Visual | Remotely (virtually) |
Jona Leka | UCL | NeuroML | In person |
Kathleen Zhang | UCL | BioPAX, CellML, COMBINE Archive, Multicellular modeling, NeuroML, OMEX Metadata, SBGN, SBML, SBOL and SBOL Visual, SED-ML, PE-TAB, FROG | In person |
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. | Remotely (virtually) |
Louie Destouches | UCL | Multicellular modeling, SBML, SBOL and SBOL Visual | In person |
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/) | In person |
Lukas Buecherl | University of Colorado Boulder | COMBINE Archive, SBML, SBOL and SBOL Visual, SED-ML | In person |
Manuel Lera Ramirez | UCL | SBOL and SBOL Visual, https://genestorian.org/ | In person |
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/ | In person |
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/ | Remotely (virtually) |
Nicholas Owen | UCL | Multicellular modeling, SBML, SBOL and SBOL Visual, Data Stewardship at UCL | Remotely (virtually) |
Padraig Gleeson | UCL, London | CellML, Multicellular modeling, NeuroML, OMEX Metadata, SBML, SED-ML, Open Source Brain | In person |
Paola Dr Di Maio | IGDORE | BioPAX, CellML, COMBINE Archive, Multicellular modeling, NeuroML, SED-ML, Model Cards ML, Neuroscience Model Cards | Remotely (virtually) |
Pedro Fontanarrosa | UCL | SBOL and SBOL Visual | In person |
Rahuman Sheriff | EMBL-EBI | COMBINE Archive, Multicellular modeling, NeuroML, OMEX Metadata, SBML, SED-ML, PE-TAB, FROG, Stochastic Reproducibility, BioModels | In person |
Robert Vickerstaff | UCL | NeuroML, SBML, SED-ML | In person |
Sarah Keating | UCL, London | NeuroML, SBML, SED-ML, FROG, CHIMERA | In person |
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) | In person |
Thomas Gorochowski | University of Bristol | SBOL and SBOL Visual | Remotely (virtually) |
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/) | In person |
Yan-Kay Ho | University of Cambridge | SBOL and SBOL Visual | In person |
Last updated 2 March 2024