COMBINE

Coordinating standards for modeling in biology

The “COmputational Modeling in BIology NEtwork” (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models. By doing so, it is expected that the federated projects will develop a set of interoperable and non-overlapping standards covering all aspects of modeling in biology. The global COMBINE effort is led by the COMBINE Coordination Board.

Building on the experience of mature projects, which already have stable specifications, software support, user-base and community governance, COMBINE will help foster or support fledgling efforts aimed at filling gaps or new needs. As those efforts mature, they may become part of the core set of COMBINE standards.

One of the initial activities of COMBINE is to coordinate the organization of scientific and technical events common to several standards. Those events, as others related to our field of research are gathered in a calendar.

To discuss the goals, organization and operation of COMBINE, subscribe to COMBINE discuss mailing list.

To report issues about the co.mbine.org website, send a mail to combine-support @ googlegroups.com

Upcoming Conferences

HARMONY 2024

Conference Date

8-11 April, 2024

Conference Location

UCL, London, UK

Important Dates

Breakouts and tutorials submission deadline

NOW CLOSED

Notification of acceptance for breakout and tutorials

3 Apr, 2024

Lightning talk and poster submission deadline

NOW CLOSED

Notification of acceptance for lightning talks and posters

3 Apr, 2024

Travel support applications NOW CLOSED

Notification of travel support awards

21 February, 2024

Important Links

Registration

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.

Schedule

Abstract book

Break out booklet

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

COMBINE

Coordinating standards for modeling in biology

Coordination

Coordinators

SBOL Delegate

Semantic Annotation Delegate

SBML Delegate

CellML Delegate (Chair)

SBGN Delegate

BioPAX Delegate

Data Processing and Integration

SED-ML Delegate

NeuroML Delegate (Vice Chair)

SBOL Visual Delegate

Past Coordinators

SBML Delegate

Past Delegate

Upcoming Conferences

HARMONY 2024

Conference Date

Conference Location

Important Dates

Important Links

Workshop Location

Schedule

Arrival and Transportation

Accommodations and meals

Visa

Power outlet

Support

Attendees - in person

Attendees - remote

Topics of Interest

Contact