COMBINE

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

Coordination

Coordinators

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Chris Myers

SBOL Delegate

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Dagmar Waltemath

Semantic Annotation Delegate (Chair)

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Sarah Keating

SBML Delegate

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David Nickerson

CellML Delegate (Vice Chair)

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Falk Schreiber

SBGN Delegate

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Gary Bader

BioPAX Delegate

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Martin Golebiewski

Data Processing and Integration

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Matthias König

SED-ML Delegate

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Padraig Gleeson

NeuroML Delegate

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Thomas Gorochowski

SBOL Visual Delegate

Past Coordinators

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Michael Hucka

SBML Delegate

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Nicolas Le Novere

Past Delegate

Upcoming Conferences

Harmony 2022

Conference Date

26-30, April 2022

Conference Location

Washington, DC - Hybrid (Online and Offline)

Important Dates

Breakout submission deadline
April 4, 2022

Lightning talk submission deadline
April 4, 2022

Notification of acceptance of breakouts
April 6, 2022

HARMONY Workshop
April 26 to 30, 2022

Important 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 2022 is going to be organized as a hybrid event with in-person and online participants. In particular:

  • April 26 : Online lightning talks (EST afternoon)
  • April 27-29 : in-person breakouts with online participants (8am to 5pm EST)
  • April 30 : online breakouts (8am to 5pm EST)

This event is co-located with 2022 Synthetic Biology: Engineering, Evolution & Design (SEED). Most of the day will be scheduled by the communities as breakouts. In addition, we will have some time each day for community discussion and wrap-ups of breakouts and advertisements for following breakouts.

Please see this Google Calendar for the live HARMONY 2022 Schedule. This calendar is only accessible to registered attendees. If you have difficulties accessing the calendar please contact the organisers.

Workshop Location Details

The site is the Institute for Bioscience and Biotechnology Research (https://www.ibbr.umd.edu). The address is 9600 Gudelsky Drive, Rockville, Maryland 20850 (https://www.ibbr.umd.edu/about)

Attendees should park in the garage at 9621 Gudelsky Drive, Rockville, Maryland 20850. NIST will validate parking, so attendees don’t have to pay the $15/day fee. Please enter through the double doors located to the right of the flag poles in front of the circular drive.

Registration

Registration for the meeting is open and 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 video conferencing links, etc.

Call for Breakout Sessions

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.

Call for Lightning Talks

Requests for a lightning talk (3 min max.) 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.

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