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

COMBINE 2022

Conference Date

06-08 October 2022

Conference Location

Humboldt University of Berlin, Philippstraße 13, Haus 20, Berlin (In Person)

Important Dates

Breakout/tutorial submission deadline

August 26, 2022

Forum abstract submission deadline

August 26, 2022

Notification of acceptance

September 9, 2022

Important Links

Registration

Breakouts/Tutorials submission

The “Computational Modeling in Biology” Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats in systems biology and related fields. COMBINE 2022 will be a workshop-style event with oral presentations, breakout sessions and tutorials. The three meeting days will include talks about the COMBINE standards and associated or related standardization efforts, presentations of tools using these standards, breakout sessions for detailed discussions as well as tutorials.

COMBINE 2022 will be an in-person meeting organised as a satellite to the ICSB 2022 meeting in Berlin.

Agenda

COMBINE Community meet-up

Two days of breakout sessions and tutorials related to COMBINE standards

Thus 6th & Fri 7th Oct, 9am-6pm at Humboldt University of Berlin, Philippstraße 13, Haus 20

All attendees can suggest breakout sessions for detailed discussions of certain aspects of one or several of the COMBINE standard(s), discussions on metadata and semantic annotations (format-specific or overarching), discussions on the application and implementations of the COMBINE standards, or any other topic relevant for the COMBINE community.

We also solicit applications to host tutorials on tools, standards or resources (or any other topic) which would be relevant for the COMBINE community (see Topics of Interest below). The link to submit suggestions for breakout sessions or tutorials is here, and the deadline is on the left.

COMBINE Forum

Single track session with invited and submitted talks

Sat 8th Oct, 8am-1pm at Humboldt University of Berlin, Philippstraße 13, Haus 20

To submit an abstract for the COMBINE Forum on Saturday October 8, please use the official ICSB abstract submission portal on EasyChair:

Submit your abstract at https://easychair.org/conferences/?conf=icsb2022
Select “COMBINE: Satellite Event” as your submission topic

Detailed Agenda

Thursday Oct. 6 - COMBINE Community meet-up Day 1


8:30am	Welcome
9am	*Breakouts & Tutorials 1*	Submit further suggestions here
10:30am	Break
11am	*Breakouts & Tutorials 2*	Submit further suggestions here
12:30pm	Lunch
2pm	*Breakouts & Tutorials 3*	Submit further suggestions here
3:30pm	Break
4pm	*Breakouts & Tutorials 4*	Submit further suggestions here
5:30pm	Wrap-up

Friday Oct. 7 - COMBINE Community meet-up Day 2


8:30am	Welcome
9am	*Breakouts & Tutorials 5*	Submit further suggestions here
10:30am	Break
11am	*Breakouts & Tutorials 6* Tutorial: CovidGraph: Interfaces and Usage	Submit further suggestions here
12:30pm	Lunch
2pm	*Breakouts & Tutorials 7* Tutorial: Creating reproducible biochemical modeling workflows in Python (Part 1)	Submit further suggestions here
3:30pm	Break
4pm	*Breakouts & Tutorials 8* Tutorial: Creating reproducible biochemical modeling workflows in Python (Part 2)	Submit further suggestions here
5:30pm	Wrap-up

Saturday Oct 8 - COMBINE Forum


8am	*Poster Session* / Coffee
9am	*Invited Talk*
9:30am	*Contributed Talks*	Submit abstract here
10:30am	*Poster Session* / Break
11am	*Invited Talk*
11:30am	*Contributed Talks*	Submit abstract here
12:30pm	*Poster Session* / Coffee
1pm	Adjourn

Registration

Registration for the meeting is open and is free. Please register at the link on the left as soon as possible. This will help us plan the schedule and match your interests to the timing of the breakouts, etc.

Organizers

The COMBINE 2022 meeting is organised by Dagmar Waltemath and Matthias König.

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 (Chair)

SBML Delegate

CellML Delegate (Vice Chair)

SBGN Delegate

BioPAX Delegate

Data Processing and Integration

SED-ML Delegate

NeuroML Delegate

SBOL Visual Delegate

Past Coordinators