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 September 10, 2022

Forum abstract submission deadline
August 26, 2022 September 30, 2022

Initial notification of acceptance (and then ongoing)
September 9, 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 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.

Overview

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:

Agenda

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

 
8:30amWelcome                                                                                                                   
9amBreakouts & Tutorials 1
Breakouts:
- Room 1: SEP 55 (Prashant Vaidyanathan)
- Room 2: SED-ML Level 2: Proposals and Requirements (Lucian Smith)
- Room 3: Protocol Activity Modeling Language Standard Working Group (Daniel Bryce)
Submit further suggestions here
10:30amBreak
11amBreakouts & Tutorials 2
Tutorial: CovidGraph: Interfaces and Usage
Breakouts:
- Room 1: Parametric SVG for SBOL Visual (Thomas Gorochowski)
- Room 2: SED-ML Level 2: Proposals and Requirements
- Room 3: Protocol Activity Modeling Language Standard Working Group
Submit further suggestions here
12:30pmLunch
2pmBreakouts & Tutorials 3
Tutorial: Clinical trial simulations with the Jinkō modeling platform
Breakouts:
- Room 1: SBOL 3.1 (Gonzalo Vidal)
- Room 2: Curating models and simulations for BioSimulations (David Nickerson)
- Room 3: Protocol Activity Modeling Language Standard Working Group
Submit further suggestions here
3:30pmBreak
4pmBreakouts & Tutorials 4
Tutorial: Modelling with VCell
Breakouts:
- Room 1: Representation of Site-Variant Libraries (James Diggans)
- Room 2:
- Room 3: Protocol Activity Modeling Language Standard Working Group
Submit further suggestions here
5:30pmWrap-up

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

 
8:30amWelcome                                                       
9amBreakouts & Tutorials 5
Tutorial: Morpheus: Multi-scale, Multi-cellular, Spatio-temporal Modeling with Hands-on for Your Own Projects
Breakouts:
- Room 1: Managing RDF Packages (Jacob Beal)
- Room 2: FROG Analysis - a community standard to foster reproducibility and curation of constraint-based models (Rahuman Sheriff)
- Room 3: Similarity Computation of Small Molecule Names (Lukrécia Mertová)
Submit further suggestions here
10:30amBreak
11amBreakouts & Tutorials 6
Tutorial:
Breakouts:
- Room 1: SBOL Examples (Prashant Vaidyanathan)
- Room 2: FAIRness assessment of COMBINE archives (Irina Balaur, Dagmar Waltemath)
- Room 3: MutliCellML – a “to-be” Multi-cellular Modelling language
- Room 4 SBML FBC
Submit further suggestions here
12:30pmLunch
2pmBreakouts & Tutorials 7
Tutorial: Creating reproducible biochemical modeling workflows in Python (Part 1)
Breakouts:
- Room 1: RNA Working Group Discussions (Thomas Gorochowski)
- Room 2: FAIRness assessment of COMBINE archives
- Room 3: MutliCellML – a “to-be” Multi-cellular Modelling language (Jörn Starruß)
Submit further suggestions here
3:30pmBreak
4pmBreakouts & Tutorials 8
Tutorial: Creating reproducible biochemical modeling workflows in Python (Part 2)
Breakouts:
- Room 1: RNA Working Group Discussions
- Room 2: “Data Hazards: framework for thinking ethics in computational systems biology (Susana Roman Garcia)”
- Room 3: SBGN general discussion (Adrien Rougny)
Submit further suggestions here
5:30pmWrap-up

Saturday Oct 8 - COMBINE Forum

 
8amPoster Session / Coffee                                                                                                      
8:45amWelcome
9amInvited Talk
9:30amContributed Talks
FROG Analysis - a community standard to foster reproducibility and curation of constraint-based models Rahuman Malik Sheriff
BioCypher: an ontology-driven framework for flexible harmonisation of large-scale biomedical knowledge graphs Sebastian Lobentanzer
Implementing Safe Cross-Document RDF References Jacob Beal
The Protocol Activity Modeling Language Jacob Beal
10:30amPoster Session / Break
11amInvited Talk
Documentation of simulation studies — beyond reproducibility
Adelinde Uhrmacher, Institute for Visual and Analytic Computing, University Rostock
By storing information about a simulation study within a provenance graph the stored information becomes queryable and the dependencies between different modeling and experimenting activities and the used or generated entities become visually accessible. Combined with explicit unambiguous model and simulation experiment specifications such a documentation enhances the reproducibility of the simulation study and the credibility of its products. However, as every documentation of a simulation study, it requires additional effort by the modeler. Therefore, to make the most out of the documentation, how can it be used beyond being a source of information for the modeler about the current or a previous simulation study? In this talk we will discuss the potential, challenges, and experiences in using information stored in a provenance graph to generate and execute simulation experiments during simulation studies automatically.
11:30amContributed Talks
FAIRDOM: Promoting and Supporting FAIR Data and Model Management in Systems Biology Olga Krebs
MeDaX - our vision for bioMedical Data eXploration Judith Wodke
Morpheus: Multi-scale, Multi-cellular, Spatio-temporal Modeling Made Easy Jörn Starruß
Analyze Parameter Space for Rule-based Models with Simmune Analyzer Fengkai Zhang
12:30pmPoster Session / Coffee
1pmAdjourn

Attendees

NameAffiliationAttendance
Irina BalaurUniversity of LuxembourgThursday 6th October, Friday 7th October, Saturday 8th October
COMBINE Archive and OMEX, Personalized Medicine, SBGN
Jacob BealRaytheon BBNThursday 6th October, Friday 7th October, Saturday 8th October
SBOL, SBOL Visual
Frank BergmannHeidelberg University, BioQUANT / COSThursday 6th October, Friday 7th October, Saturday 8th October
COMBINE Archive and OMEX, FROG, PEtab, SBGN, SBML, SED-ML
Michael BlinovUConn HealthFriday 7th October, Saturday 8th October
BioPAX, COMBINE Archive and OMEX, ModeleXchange, PEtab, SBGN, SBML, SED-ML
Lutz BruschTechnische Universität DresdenFriday 7th October, Saturday 8th October
COMBINE Archive and OMEX, PEtab, MultiCellML, MorpheusML, SBML-Spatial
Lukas BuecherlUniversity of Colorado BoulderThursday 6th October, Friday 7th October, Saturday 8th October
CellML, COMBINE Archive and OMEX, Personalized Medicine, SBML, SBOL, SBOL Visual, SED-ML
Famke BäuerleUniversity of TuebingenThursday 6th October, Friday 7th October, Saturday 8th October
COMBINE Archive and OMEX, FROG, Personalized Medicine, SBGN, SBML, SED-ML
Tobias CzaudernaUniversity of Applied Sciences MittweidaFriday 7th October, Saturday 8th October
SBGN
Andreas DrägerEberhard Karls Universität TübingenThursday 6th October, Friday 7th October, Saturday 8th October
COMBINE Archive and OMEX, FROG, SBGN, SBML, SED-ML
Fabian FröhlichHarvard Medical SchoolFriday 7th October, Saturday 8th October
BioPAX, PEtab, SBML, SED-ML
Mose GiordanoUCLThursday 6th October, Friday 7th October, Saturday 8th October
SBML
Thomas GorochowskiUniversity of BristolThursday 6th October, Friday 7th October, Saturday 8th October
SBOL, SBOL Visual
Lea GütebierDepartment of Medical Informatics, Institute for Community Medicine, University Medicine GreifswaldThursday 6th October, Friday 7th October, Saturday 8th October
CellML, Personalized Medicine, SBML, SED-ML
Joseph HellersteineScience Institute, University of WashingtonThursday 6th October
SBML, SED-ML
Sebastian HöpflInstitute for Systems Theory and Automatic Control (IST)Thursday 6th October, Friday 7th October, Saturday 8th October
COMBINE Archive and OMEX, Personalized Medicine, PEtab, SBML
Miroslav KratochvílLuxembourg Centre for Systems BiomedicineSaturday 8th October
FROG, SBML
Olga KrebsHeidelberg Institute for Theoretical StudiesThursday 6th October, Friday 7th October, Saturday 8th October
Personalized Medicine, PEtab, SBML, SBOL, SBOL Visual, SED-ML
Matthias KönigHumboldt-University BerlinThursday 6th October, Friday 7th October, Saturday 8th October
COMBINE Archive and OMEX, FROG, Personalized Medicine, PEtab, SBML, SED-ML
Paul LangUniversity of Oxford; Julia ComputingSaturday 8th October
Personalized Medicine, PEtab, SBML
Sebastian LobentanzerUniversity Hospital HeidelbergThursday 6th October, Friday 7th October, Saturday 8th October
BioPAX, Personalized Medicine, PEtab, SBGN, SBML
Karin LundengårdAuckland Bioengineering InstituteThursday 6th October, Friday 7th October
Lukrécia MertováHeidelberg Institute for Theoretical Studies HITS gGmbHThursday 6th October, Friday 7th October, Saturday 8th October
BioPAX, ModeleXchange, Personalized Medicine, SBML, SBOL
Sébastien MorettiSIB Swiss Institute of BioinformaticsThursday 6th October, Friday 7th October
SBML
Chris MyersUniversity of Colorado BoulderThursday 6th October, Friday 7th October, Saturday 8th October
SBOL, SBOL Visual, SBML, SED-ML
Tung NguyenEMBL-EBIThursday 6th October, Friday 7th October, Saturday 8th October
BioPAX, CellML, COMBINE Archive and OMEX, FROG, ModeleXchange, Personalized Medicine, PEtab, SBGN, SBML, SED-ML
David NickersonAuckland Bioengineering Institute, University of AucklandThursday 6th October, Friday 7th October, Saturday 8th October
CellML, COMBINE Archive and OMEX, ModeleXchange, Personalized Medicine, PEtab, SED-ML
Dilan PathiranaUniversity of BonnThursday 6th October, Friday 7th October, Saturday 8th October
PEtab, SBML
Fronth nyhus PiQuantum4Life SensonomiqsThursday 6th October, Friday 7th October, Saturday 8th October
CellML, COMBINE Archive and OMEX, NeuroML, SBML, SBOL
Gianmarco RasinoneThursday 6th October, Friday 7th October, Saturday 8th October
SBML
Susana Roman garciaUniversity of EdinburghThursday 6th October, Friday 7th October, Saturday 8th October
BioPAX, CellML, COMBINE Archive and OMEX, ModeleXchange, NeuroML, Personalized Medicine, PEtab, SBGN, SBML, SBOL, SBOL Visual, SED-ML
Herbert SauroUniversity of WashingtonThursday 6th October, Friday 7th October, Saturday 8th October
COMBINE Archive and OMEX, SBML, SED-ML
Falk SchreiberUniversity of KonstanzThursday 6th October, Friday 7th October, Saturday 8th October
SBGN, SBML, SBOL Visual
Woosub ShinAuckland Bioengineering Institute, University of Washington
SBML
Jörn StarrußTU DresdenThursday 6th October, Friday 7th October, Saturday 8th October
PEtab, SBML, MultiCellML
Krishna kumar TiwariEMBL-EBIThursday 6th October, Friday 7th October, Saturday 8th October
FROG, ModeleXchange, Personalized Medicine, SBGN
Matej TrojákMasaryk universityThursday 6th October, Friday 7th October, Saturday 8th October
SBML
Gonzalo VidalICOS, Newcastle UniversityThursday 6th October, Friday 7th October, Saturday 8th October
SBOL, SBOL Visual
Dagmar WaltemathUniversity Medicine GreifswaldThursday 6th October, Friday 7th October, Saturday 8th October
COMBINE Archive and OMEX, ModeleXchange, Personalized Medicine, SBML, SED-ML, FAIR model indicators
St. elmo WilkenHeinrich Heine UniversitySaturday 8th October
Fengkai ZhangNIAID/NIHThursday 6th October, Friday 7th October, Saturday 8th October
COMBINE Archive and OMEX, ModeleXchange, SBGN, SBML, SED-ML

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