COMBINE 2022

Conference Date

06-08 October 2022

Conference Location

Humboldt University of Berlin, Philippstraße 13, House 4, Berlin (In Person)

Important Links

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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.

The daily welcomes, wrap-up and the COMBINE forum will be streamed online. Please register via the following link for the stream: https://hu-berlin.zoom.us/meeting/register/u5EocOGoqzgiE9LPwbHLtC-m_6UTn7LCXx6X

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

Overview

COMBINE Community meet-up

Two days of breakout sessions and tutorials related to COMBINE standards

Thus 6th & Fri 7th Oct, 8:30am-6pm at Humboldt University of Berlin, Philippstraße 13, House 4

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.

COMBINE Forum

Single track session with invited and submitted talks

Sat 8th Oct, 8am-1pm at Humboldt University of Berlin, Philippstraße 13, House 4

How to get there?

COMBINE2022 is located at Humboldt University of Berlin, Philippstraße 13, House 4

The main entry is at Philippstraße 13. The main event site is in House 4, where the daily welcomes, wrap-ups and the COMBINE Forum will take place. In addition, some breakouts will take place in House 20 and House 18. Please see the following plan for details:

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Agenda

Thursday Oct 6 - COMBINE Community meet-up Day 1

  
8:30amWelcome (Matthias König, House 4, Lecture Hall)
9amBreakouts & Tutorials 1
Breakouts:
- Room 2 (House 4, 012a): SEP 55 (Prashant Vaidyanathan)
- Room 1 (House 4, Lecture Hall): SED-ML Level 2: Proposals and Requirements (Lucian Smith)
10:30amBreak / Coffee
11amBreakouts & Tutorials 2
Tutorial:
- Room 3 (House 18, Maut Menten): CovidGraph: Interfaces and Usage (Lea Gütebier)
Breakouts:
- Room 2 (House 4, 012a): Parametric SVG for SBOL Visual (Thomas Gorochowski)
- Room 1 (House 4, Lecture Hall): SED-ML Level 2: Proposals and Requirements
12:30pmLunch (self organized)
2pmBreakouts & Tutorials 3
Tutorial:
- Room 3 (House 18, Maud Menten): Clinical trial simulations with the Jinkō modeling platform
Breakouts:
- Room 2 (House 4, 012a): SBOL 3.1 (Gonzalo Vidal)
- Room 1 (House 4, Lecture hall): Curating models and simulations for BioSimulations (David Nickerson)
- online: Protocol Activity Modeling Language Standard Working Group (Daniel Bryce)
3:30pmBreak / Coffee
4pmBreakouts & Tutorials 4
Breakouts:
- Room 2 (House 4, 012a): Representation of Site-Variant Libraries (James Diggans)
- Room 1 (House 4, Lecture Hall): VSCode-Antimony: A Smart Editor for Developing Models in Systems Biology (Joe Hellerstein/Herbert Sauro)
- online: Protocol Activity Modeling Language Standard Working Group
5:30pmWrap-up (House 4, Lecture Hall)

Friday Oct 7 - COMBINE Community meet-up Day 2

  
8:30amWelcome (Matthias König, House 4, Lecture Hall)
9amBreakouts & Tutorials 5
Tutorial:
- Room 1 (House 4, Lecture Hall): Morpheus: Multi-scale, Multi-cellular, Spatio-temporal Modeling with Hands-on for Your Own Projects
Breakouts:
- Room 3 (House 20, Seminar Room 1): Managing RDF Packages (Jacob Beal)
- Room 2 (House 4, 012a): FROG Analysis - a community standard to foster reproducibility and curation of constraint-based models (Rahuman Sheriff)
- Room 4 (House 20, Seminar Room 2): Similarity Computation of Small Molecule Names (Lukrécia Mertová)
10:30amBreak / Coffee
11amBreakouts & Tutorials 6
Breakouts:
- Room 3 (House 20, Seminar Room 1): SBOL Examples (Prashant Vaidyanathan)
- Room 2 (House 4, 012a): FAIRness assessment of COMBINE archives (Irina Balaur, Dagmar Waltemath)
- Room 1 (House 4, Lecture Hall): MultiCellML – a “to-be” Multi-cellular Modelling language (Jörn Starruß)
- Room 4 (House 20, Seminar Room 2): SBML FBC Package Finalization (Matthias König)
12:30pmLunch (self organized)
2pmBreakouts & Tutorials 7
Tutorial:
- Room 1 (House 4, Lecture Hall): Creating reproducible biochemical modeling workflows in Python (Part 1)
Breakouts:
- Room 3 (House 20, Seminar Room 1): RNA Working Group Discussions (Thomas Gorochowski)
- Room 2 (House 4, 012a): FAIRness assessment of COMBINE archives
- Room 4 (House 20, Seminar Room 2): MultiCellML – a “to-be” Multi-cellular Modelling language (Jörn Starruß)
- online: Protocol Activity Modeling Language Standard Working Group (Daniel Bryce)
3:30pmBreak / Coffee
4pmBreakouts & Tutorials 8
Tutorial:
- Room 1 (House 4, Lecture Hall): Creating reproducible biochemical modeling workflows in Python (Part 2)
Breakouts:
- Room 3 (House 20, Seminar Room 1): RNA Working Group Discussions
- Room 4 (House 20, Seminar Room 2): “Data Hazards: framework for thinking ethics in computational systems biology (Susana Roman Garcia)”
- Room 2 (House 4, 012a): SBGN general discussion (Adrien Rougny)
- online: Protocol Activity Modeling Language Standard Working Group (Daniel Bryce)
5:30pmWrap-up (House 4, Lecture Hall)
  
2:30pm - 5.00pm- different location: Workshop on statistical inference for dynamical models, PETab (Jan Hasenauer, Daniel Weindl)

Saturday Oct 8 - COMBINE Forum

  
8amPoster Session / Coffee
8:45amWelcome (Dagmar Waltemath and Matthias König)
9amInvited Talk
F.A.I.R. Bayesian Workflows and Model Citation Analysis
Nicole Radde, University of Stuttgart
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 / Coffee
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 AnalyzerFengkai Zhang
12:30pmPoster Session / Coffee
1pmAdjourn

Attendees

86 participants have registered for COMBINE2022 so far.
NameAffiliationAttendance
Mihail AntonChalmers University of TechnologyFriday 7th October
COMBINE Archive and OMEX, FROG, ModeleXchange, Personalized Medicine, SBGN
Lara BRUEZIERENovadiscoveryThursday 6th October, Friday 7th October, Saturday 8th October
SBGN, SBML, SED-ML
Irina BalaurUniversity of LuxembourgThursday 6th October, Friday 7th October, Saturday 8th October
COMBINE Archive and OMEX, Personalized Medicine, SBGN
Jacob BarhakJacob Barhak AnalyticsFriday 7th October, Saturday 8th October
ModeleXchange, SBML
Bryan BartleyRaytheon BBNThursday 6th October, Friday 7th October, Saturday 8th October
SBOL, SBOL Visual
Florian BartschInstitut für theoretische Biologie, Humboldt-Universität zu BerlinThursday 6th October, Friday 7th October
Personalized Medicine, SBML
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
Daniel BryceSIFT, LLC.Thursday 6th October, Friday 7th October, Saturday 8th October
-
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
Zsófia BujtárMax Delbrück Center for Molecular Medicine in the Helmholtz Association (Berlin)Friday 7th October, Saturday 8th October
SBGN, SBML, DDE-BIFTOOL
Famke BäuerleUniversity of TuebingenThursday 6th October, Friday 7th October, Saturday 8th October
COMBINE Archive and OMEX, FROG, Personalized Medicine, SBGN, SBML, SED-ML
Jeremy CahillMetamer LabsThursday 6th October, Friday 7th October, Saturday 8th October
BioPAX, CellML, COMBINE Archive and OMEX, FROG, ModeleXchange, NeuroML, Personalized Medicine, PEtab, SBGN, SBML, SBOL, SBOL Visual, SED-ML
Marie CoutelierParis Brain Institute-
CellML, COMBINE Archive and OMEX, NeuroML, Personalized Medicine
Tobias CzaudernaUniversity of Applied Sciences MittweidaFriday 7th October, Saturday 8th October
SBGN
James DiggansTwist BioscienceThursday 6th October
SBOL, SBOL Visual
Andreas DrägerEberhard Karls Universität TübingenThursday 6th October, Friday 7th October, Saturday 8th October
COMBINE Archive and OMEX, FROG, SBGN, SBML, SED-ML
Dorotea DudasHITS gGmbHThursday 6th October, Friday 7th October, Saturday 8th October
SBML
Ibrahim Dulijanstevens.eduThursday 6th October, Friday 7th October, Saturday 8th October
SBML, SBOL, SBOL Visual
Longxuan FanUniversity of WashingtonThursday 6th October
SBML
Fabian FröhlichHarvard Medical SchoolFriday 7th October, Saturday 8th October
BioPAX, PEtab, SBML, SED-ML
Alan GarnyUniversity of AucklandThursday 6th October, Friday 7th October, Saturday 8th October
CellML, COMBINE Archive and OMEX, SED-ML
Robert T. GiessmannInstitute for globally distributed open research and education (IGDORE)-
BioPAX, COMBINE Archive and OMEX, SBML, SBOL, SBOL Visual, SED-ML, thermodynamic data, openTECR
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
Alexander GowerChalmers University of TechnologyThursday 6th October, Friday 7th October, Saturday 8th October
BioPAX, CellML, COMBINE Archive and OMEX, FROG, ModeleXchange, PEtab, SBGN, SBML, SED-ML
Niklas GröneUniversität KonstanzThursday 6th October, Friday 7th October, Saturday 8th October
-
Roy GusinowUniversity of BonnThursday 6th October, Friday 7th October, Saturday 8th October
NeuroML, PEtab, SBML
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
Jan HasenauerUniversity of BonnThursday 6th October, Friday 7th October, Saturday 8th October
ModeleXchange, Personalized Medicine, PEtab, SBGN, SBML, SED-ML
Joseph HellersteineScience Institute, University of WashingtonThursday 6th October
SBML, SED-ML
Joseph HellersteinUniversity of WashingtonThursday 6th October
PEtab, SBML, SED-ML
Ron HenkelUniversity Medicine GreifswaldThursday 6th October, Friday 7th October, Saturday 8th October
CellML, COMBINE Archive and OMEX, ModeleXchange, SBGN, SBML, SBOL, SED-ML
Henning HermjakobEMBL-EBIFriday 7th October, Saturday 8th October
BioPAX, COMBINE Archive and OMEX, FROG, ModeleXchange, SBML
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
Johann Fredrik JadebeckIBG-1 Forschungszentrum JülichThursday 6th October, Saturday 8th October
FROG, SBML
João JúniorCentro de Tecnologia CanavieiraThursday 6th October, Friday 7th October, Saturday 8th October
CellML, ModeleXchange, Personalized Medicine, SED-ML
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
Adrian KöllerInstitut für theoretische Biologie, Humboldt-Universität zu BerlinThursday 6th October, Friday 7th October
SBML
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
Eva LiuUniversity of Washington Bioengineering Sys-Bio LabThursday 6th October
-
Sebastian LobentanzerUniversity Hospital HeidelbergThursday 6th October, Friday 7th October, Saturday 8th October
BioPAX, Personalized Medicine, PEtab, SBGN, SBML
Augustin LunaHarvard Medical SchoolThursday 6th October, Friday 7th October, Saturday 8th October
BioPAX, SBGN
Karin LundengårdAuckland Bioengineering InstituteThursday 6th October, Friday 7th October
-
Steve MaNVIDIAThursday 6th October
SBML
Simon MerktUniversity of BonnThursday 6th October, Friday 7th October, Saturday 8th October
NeuroML, PEtab, SBGN, SBML
Lukrécia MertováHeidelberg Institute for Theoretical Studies HITS gGmbHThursday 6th October, Friday 7th October, Saturday 8th October
BioPAX, ModeleXchange, Personalized Medicine, SBML, SBOL
Goksel MisirliKeele UniversityThursday 6th October, Friday 7th October
SBOL, SBOL Visual
Ion MoraruUConn HealthThursday 6th October, Friday 7th October
COMBINE Archive and OMEX, SBML, SED-ML
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
Clemens PeiterIRU MLS, LIMES, University of BonnThursday 6th October, Friday 7th October
PEtab, SBGN, SBML
Sathish PeriyasamyQueensland Brain InstituteFriday 7th October, Saturday 8th October
CellML, NeuroML, Personalized Medicine, SBGN, SBML
Fronth Nyus PiQuantum4Life SensonomiqsThursday 6th October, Friday 7th October, Saturday 8th October
CellML, COMBINE Archive and OMEX, NeuroML, SBML, SBOL
Veronica PorubskyUniversity of WashingtonThursday 6th October, Friday 7th October, Saturday 8th October
NeuroML
Nicole RaddeUniversity of StuttgartFriday 7th October, Saturday 8th October
COMBINE Archive and OMEX, ModeleXchange, Personalized Medicine, PEtab, SBML
Karthik RamanIndian Institute of Technology MadrasThursday 6th October, Friday 7th October, Saturday 8th October
FROG
Gianmarco Rasi-Thursday 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
Adrien RougnyIndependent researcher (former AIST)Friday 7th October, Saturday 8th October
SBGN
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
James Scott-BrownUniversity of EdinburghThursday 6th October, Friday 7th October
SBOL, SBOL Visual
Vinoo SelvarajahiGEM FoundationThursday 6th October, Friday 7th October
SBOL, SBOL Visual
Woosub ShinAuckland Bioengineering Institute, University of Washington-
SBML
Lucian SmithUniversity of WashingtonThursday 6th October, Friday 7th October, Saturday 8th October
CellML, COMBINE Archive and OMEX, FROG, PEtab, SBML, SED-ML
Jörn StarrußTU DresdenThursday 6th October, Friday 7th October, Saturday 8th October
PEtab, SBML, MultiCellML
Melanie StefanMedical School BerlinThursday 6th October, Friday 7th October, Saturday 8th October
COMBINE Archive and OMEX, Personalized Medicine, SBGN, SBML
Abel SzkalisityUniversity of HelsinkiThursday 6th October, Friday 7th October, Saturday 8th October
BioPAX, SBML
Baishakhi TikaderIndian Institute of Bombay, IndiaFriday 7th October
SBML
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
Adelinde UhrmacherUniversity of RostockSaturday 8th October
CellML, COMBINE Archive and OMEX, SBGN, SBML, SED-ML
Prashant VaidyanathanOxford BiomedicaThursday 6th October, Friday 7th October
SBOL
Paola Vera-LiconaUConn HealthFriday 7th October
BioPAX, Personalized Medicine, 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
Daniel WeindlHelmholtz MunichThursday 6th October, Friday 7th October, Saturday 8th October
PEtab, SBML, SED-ML
St. Elmo WilkenHeinrich Heine UniversitySaturday 8th October
-
Pia WilsdorfUniversity of RostockSaturday 8th October
COMBINE Archive and OMEX, PEtab, SED-ML
Fengkai ZhangNIAID/NIHThursday 6th October, Friday 7th October, Saturday 8th October
COMBINE Archive and OMEX, ModeleXchange, SBGN, SBML, SED-ML
kristina grudenNIBSaturday 8th October
CellML, SBGN, SBML, SBOL

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