COMBINE 2019 - Agenda

Agenda (tentative, under development)

Contributed talks and lightning talks in the different sessions will be selected from the submitted abstracts.
Abstracts can be submitted by the Abstract Submission Form.

Day 1 (Monday, July 15th)

Speaker Title Slides
09:15-10:00 Registration & Coffee Foyer Studio Villa Bosch

10:00 – 11:00 Opening Session
Chair: Martin Golebiewski (HITS)
Welcome
10:00-10:05 Martin Golebiewski Welcome by the host
10:05-10:15 Gesa Schönberger Welcome address by the Managing Director of HITS
10:15-10:25 Wolfgang Müller Welcome address by the Scientific Director of HITS
10:25-11:00
Michael Hucka, California Institute of Technology, Pasadena, CA (USA)
The History of COMBINE

11:00 – 12:00 HITS Colloquium
Chair: Wolfgang Müller (HITS)
11:00 – 12:00 Peter Hunter (Auckland, New Zealand) Keynote: Computational Physiology and the Physiome Project

12:00 – 13:00 Lunch Foyer Studio Villa Bosch

13:00 – 15:00 COMBINE Colloquium
Chair: Martin Golebiewski (HITS)
13:00-13:45 Thomas Lemberger (EMBO press) Keynote: Implementing Open Science in publishing
13:45-14:30 Ursula Kummer, University of Heidelberg (Germany) Keynote: Modeling projects across platforms - the reality and how reality should be
14:30 – 15:00 Lightning talks 3 min talks selected from the submitted abstracts

15:00-15:30 Poster Session & Coffee Break Foyer Studio Villa Bosch

15:30 – 17:30 de.NBI Colloquium
Chair: Dagmar Waltemath (Greifswald, D)
15:30-16:00 Judith Wodke, Humboldt University Berlin (Germany) How (not) to Apply (COMBINE) Standards in Agent-Based Modeling
16:00-16:30 Matthias König, Humboldt University Berlin (Germany) Computational modeling of liver function tests - Stratification and individualization based on semantic annotations of models and data
16:30-17:00 Heidi Seibold, Ludwig-Maximilians-Universität München (Germany) Research software engineers and their role for open and reproducible research
17:00 – 17:30 Lightning talks 3 min talks selected from the submitted abstracts

17:30-19:00 Poster Session & Welcome Reception: 10 years COMBINE - Happy Birthday ! Foyer Studio Villa Bosch


Day 2 (Tuesday, July 16th)

Speaker Title Slides
09:30 – 11:00 Session 1: Synthetic Biology
Chair: Ernst Oberortner (Lawrence Berkeley National Laboratory, CA, USA)
09:30-10:00 Chris Myers, University of Utah, Salt Lake City, UT (USA) A Standard Enabled Workflow for Synthetic Biology
10:00-10:10 speaker: TBA Title of contributed talk
10:10-10:20 speaker: TBA Title of contributed talk
10:20-10:30 speaker: TBA Title of contributed talk
10:30-11:00 all speakers of Session 1 Discussion

11:00 – 11:30 Poster Session & Coffee Break Foyer Studio Villa Bosch

11:30 – 13:00 Session 2: Reproducibility in Synthetic and Systems Biology
Chairs: Dagmar Waltemath (Greifswald, D) & David Nickerson (Auckland, NZ)
11:30-12:00 Herbert Sauro, Seattle, WA (USA) The Center for Reproducible Biomedical Modeling
12:00-12:10 speaker: TBA Title of contributed talk
12:10-12:20 speaker: TBA Title of contributed talk
12:20-12:30 speaker: TBA Title of contributed talk
12:30-13:00 all speakers of Session 2 Discussion

13:00 – 14:00 Lunch Foyer Studio Villa Bosch Lobby

14:00 – 15:30 Session 3: Reproducibility workshop
Chair: Herbert Sauro, Seattle, WA (USA)

& Breakouts (up to 2 parallel sessions)


Breakout session for specific topics can be proposed using the Abstract Submission Form.
15:30 – 16:00 Poster Session & Coffee Break Foyer Studio Villa Bosch

16:00 – 17:30 Session 4: Reproducibility workshop
Chair: Herbert Sauro, Seattle, WA (USA)

& Breakouts (up to 2 parallel sessions)


Breakout session for specific topics can be proposed using the Abstract Submission Form.

17:30 – 17:45

Plenary Wrapup

18:30-20:30

Guided Tour through the old town of Heidelberg (optional)


Day 3 (Wednesday, July 17th)

Speaker Title Slides
09:30 – 11:00 Session 5: Modeling Approaches and Tools
Chairs: Matthias König (Berlin, D) & Melanie Stefan (Edinburgh, UK)
09:30-10:00 Caroline Mendonça Costa, King's College London (UK) Improving reproducibility of cardiac electrophysiology simulations via standardized modelling pipelines
10:00-10:10 speaker: TBA Title of contributed talk
10:10-10:20 speaker: TBA Title of contributed talk
10:20-10:30 speaker: TBA Title of contributed talk
10:30-11:00 all speakers of Session 5 Discussion

11:00 – 11:30 Poster Session & Coffee Break Foyer Studio Villa Bosch

11:30 – 13:00 Session 6: Visualization
Chairs: Falk Schreiber (Konstanz, D) & Michael Blinov (Farmington, CT, USA)
11:30-12:00 Akira Funahashi, Keio University, Yokohama (Japan) Invited talk: Title TBA
12:00-12:10 speaker: TBA Title of contributed talk
12:10-12:20 speaker: TBA Title of contributed talk
12:20-12:30 speaker: TBA Title of contributed talk
12:30-13:00 all speakers of Session 6 Discussion

13:00 – 14:00 Lunch Foyer Studio Villa Bosch Lobby

14:00-14:30 Michael Blinov, UConn Health, Farmington, CT (USA) Visualization of Rule-Based Modeling
14:30 – 15:30 Session 7: SBGN workshop
Chairs: Falk Schreiber & Michael Blinov

& Breakouts (up to 2 parallel sessions)


Breakout session for specific topics can be proposed using the Abstract Submission Form.
15:30 – 16:00 Poster Session & Coffee Break Foyer Studio Villa Bosch

16:00 – 17:30 Session 8: COMBINE as Legal Entity
Chairs: Martin Golebiewski & Herbert Sauro

SBGN workshop
Chairs: Falk Schreiber & Michael Blinov

& Breakouts (up to 2 parallel sessions)






Breakout session for specific topics can be proposed using the Abstract Submission Form.



17:30 – 17:45

Plenary Wrapup

19:30-23:00

Conference Dinner at the restaurant S'Kastanie


Day 4 (Thursday, July 18th) - EU-STANDS4PM workshop

Speaker Title Slides
09:30 – 11:00 Session 9: Model and Data Management
Chair: Wolfgang Müller (HITS)
09:30-10:15 Carole Goble, University of Manchester (UK) Keynote: Title TBA
10:15-10:25 speaker: TBA Title of contributed talk
10:25-10:35 speaker: TBA Title of contributed talk
10:35-11:00 all speakers of Session 9 Discussion

11:00 – 11:30 Poster Session & Coffee Break Foyer Studio Villa Bosch

11:30 – 13:00 Session 10: Standards for Personalized Medicine
Chairs: Niklas Blomberg (ELIXIR) & Martin Golebiewski (HITS)
11:30-11:45 Niklas Blomberg, Director ELIXIR, Hinxton (UK) EU-STANDS4PM: Data sources and standards for personalized medicine (tentative title)
11:45-12:15 Norbert Graf, Saarland University Medical Center, Homburg (Germany) Keynote: From data via models to personalized medicine – An example in Pediatric Oncology
12:15-12:30 Petr Holub, BBMRI-ERIC, Masaryk University (Czech Republic) Standards in Biobanking (title TBC)
12:30-12:45 Søren Brunak, University of Copenhagen (DK) Standards for Clinical Data and Systems Medicine (title TBC)
12:45-13:00 Katharina Eva Ó Cathaoir, Faculty of Law, University of Copenhagen (DK) Using patient-derived data for personalized medicine: Ethical and Legal Aspects (title TBC)

13:00 – 14:00 Lunch Foyer Studio Villa Bosch Lobby

14:00-14:30 Adriano Henney, Avicenna Alliance for Predictive Medicine (UK) title TBA
14:30 – 15:30 Session 11: EU-STANDS4PM workshop
Chairs: Niklas Blomberg (ELIXIR) & Martin Golebiewski (HITS)

& Breakouts (up to 2 parallel sessions)



Breakout session for specific topics can be proposed using the Abstract Submission Form.


15:30 – 16:00 Poster Session & Coffee Break Foyer Studio Villa Bosch

16:00 – 17:30 Session 12: EU-STANDS4PM workshop
Chairs: Niklas Blomberg (ELIXIR) & Martin Golebiewski (HITS)

& Breakouts (up to 2 parallel sessions)



Breakout session for specific topics can be proposed using the Abstract Submission Form.

17:30 – 17:45

Plenary Wrapup


Day 5 (Friday, July 19th)

Speaker Title Slides
09:30 – 11:00 Session 13: Semantic Model Annotation
Chair: Dagmar Waltemath (Greifswald, D)
09:30-10:00 David Nickerson, Auckland Bioengineering Institute, University of Auckland (New Zealand) Semantic annotation in the Physiome Model Repository
10:00-10:30 Huaiyu Mi, Keck School of Medicine of the University of Southern California (USC), Los Angeles, CA (USA) Gene Ontology Causal Activity Modeling (GO-CAM)
10:30-10:45 speaker: TBA Title of contributed talk
10:45-11:00 speaker: TBA Title of contributed talk

11:00 – 11:30 Poster Session & Coffee Break Foyer Studio Villa Bosch

11:30 – 13:00 Session 14: Emerging Standardization Needs and Multicellular Modeling
Chairs: Dirk Drasdo (Paris, F) & Tim Johann (Dortmund, D)
11:30-11:50 Padraig Gleeson, University College London (UK) Title of invited talk
11:50-12:10 Melanie Stefan, University of Edinburgh (UK) Multi-method modelling of synaptic plasticity and the challenges it brings
12:10-12:20 speaker: TBA Title of contributed talk
12:20-12:30 speaker: TBA Title of contributed talk
12:30-13:00 all speakers of Session 14 Discussion

13:00 – 14:00 Lunch Foyer Studio Villa Bosch Lobby

14:00 – 15:30 Session 15: FAIRDOM PALs and User Workshop
Chair: Olga Krebs (HITS)

& Breakouts (up to 2 parallel sessions)



Breakout session for specific topics can be proposed using the Abstract Submission Form.


15:30 – 16:00 Poster Session & Coffee Break Foyer Studio Villa Bosch

16:00 – 17:30 Session 16: FAIRDOM PALs and User Workshop
Chair: Olga Krebs (HITS)

& Breakouts (up to 2 parallel sessions)



Breakout session for specific topics can be proposed using the Abstract Submission Form.

17:30 – 17:45

Plenary Wrapup

HITS

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EU-STANDS4PM_COMBINE_workshop_published.pdf1.45 MB