COMBINE 2019 - Agenda (old)
Agenda
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 | |
| 10:05-10:20 | Gesa Schönberger and Wolfgang Müller | Welcome addresses from the HITS Management | |
| 10:20-11:00 | 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 – 11:05 | Session 1: Synthetic Biology | Chairs: Ernst Oberortner (Lawrence Berkeley National Laboratory, CA, USA) & Chris Myers (Salt Lake City, UT, USA) | |
| 09:30-10:00 | Chris Myers, University of Utah, Salt Lake City, UT (USA) | A Standard Enabled Workflow for Synthetic Biology | |
| 10:00-10:30 | Manuel Porcar Miralles, Institute for Integrative Systems Biology, València (Spain) | BioRoboost: A last chance for standardisation in biology? | |
| 10:30-10:40 | Pedro Fontanarrosa, University of Utah, Salt Lake City, UT (USA) | Analyzing Genetic Circuits for Hazards and Glitches | |
| 10:40-10:50 | Ernst Oberortner, Lawrence Berkeley Nat. Laboratory (USA) | SBOL and its applicability in partially and fully automated design workflows: Three success stories | |
| 10:50-11:05 | all speakers of Session 1 | Discussion | |
| 11:05 – 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, University of Washington, Seattle, WA (USA) | The Center for Reproducible Biomedical Modeling | |
| 12:00-12:10 | Karin Lundengård, University of Auckland (NZ) | Physiome - Publish your models curated for reproducibility and reusability to increase research quality for everyone | |
| 12:10-12:20 | Jacky Snoep, Stellenbosch University (South Africa) | Reproducibility in model construction, validation and analysis workflows in systems biology projects; Xylose metabolism in Caulobacter crescentus as a case study, using JWS Online and the FAIRDOMHub | |
| 12:20-12:30 | Emek Demir, Oregon Health and Science University, Portland (USA) | Causal, Mechanistic Pathway Based Analysis of -Omic Profiles | |
| 12:30-12:40 | Polyxeni Gkontra, La Fe Health Research Institute (IIS La Fe), Valencia (Spain) | Predictive in-silico multiscale analytics to support cancer personalized diagnosis and prognosis, empowered by imaging biomarkers | |
| 12:40-13:00 | all speakers of Session 2 | Discussion | |
| 13:00 – 14:00 | Lunch | Foyer Studio Villa Bosch Lobby | |
| 14:00 – 15:30 | Session 3a: Sharing experiences in building a standards community | Chairs: Dagmar Waltemath (Greifswald, D) & Mike Hucka (Pasadena, CA, USA) | |
| 14:00 – 15:30 | Session 3b: Reproducibility - SED-ML Script: a Proposal | Chairs: Herbert Sauro & Lucian Smith (Seattle, WA, USA) | |
| 15:30 – 16:00 | Poster Session & Coffee Break | Foyer Studio Villa Bosch | |
| 16:00 – 17:30 | Session 4: COMBINE as Legal Entity | Chairs: Martin Golebiewski (Heidelberg, D) & Herbert Sauro (Seattle, WA, USA) | |
| 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) | A personalized modeling pipeline for cardiac electrophysiology simulations of cardiac resynchronization therapy in infarct patients | |
| 10:00-10:10 | Yosef Roth, Icahn School of Medicine at Mount Sinai, New York City, NY (USA) | Datanator: Tools for Aggregating Data for Large-Scale Biomodeling | |
| 10:10-10:20 | Fabian Fröhlich, Harvard Medical School, Boston, MA (USA) | Simulation and Sensitivity Analysis for Large Kinetic Models in AMICI | |
| 10:20-10:30 | Alan Garny, University of Auckland (NZ) | OpenCOR: current status and future plans | |
| 10:30-10:45 | all speakers of Session 5 | Discussion | |
| 10:45 – 11:15 | Poster Session & Coffee Break | Foyer Studio Villa Bosch | |
| 11:15 – 13:00 | Session 6: Visualization | Chairs: Falk Schreiber (Konstanz, D) & Michael Blinov (Farmington, CT, USA) | |
| 11:15-11:45 | Akira Funahashi, Keio University, Yokohama (Japan) | CellDesigner: A modeling tool for biochemical networks | |
| 11:45-12:15 | Michael Blinov, UConn Health, Farmington, CT (USA) | Virtual Cell: Modeling and Visualization of Reaction Rules | |
| 12:15-12:25 | Jeanet Mante, University of Utah, Salt Lake City, UT (USA) | Visualization of Part Use in SynBioHub | |
| 12:25-12:35 | Oscar O Ortega, Vanderbilt University, Nashville, TN (USA) | PySB framework: Tools to build, calibrate and visualize biochemical models | |
| 12:35-12:45 | Augustin Luna, Harvard Medical School, Boston, MA (USA) | Visualization, Access, and Exploration of Biological Pathway Information from Pathway Commons | |
| 12:45-13:00 | all speakers of Session 6 | Discussion | |
| 13:00 – 14:00 | Lunch | Foyer Studio Villa Bosch Lobby | |
| 14:00-15:30 | Session 7a: SBGN workshop | Chairs: Falk Schreiber (Konstanz, D) & Michael Blinov (Farmington, CT, USA) | |
| 14:00-15:30 | Session 7b: MIRIAM 2 & the OMEX Metadata Specification | Chairs: Dagmar Waltemath (Greifswald, D) & David Nickerson (Auckland, NZ) | |
| 14:00-15:30 | Session 7c: SBOL | Chairs: Ernst Oberortner (Berkeley, CA, USA) & Chris Myers (Salt Lake City, UT, USA) | |
| 15:30 – 16:00 | Poster Session & Coffee Break | Foyer Studio Villa Bosch | |
| 16:00 – 17:30 | Session 8a: SBGN workshop | Chairs: Falk Schreiber (Konstanz, D) & Michael Blinov (Farmington, CT, USA) | |
| 16:00 – 17:30 | Session 8b: Model eXchange consortium: Inaugural meeting | Chairs: Henning Hermjakob & Rahuman Sheriff (EMBL-EBI, Hinxton, UK) | |
| 14:00-15:30 | Session 8c: SBOL | Chairs: Ernst Oberortner (Berkeley, CA, USA) & Chris Myers (Salt Lake City, UT, USA) | |
| 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 & Ulrike Wittig (Heidelberg, D) | |
| 09:30-10:15 | Carole Goble, University of Manchester (UK) | Keynote:Let’s go on a FAIR asset management safari | |
| 10:15-10:25 | Susheel Varma, EMBL-EBI, Hinxton (UK) | ELIXIR Cloud & AAI: Standardised and Interoperable Services for Human Data Communities | |
| 10:25-10:35 | Rahuman Sheriff, EMBL-EBI, Hinxton (UK) | BioModels Parameters: A resource to search and access parameters from published systems models | |
| 10:35-10:45 | Martin Golebiewski, HITS, Heidelberg (D) | Two universes – one world: Community standards vs. formal standards in systems biology and systems medicine | |
| 10:45-11:00 | 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: Marc Kirschner (Jülich, D) & Martin Golebiewski (HITS) | |
| 11:30-11:45 | Marc Kirschner, PTJ (Germany) & Ingrid Skelton Kockum, Karolinska Institutet (Sweden) | EU-STANDS4PM: A pan-European Expert Forum joined forces to tackle the complexity of big data integration for in silico methodologies in personalised medicine | |
| 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 | |
| 12:30-12:45 | Søren Brunak, University of Copenhagen (DK) | Standards for Clinical Data and Systems Medicine | |
| 12:45-13:00 | Katharina Eva Ó Cathaoir, Faculty of Law, University of Copenhagen (DK) | A Bird's Eye view of Legal and Ethical aspects of EU-STANDS4PM | |
| 13:00 – 14:00 | Lunch | Foyer Studio Villa Bosch Lobby | |
| 14:00-14:30 | Liesbet Geris, Executive Director VPH Institute, KU Leuven (Belgium) | In silico medicine and the VPH institute: bringing the community together and the field forward | |
| 14:30 – 15:30 | Session 11a: EU-STANDS4PM workshop | Chairs: Marc Kirschner (Jülich, D) & Martin Golebiewski (HITS) | |
| 14:00 – 15:30 | Session 11b: Something old, something new: constraint-based modelling and SBML | Chair: Brett Olivier (VU University Amsterdam, NL) | |
| 14:00 – 15:30 | Session 11c: SBOL | Chairs: Ernst Oberortner (Berkeley, CA, USA) & Chris Myers (Salt Lake City, UT, USA) | |
| 15:30 – 16:00 | Poster Session & Coffee Break | Foyer Studio Villa Bosch | |
| 16:00 – 17:30 | Session 12a: EU-STANDS4PM workshop | Chairs: Marc Kirschner (Jülich, D) & Martin Golebiewski (HITS) | |
| 16:00 – 17:30 | Session 12b: SBML L3 Packages - An Introduction to SBML packages | Chair: Sarah Keating (University College London, UK) | |
| 16:00 – 17:30 | Session 12c: SBOL | Chairs: Ernst Oberortner (Berkeley, CA, USA) & Chris Myers (Salt Lake City, UT, USA) | |
| 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) | |
| 10:30-10:40 | Anand Rampadarath, University of Auckland (NZ) | Model curation and annotation | |
| 10:40-10:50 | Henning Hermjakob, EMBL-EBI, Hinxton (UK) | Identifiers.org Compact Identifiers for robust data citation | |
| 10:50-11:00 | all speakers of session 13 | Discussion | |
| 11:00 – 11:30 | Poster Session & Coffee Break | Foyer Studio Villa Bosch | |
| 11:30 – 13:00 | Session 14: Emerging Standardization Needs and Multicellular Modeling Chair: Tim Johann (Dortmund, D) | ||
| 11:30-11:50 | Padraig Gleeson, University College London (UK) | Sharing standardised models and data on the Open Source Brain platform | |
| 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 | Jörn Starruß, TU Dresden (D) | Principles for declarative multicellular modelling | |
| 12:20-12:30 | Guillerm Yanez, Pontificia Universidad Católica de Chile (CL) | Flapjack: an open-source tool for storing, visualising, analysing and modelling kinetic gene expression data | |
| 12:30-12:45 | all speakers of Session 14 | Discussion | |
| 13:00 – 14:00 | Lunch | Foyer Studio Villa Bosch Lobby | |
| 12:45 – 13:00 | CLOSING PLENARY; Chairs: Martin Golebiewski (HITS, Heidelberg, D) & Dagmar Waltemath (University of Greifswald, D) | Foyer Studio Villa Bosch Lobby | |
| 13:00 – 14:00 | Lunch | Foyer Studio Villa Bosch Lobby | |
| 14:00 – 15:30 | Session 15a: FAIRDOM PALs and User Workshop | Chair: Olga Krebs (HITS) | |
| 14:00 – 15:30 | Session 15b: Model eXchange consortium | Chairs: Henning Hermjakob & Rahuman Sheriff (EMBL-EBI, Hinxton, UK) | |
| 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) | |
| 17:30 | End of Meeting |
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| Attachment | Size |
|---|---|
| EU-STANDS4PM_COMBINE_workshop_published.pdf | 1.45 MB |