COMBINE 2016 - Agenda
Agenda
All meetings will be held at the Crowne Plaza, Newcastle.
Day 1 (Monday, September 19)
| Speaker | Title | Slides | Recordings | |
|---|---|---|---|---|
| 8:15am | Paolo Zuliani & Anil Wipat, Newcastle | Welcome | Slides | |
| 8:30am - 10:00am | Session 1 Chair: Chris J. Myers | Modeling | ||
| 8:30am | Sarah Keating, EMBL-EBI | SBML in 2016 | Slides | |
| 9:15am | David Nickerson, Auckland | CellML, SED-ML, and the Physiome Model Repository | Slides | |
| 10:00am | Break | |||
| 10:30am - noon | Session 2 Chair: Herbert Sauro | Modeling | ||
| 10:30am | Dagmar Iber, ETH Zurich | From Networks to Function - Computational Models of Organogenesis | Slides | |
| 11:15am | Andrew Millar, Edinburgh | What infrastructure to cross the genotype-to-phenotype gap: foundations or flying buttresses? | ||
| noon | Lunch | |||
| 1:30pm - 3:00pm | Session 3 Chair: Paolo Zuliani | Medical Applications | ||
| 1:30pm | Yujiang Wang, Newcastle | Control of epileptic seizures - a computational perspective | ||
| 2:15pm | Alfonso Bueno-Orovio, Oxford | Delivering cardiac computational biology to industry and the clinic: Advances towards reshaping future health and care | ||
| 3:00pm | Break | |||
| 3:30pm - 5:00pm | Session 4 Chair: David Nickerson | Models and Data Exchange | ||
| 3:30pm | Carole Goble, Manchester | FAIRDOM - FAIR asset management and sharing experiences in Systems and Synthetic Biology | Slides | |
| 4:15pm | Chris J. Myers, Utah | A Standard Enabled Workflow for Synthetic Biology | Slides | |
| 5:00pm | Wrapup | |||
| 5:30pm | Social Event | |||
| 7:00pm | Banquet (Crowne Plaza) |
Day 2 (Tuesday, September 20)
| Speaker | Title | Slides | Recordings | |
|---|---|---|---|---|
| 8:30am - 10:00am | Session 5 Chair: Goksel Misirli | Software | ||
| 8:30am | David Nickerson, Auckland | OpenCMISS-Osmium: helping PMR support the VPH requirements for identifiable and discoverable computational models | Slides | |
| 8:45am | Herbert Sauro, Washington | pathwayDesigner: A SBML compliant network simulation and design tool | Slides | |
| 9:00am | Matthias König, Humboldt | cy3sbml: a Cytoscape app for SBML | Slides | |
| 9:15am | Curtis Madsen & Nicholas Roehner, Boston | Nona Research Foundation - Creating a SynBio Software Commons | Slides | |
| 9:30am | Discussion | |||
| 10:00am | Break/Posters | |||
| 10:30am - noon | Session 6 Chair: Curtis Madsen | Synthetic Biology | ||
| 10:30am | Goksel Misirli, Newcastle | Data Integration and Mining for Synthetic Biology Design | Slides | |
| 10:45am | Hiroyuki Kuwahara, KAUST | A new thermodynamics-based approach to aid the design of natural-product biosynthetic pathways | Slides | |
| 11:00am | Nicholas Roehner, Boston | How to Remember and Revisit Many Genetic Design Variants Automatically | Slides | |
| 11:15am | Bryan Bartley, Washington | Version and Variant Control for Synthetic Biology | Slides | |
| 11:30am | Discussion | |||
| noon | Lunch | |||
| 1:30pm - 3:00pm | Session 7 | Breakouts | ||
| Leader: Anil Wipat, Track: SBOL | SBOL: Host Context (remote attendance via BlueJeans) | |||
| Leader: David Nickerson | SED-ML: L1V3 Status/Review (remote attendance via BlueJeans) | |||
| 3:00pm | Break/Posters | |||
| 3:30pm - 5:00pm | Session 8 | Breakouts | ||
| Leader: Lucian Smith, Track: SBML | SBML L3v2 (and libsbml/test suite support) (remote attendance via BlueJeans) | |||
| Leader: Herbert Sauro, Track: SBOL | SBOL: Website, FAQ, and Tutorials (remote attendance via BlueJeans) | |||
| 5:00pm | Wrapup |
Day 3 (Wednesday, September 21)
| Speaker | Title | Slides | Recordings | |
|---|---|---|---|---|
| 8:30am - 10:00am | Session 9 Chair: Anil Wipat | Invited Talks | ||
| 8:30am | Martin Golebiewski, HITS | COMBINE and ISO/TC 276 Biotechnology: From grassroots community standards to official ISO standards | Slides | |
| 9:15am | Daryl Shanley, Newcastle | Modelling ageing to enhance a healthy lifespan | Slides | |
| 10:00am | Break/Posters | |||
| 10:30am - noon | Session 10 Chair: Frank Bergmann | Web | ||
| 10:30am | Vincent Noel, Instituto Butantan | SigNetSim : A web-based framework for designing kinetic models of molecular signaling networks | Slides | |
| 10:45am | Andreas Draeger, Tuebingen | The ZBIT Systems Biology Software and Web Service Collection | Slides | |
| 11:00am | Martin Peters, Rostock | SED-ML support in JWS Online | Slides | |
| 11:15am | Martin Golebiewski, HITS | The NormSys registry for modeling standards in systems and synthetic biology | Slides | |
| 11:30am | Discussion | |||
| noon | Lunch | |||
| 1:30pm - 3:00pm | Session 11 | Breakouts | ||
| Leader: Sarah Keating, Track: SBML | SBML Math packages (remote attendance via BlueJeans) | |||
| Leader: Robert Sydney Cox, Track: SBOL | SBOL Visual / SBGN (remote attendance via BlueJeans) | |||
| 3:00pm | Break/Posters | |||
| 3:30pm - 5:00pm | Session 12 | Breakouts | ||
| Leader: James McLaughlin, Track: SBOL | SBOL: Ontologies and URI Best Practices (remote attendance via BlueJeans) | |||
| Leader: Kieran Alden | Standards for storing and exchanging agent-based models (remote attendance via BlueJeans) | |||
| 5:00pm | Wrapup |
Day 4 (Thursday, September 22)
| Speaker | Title | Slides | Recordings | |
|---|---|---|---|---|
| 8:30am - 10:00am | Session 13 Chair: Martin Golebiewski | Ermerging Standards | ||
| 8:30am | Fengkai Zhang, NIH | SBML Multi - From Specification to Application | Slides | |
| 8:45am | Samuel Friedman, USC | MultiCellDS: a community-developed standard for curating microenvironment-dependent multicellular phenotype data as digital cell lines, snapshots, and collections | ||
| 9:00am | David Nickerson, Auckland | Exploiting Electronic Health Record Standard openEHR to Manage Experimental Data in Computational Physiology | Slides | |
| 9:15am | Kieran Alden, York | Approaches for Developing Computational Models of Immune System Formation and Function | Slides | |
| 9:30am | Discussion | |||
| 10:00am | Break/Posters | |||
| 10:30am - noon | Session 14 Chair: Andreas Draeger | Simulation | ||
| 10:30am | Kiri Choi, Washington | Tellurium: A Python Based Modeling and Reproducibility Platform for Systems Biology | Slides | |
| 10:45am | Leandro Watanabe, Utah | Modeling and Simulating Hybrid SBML Models | Slides | |
| 11:00am | Fabian Fröhlich, Helmholtz Zentrum München | AMICI: An ODE simulation framework for sensitivity analysis of large-scale models | Slides | |
| 11:15am | J Kyle Medley, Washington | High-performance Model Simulation with libRoadRunner | ||
| 11:30am | Discussion | |||
| noon | Lunch | |||
| 1:30pm - 3:00pm | Session 15 | Breakouts | ||
| Leader: Bryan Bartley, Track: SBOL | SBOL Sequence Layer (remote attendance via BlueJeans) | |||
| Leader: Dagmar Waltemath, Track: SED-ML/SBML | SED-ML/SBML & qual (remote attendance via BlueJeans) | |||
| 3:00pm | Break/Posters | |||
| 3:30pm - 5:00pm | Session 16 | Breakouts | ||
| Leader: Tramy Nguyen, Track: SBOL | SBOL Interaction Definitions (remote attendance via BlueJeans) | |||
| Leader: Fengkai Zhang, Track: SBML | SBML Multi Package (remote attendance via BlueJeans) | |||
| 5:00pm | Wrapup |
Day 5 (Friday, September 23)
| Speaker | Title | Slides | Recordings | |
|---|---|---|---|---|
| 8:30am - 10:00am | Session 17 Chair: Dagmar Waltemath | Model Exchange | ||
| 8:30am | Maciej J Swat, EMBL-EBI | PharmML - exchange format for models used in quantitative system pharmacology and pharmacometrics | Slides | |
| 8:45am | Augustin Luna, BioPAX Consortium | Biological Pathway Exchange (BioPAX) Format and Pathway Commons Update | Slides | |
| 9:00am | Miguel de Alba, Federal Institute for Risk Assessment (BfR) | Introducing FSK-ML - an SBML derivate for description and exchange of executable script based models | Slides | |
| 9:15am | Tramy Nguyen, Utah | Interconversion Between BioPAX and SBML | Slides | |
| 9:30am | Discussion | |||
| 10:00am | Break/Posters | |||
| 10:30am - noon | Session 18 Chair: Nicholas Roehner | Visual Standards | ||
| 10:30am | Alexander Mazein, European Institute for Systems Biology and Medicine | Comprehensive representation of disease mechanisms on multiple layers of granularity in SBGN PD and AF | Slides | |
| 10:45am | Robert Sidney Cox, Caltech | The Visual Protein Design Language | Slides | |
| 11:00am | Jacob Beal, BBN | Progress Report on Development of SBOL Visual 2.0 | Slides | |
| 11:15am | Vasundra Toure, Rostock | Visualising differences in SBML models using SBGN and BiVeS | Slides | |
| 11:30am | Discussion | |||
| noon | Lunch | |||
| 1:30pm - 3:00pm | Session 19 | Breakouts | ||
| Leader: Anil Wipat, Track: SBOL | General Discussion/Hacking (remote attendance via BlueJeans) | |||
| Leader: David Nickerson, Track: SED-ML | SED-ML: New Output Types, Plots, Roadmap (remote attendance via BlueJeans) | |||
| 3:00pm | Break/Posters | |||
| 3:30pm - 5:00pm | Session 20 | Breakouts | ||
| Leader: Dagmar Waltemath | COMBINEd Annotations (remote attendance via BlueJeans) | |||
| 5:00pm | Wrapup |
Day 6 (Saturday, September 24)
The SBGN Workshop/Hackathon will be held in the same venue (Crowne Plaza).
Posters
| Presenter | Title | Poster |
|---|---|---|
| Nima Afshar, Auckland | Computational Modelling of Glucose uptake in enterocytes using CellML |
|
| Kieran Alden, York | Approaches for Understanding the Relationship Between a Computational Model and Captured Real-World Phenomena |
|
| Florian Auer, Goettingen | Bringing Pathway Knowledge to Systems Medicine Approaches |
|
| Petronela Buiga, Manchester | Application of systems biology regulation of HER2 signalling in breast cancer therapy |
|
| Kiri Choi, University of Washington | Using SBML to Model Cellular Automata |
|
| Harold Fellerman, Newcastle | A temperature-dependent computational model of the PCR reaction |
|
| Matthias König, Humboldt University | Personalized liver function tests: A Multiscale Computational Model Predicts Individual Human Liver Function From Single-Cell Metabolism |
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| Goksel Misirli, Newcastle | Data Integration and Mining for Synthetic Biology Design |
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| Goksel Misirli, Newcastle | Modular Composition of Synthetic Biology Designs using Rule-Based Models |
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| Jeremy Revell, Newcastle | Cross Entropy Method For Stochastic Parameter Inference |
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| James Scott-Brown, Oxford | Visual Comparison of SBML Models |
|
| Vasundra Toure, Rostock | A demonstration of a fully-featured COMBINE Archive |
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| Vasundra Toure, Rostock | Designing informative SBGN maps using SBGN-ED |
|
| Brijesh S. Yadav, Tel Aviv | Multidimensional patterns of metabolic response in abiotic stress-induced growth of Arabidopsis thaliana |