HARMONY 2017 - Agenda
Agenda
All meetings have been held in the William H. Foege Bioengineering building, at the University of Washington, Seattle.
Day 1 (Monday, June 26)
| Speaker | Title | Slides | |
|---|---|---|---|
| 9:00 | Prof. Hao Y. Kueh, UW Dept. Bioengineering | Plenary talk | |
| 9:30 - 10:30 | Session 1 Chair: Kyle/Sarah | Flash presentations | |
| Kyle Medley, Univ. Washington | Tellurium 2.0: Revamped Notebook Interface & COMBINE Archive Support | ||
| Chris Myers, Univ. Utah | Model generation in iBioSim using SBOL and SBML | ||
| Frank Bergmann, Heidelberg Univ. | COPASI new features and support of standards | ||
| Matthias König, Humboldt University | sbmlutils: sbml reports, annotation, DFBA | <html><a href="http://old_co.mbine.org/sites/combine/files/harmony2017/sbmlutils-HARMONY2017-flash-talk.slides.html">Slides</a></html> | |
| Ernst Oberortner, Lawrence Berkeley Labs | SBOL.assembly: Automated Design to Build Transition using SBOL 2.0 | ||
| Tom Gebhardt, University of Rostock | ModelStats: Visualize statistics of model versions dynamically | ||
| Lucian Smith, Caltech | SBML Test Suite | <html><a href="http://old_co.mbine.org/sites/combine/files/harmony2017/LucianSmith_Test_suite_lightTalk.pptx">Slides</a></html> | |
| Robert Sidney Cox, Prospect Bio | The Protein Design Language | ||
| Joe Hellerstein, Univ. Washington | Kinetics modeling with templates | ||
| JohnGennari/MaxNeal, Univ. Washington | Annotation and model merging in SemGen | ||
| Augustin Luna, Dana-Farber Cancer Institute | Javascript-based SBGN tools: Newt/SBGNViz.js and libSBGN.js | <html><a href="http://old_co.mbine.org/sites/combine/files/harmony2017/AugustinLuna_harmony_2017_lightTalk.pptx">Slides</a></html> | |
| James McLaughlin, Newcastle University | SynBioHub: A Design Repository for Synthetic Biology | ||
| 10:30 | Break |
| Track 1 | Track 2 | Track 3 | |
|---|---|---|---|
| 10:30 - 12:30 | SBML L3V2 Implementation | SBOL Visual 2.0 (Led by Jake) | Meet with SBOL |
| 12:30am | Lunch | ||
| 14:00 - 15:30 | SBML Package Status updates (Lucian) <html><a href="http://old_co.mbine.org/sites/combine/files/harmony2017/LucianSmith_SBML_Packages_update.pptx">Slides</a></html> | Combinatorial Design (Led by Nic) <html><a href="http://old_co.mbine.org/sites/combine/files/harmony2017/NicholasRoehner_Combinatorial_design_in_SBOL.pptx">Slides</a></html> | Biological semantics and annotation (Max) |
| 15:30 | Coffee break | ||
| 16:00 - 17:30 | libSBML and JSBML Developers available for discussion | Combinatorial Design (Led by Nic) | Biological semantics and annotation (Max) |
| 17:30 - 18:00 | Wrap-up |
Day 2 (Tuesday, June 27)
| Track 1 | Track 2 | Track 3 | |
|---|---|---|---|
| 09:00 - 10:30 | SED-ML current status (David) <html><a href="http://old_co.mbine.org/sites/combine/files/harmony2017/SED-MLdiscussionsHARMONY2017-2017-06-30.pdf">Minutes (pdf)</a> <a href="https://docs.google.com/document/d/1l2jx5K6msZhB-kfZKjeN2WgRVgfkVuCYnM8yYhIsUsw/edit?usp=sharing">Minutes (google doc)</a></html> | iGEM Vision (Led by Vinoo) | SBGN Specifications (Augustin) |
| 10:30am | Coffee break | ||
| 10:30 - 12:30 | SED-ML and Data (Frank) | iGEM Vision (Led by Vinoo) | SBGN Specifications (Augustin) |
| 12:30am | Lunch | ||
| 14:00 - 15:30 | SBML/CellML/SED-ML Hacking | Workflow Hacking | Linking CellML to Clinical Data (David) |
| 15:30 | Coffee break | ||
| 16:00 - 17:30 | SBML/CellML/SED-ML Hacking | Workflow Hacking | Linking CellML to Clinical Data (David) |
| 17:30 - 18:00 | Wrap-up |
Day 3 (Wednesday, June 28)
| Track 1 | Track 2 | Track 3 | |
|---|---|---|---|
| 09:00 - 10:30 | SED-ML Specification Hacking <html><a href="http://old_co.mbine.org/sites/combine/files/harmony2017/SED-MLdiscussionsHARMONY2017-2017-06-30.pdf">Minutes (pdf)</a> <a href="https://docs.google.com/document/d/1l2jx5K6msZhB-kfZKjeN2WgRVgfkVuCYnM8yYhIsUsw/edit?usp=sharing">Minutes (google doc)</a></html> | Provenance/Assembly (Led by James) | SBGN Specifications (Augustin) |
| 10:30am | Coffee break | ||
| 10:30 - 12:30 | SED-ML specification issues (David) | Provenance/Assembly (Led by James) | SBGN Specifications (Augustin) |
| 12:30am | Lunch | ||
| 14:00 - 15:30 | SBML Math packages progress (Sarah) <html><a href="http://old_co.mbine.org/sites/combine/files/harmony2017/SarahKeating_Math_packages.pptx">Slides</a></html> | Experimental Data (Sid) | SBGNML Storing IDs/Annotations (libSBGN.js) |
| 15:30 | Coffee break | ||
| 16:00 - 17:30 | SBML/CellML/SED-ML Hacking | Experimental Data (Sid) <html><a href="https://docs.google.com/document/d/1HRfeph-ieygm3Sfw34yFs0PDxEB6cSx3dBf8_DRncXc/edit?usp=sharing%E2%80%8B">Agenda/Minutes (gdoc)</a></html> | SBGNML Storing IDs/Annotations (libSBGN.js) |
| 17:30 - 18:00 | Wrap-up |
Day 4 (Thursday, June 29)
| Track 1 | Track 2 | Track 3 | |
|---|---|---|---|
| 09:00 - 10:30 | SBML Distrib Package (Lucian) <html><a href="http://old_co.mbine.org/sites/combine/files/harmony2017/LucianSmith_Distributions.pptx">Lucian - Distrib package overwiew</a> <a href="http://old_co.mbine.org/sites/combine/files/harmony2017/Swat_ProbOnto.ppt">Swat - ProbOnto overwiew</a></html> | SBOL Hacking | SBGN Specifications (Augustin) |
| 10:30am | Coffee break | ||
| 10:30 - 12:30 | FBC units and progressing to Dynamical FBA (Matthias) <html><a href="http://old_co.mbine.org/sites/combine/files/harmony2017/Koenig_DFBA.v9.pdf">Slides</a></html> | SBOL Hacking | SBGN Specifications (Augustin) |
| 12:30am | Lunch | ||
| 14:00 - 15:30 | SED-ML with data (Frank) | SBOL Visual 2 (Led by Jake) | SBGNViz.js |
| 15:30 | Coffee break | ||
| 16:00 - 17:30 | COMBINE archive status and plans | SBOL Visual 2 (Led by Jake) | SBGNViz.js |
| 17:30 - 18:00 | Wrap-up |
Day 5 (Friday, June 30)
| Track 1 | Track 2 | Track 3 | |
|---|---|---|---|
| 09:00 - 10:30 | COMBINE Annotations (John Gennari) <html><a href="http://old_co.mbine.org/sites/combine/files/harmony2017/GennariJohn_SemanticAnnotationsForCombine.pptx ">Slides</a></html> | ||
| 10:30am | Coffee break | ||
| 10:30 - 11:00 | COMBINE Annotations (John Gennari) | ||
| 11:00 - 12:00 | Wrap-up | ||
| 12:30am | Lunch |