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 Slides
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 Slides
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 Slides
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)
Slides
Combinatorial Design
(Led by Nic)
Slides
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)
Minutes (pdf)
Minutes (google doc)
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
Minutes (pdf)
Minutes (google doc)
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)
Slides
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)
Agenda/Minutes (gdoc)
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)
Lucian - Distrib package overwiew
Swat - ProbOnto overwiew
SBOL Hacking SBGN Specifications
(Augustin)
10:30am Coffee break
10:30 - 12:30 FBC units and progressing to Dynamical FBA
(Matthias)
Slides
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)
Slides
10:30am Coffee break
10:30 - 11:00 COMBINE Annotations
(John Gennari)
11:00 - 12:00 Wrap-up
12:30am Lunch