Full agenda


Day 1 (Monday, August 18)

Speaker Title Slides Recordings
10:00 - 10:10 Huaiyu Mi Welcome Slides Video
10:10 - 10:20 Michael Hucka Introduction Slides
10:10 - 12:00 Session 1 Chair: Huaiyu Mi
10:20 - 10:50 Michael Hucka, Caltech SBML and recent developments: the 2014 edition Slides Video
10:50 - 11:20 Frank Bergmann, Heidelberg University The Simulation Experimental Description Markup Language, an update Slides Video
11:20-12:00 Christina Curtis, USC Norris Comprehensive Cancer Center, USC Keck Medical Center Inference of human tumor growth dynamics through integrative genomics and spatial mathematical modeling n/a Video
12:00-13:30 Lunch
13:30 - 15:00 Session 2 Chair: Falk Schreiber
13:30-14:00 Paul Sternberg, Biology and Biological Engineering, Caltech Curated Systems Biology: solving the Worm and presenting it in computable form Slides Video
14:00 -14:30 Fengzhu Sun, Department of Molecular and Computational Biology, USC Integrated approaches for gene prioritization and pathway inference for complex traits n/a Video
14:30 -15:00 Herbert Sauro, University of Washington Developing Standards in Synthetic Biology: the needs for a broad new engineering discipline Slides Video
15:00-15:30 Break
15:30 - 17:00 Session 3 Chair: Chris Myers
15:30 - 16:00 Falk Schreiber, Monash University, Australia An update on Systems Biology Graphical Notation Slides Video
16:00 -16:30 Emek Demir, Path Information Resource, Memorial Sloan Kettering Cancer Center Building Cell Maps:Status and Challenges
Slides Video
16:30 - 17:00 Paul Macklin, Center for Applied Molecular Medicine, USC Keck Medical Center Digital cell lines and MultiCellDS: Standardizing cell phenotype data for data-driven cancer simulations n/a
19:00 - 22:00 COMBINE Reception Ballroom Center, Radisson Hotel Los Angeles at USC, 3540 South Figueroa Street, Los Angeles California 90007

Day 2 (Tuesday, August 19)

Speaker Title Slides Recordings
08:30 breakfast
SBGN Chair: Falk Schreiber
09:00 Falk Schreiber Introduction to SBGN Slides
09:10 Stuart Moodie SBGN PD L1 V2.0 Video
09:30 Anatoly Sorokin SBGN ER L1 V2.0 n/a Video
09:50 Huaiyu Mi SBGN AF L1 V + SBGN AF to represent LEGO Models Slides Video
10:30 Break
SBGN + SBOL Visual Chair: Huaiyu Mi
11:00 Michael Blinov Openworld SBGN RB schema Slides Video
11:20 Robin Haw Reactome Knowledgebase - Linking biological pathways, networks and disease Slides Video
11:40 Tobias Czauderna libSBGN Slides Video
12:00 Jackie Quinn Synthetic Biology Open Language Visual: graphical notation for forward engineering of biology Slides Video
12:30 Lunch
14:00 Parallel Breakouts
Falk Schreiber SBGN + Discussion on SBGN and SBOL Visual connections n/a
Lucian Smith SBML L3 V2 Discussion Slides Video
15:30 Break
16:00 Parallel Breakouts
Jackie Quinn SBOL Visual 2.0 n/a
Lucian Smith Discussion of status of SBML Package development distrib/groups/comp/render/... Slides Video
Huaiyu Mi SBGN discussion
17:30 Breakout report and daily wrap-up
19:00 Conference Dinner at Radisson Hotel

Day 3 (Wednesday, August 20)

Speaker Title Slides Recordings
08:30 Breakfast
SBOL Chair: John Gennari
09:00 Nicholas Roehner Generating SBML models from SBOL Slides Video
09:30 Kevin Clancy Vector NTI Express Designer as a demonstration of SBOL interoperability with COMBINE standards n/a Video
10:00 Curtis Madsen SBOL Stack: The One-stop-shop to Storing and Publishing SBOL Data Slides Video
10:30 Break
Google Summer of Code
Chair: Andreas Draeger
11:00 Victor Kofia Redesign the implementation of mathematical formulas Slides Video
11:30 Leandro Watanabe Arrays Package in JSBML Slides Video
12:00 Ibrahim Vazirabad Improving the JSBML/CellDesigner Plug-in Interface Slides Video
12:30 Lunch
14:00 Parallel Breakouts
Nicholas Roehner SBOL 2.0 Hierarchical Composition n/a
Ion Moraru SBML Spatial Package n/a Video
Tobias Czauderna libSBGN Development + linking SBGN to other standards Slides
15:30 Break
16:00 Parallel Breakouts
Nicholas Roehner SBOL 2.0 Interactions and Other Issues n/a
Fengkai Zhang / Michael Blinov SBML Multi Package Slides Video
Ion Moraru SED-ML n/a
17:30 Breakout report and daily wrap-up Video

Day 4 (Thursday, August 21)

Speaker Title Slides Recordings
08:30 Breakfast
SBML I Chair: Sven Sahle
09:00 Devin Sullivan High-throughput whole-cell spatial modeling Slides Video
09:30 Endre T. Somogyi,
Herbert Sauro
Just-in-time compilation and simulation of SBML Slides Video
10:00 Alex Thomas JSBML 1.0: Providing a Smorgasbord of Options to Encode Systems Biology Models Slides Video
10:30 Break
SBML II Chair: Frank Bergmann
11:00 Martin Golebiewski Data upload into SABIO-RK Slides Video
11:30 Fengkai Zhang Simmune and COMBINE standards Slides n/a
12:00 Jose-Juan Tapia Atomizer: Extracting Implicit Molecular Structure from Reaction Network Models Slides Video
12:30 Lunch
14:00 Parallel Breakouts
Sarah Keating, Chris Myers SBML Arrays and other math extensions Slides Video
Martin Golebiewski Metadata standards n/a
SBGN and SBOL Visual focus group n/a
10:30 Break
16:00 Parallel Breakouts
Harold Gomez SBML Dynamic package and connection with other packages such as Spatial Slides Video
Frank Bergmann Combine Archive & SED-ML Discussion n/a
17:30 Breakout report and daily wrap-up Video

Day 5 (Friday, August 22)

Speaker Title Slides Recordings
08:00 Breakfast
Other Topics Chair: Pedro Mendes
08:30 Joseph Olufemi Dada Numerical Markup Language and Data Converter Slides Video
09:00 Augustin Luna PaxtoolsR: An R Package for Pathway Analysis Using Paxtools and Pathway Commons Slides Video
09:30 Samuel Friedman Using MultiCellDS and digital cell lines to initialize large-scale 3-D agent-based cancer simulations (up to 0.5M cells) Slides Video
10:00 Edwin F. Juárez Rosales A systems identification-based data pipeline to create digital cell lines from cell culture data n/a Video
10:30 Break
11:00 Areas of Collaboration and Coordination Chair: Chris Myers Slides Video
A general discussion on areas of collaboration between systems and synthetic biology standards including connections between the standards, development of repositories, establishing connections with journals, and performing compliance testing.
12:30 Lunch
COMBINE: a community of communities Chair: Michael Hucka
14:00 Martin Golebiewski From grassroots to common standards Slides Video
14:30 General discussion about future of COMBINE, liaisons with other networks and outreach
15:30 Falk Schreiber Announcement for HARMONY 2015 n/a Video
15:37 Lucian Smith The SBOL Story n/a Video
15:40 Huaiyu Mi Workshop wrap-up n/a n/a
15:45 Break
16:00 Nicholas Roehner SBOL 2.0 finalization n/a n/a