| | Speaker | Title | Slides | Recordings |
| 10:00 - 10:10 | Huaiyu Mi | Welcome | Slides | <html><a href="/sites/combine/files/combine2014/2014-08-18-mi.mov">Video</a></html> |
| 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 | <html><a href="/sites/combine/files/combine2014/2014-08-18-hucka.mov">Video</a></html> |
| 10:50 - 11:20 | Frank Bergmann, Heidelberg University | The Simulation Experimental Description Markup Language, an update | Slides | <html><a href="/sites/combine/files/combine2014/2014-08-18-bergmann.mov">Video</a></html> |
| 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 | <html><a href="/sites/combine/files/combine2014/2014-08-18-curtis.mov">Video</a></html> |
| 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 | <html><a href="/sites/combine/files/combine2014/2014-08-18-sternberg.mov">Video</a></html> |
| 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 | <html><a href="/sites/combine/files/combine2014/2014-08-18-sun.mov">Video</a></html> |
| 14:30 -15:00 | Herbert Sauro, University of Washington | Developing Standards in Synthetic Biology: the needs for a broad new engineering discipline | Slides | <html><a href="/sites/combine/files/combine2014/2014-08-18-sauro.mov">Video</a></html> |
| 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 | <html><a href="/sites/combine/files/combine2014/2014-08-18-schreiber.mov">Video</a></html> |
| 16:00 -16:30 | Emek Demir, Path Information Resource, Memorial Sloan Kettering Cancer Center | Building Cell Maps:Status and Challenges
Slides | Slides | <html><a href="/sites/combine/files/combine2014/2014-08-18-demir.mov">Video</a></html> |
| 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 | <html><a href="/sites/combine/files/combine2014/2014-08-18-macklin.mov"></a></html> |
| 19:00 - 22:00 | COMBINE Reception | Ballroom Center, Radisson Hotel Los Angeles at USC, 3540 South Figueroa Street, Los Angeles California 90007 | | |
| | 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 | | <html><a href="/sites/combine/files/combine2014/2014-08-19-moodie.mov">Video</a></html> |
| 09:30 | Anatoly Sorokin | SBGN ER L1 V2.0 | n/a | <html><a href="/sites/combine/files/combine2014/2014-08-19-sorokin.mov">Video</a></html> |
| 09:50 | Huaiyu Mi | SBGN AF L1 V + SBGN AF to represent LEGO Models | Slides | <html><a href="/sites/combine/files/combine2014/2014-08-19-mi.mov">Video</a></html> |
| 10:30 | Break | | | |
| | SBGN + SBOL Visual | Chair: Huaiyu Mi | | |
| 11:00 | Michael Blinov | Openworld SBGN RB schema | Slides | <html><a href="/sites/combine/files/combine2014/2014-08-19-blinov.mov">Video</a></html> |
| 11:20 | Robin Haw | Reactome Knowledgebase - Linking biological pathways, networks and disease | Slides | <html><a href="/sites/combine/files/combine2014/2014-08-19-haw.mov">Video</a></html> |
| 11:40 | Tobias Czauderna | libSBGN | Slides | <html><a href="/sites/combine/files/combine2014/2014-08-19-czauderna.mov">Video</a></html> |
| 12:00 | Jackie Quinn | Synthetic Biology Open Language Visual: graphical notation for forward engineering of biology | Slides | <html><a href="/sites/combine/files/combine2014/2014-08-19-quinn.mov">Video</a></html> |
| 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 | <html><a href="/sites/combine/files/combine2014/2014-08-19-sbml-l3v2-discussion.mov">Video</a></html> |
| 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 | <html><a href="/sites/combine/files/combine2014/2014-08-19-sbml-package-dev-discussion.mov">Video</a></html> |
| | Huaiyu Mi | SBGN discussion | | |
| 17:30 | | Breakout report and daily wrap-up | | |
| 19:00 | Conference Dinner at Radisson Hotel | | | |
| | Speaker | Title | Slides | Recordings |
| 08:30 | Breakfast | | | |
| | SBOL | Chair: John Gennari | | |
| 09:00 | Nicholas Roehner | Generating SBML models from SBOL | Slides | <html><a href="/sites/combine/files/combine2014/2014-08-20-roehner.mov">Video</a></html> |
| 09:30 | Kevin Clancy | Vector NTI Express Designer as a demonstration of SBOL interoperability with COMBINE standards | n/a | <html><a href="/sites/combine/files/combine2014/2014-08-20-clancy.mov">Video</a></html> |
| 10:00 | Curtis Madsen | SBOL Stack: The One-stop-shop to Storing and Publishing SBOL Data | Slides | <html><a href="/sites/combine/files/combine2014/2014-08-20-madsen.mov">Video</a></html> |
| 10:30 | Break | | | |
| | JSBML
Google Summer of Code | Chair: Andreas Draeger | | |
| 11:00 | Victor Kofia | Redesign the implementation of mathematical formulas | Slides | <html><a href="/sites/combine/files/combine2014/2014-08-20-kofia.mov">Video</a></html> |
| 11:30 | Leandro Watanabe | Arrays Package in JSBML | Slides | <html><a href="/sites/combine/files/combine2014/2014-08-20-watanabe.mov">Video</a></html> |
| 12:00 | Ibrahim Vazirabad | Improving the JSBML/CellDesigner Plug-in Interface | Slides | <html><a href="/sites/combine/files/combine2014/2014-08-20-vazirabad.mov">Video</a></html> |
| 12:30 | Lunch | | | |
| 14:00 | Parallel Breakouts | | | |
| | Nicholas Roehner | SBOL 2.0 Hierarchical Composition | n/a | |
| | Ion Moraru | SBML Spatial Package | n/a | <html><a href="/sites/combine/files/combine2014/2014-08-20-sbml-spatial-discussion.mov">Video</a></html> |
| | 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 | <html><a href="/sites/combine/files/combine2014/2014-08-20-sbml-multi-discussion.mov">Video</a></html> |
| | Ion Moraru | SED-ML | n/a | |
| 17:30 | | Breakout report and daily wrap-up | | <html><a href="/sites/combine/files/combine2014/2014-08-20-breakout-reports.mov">Video</a></html> |
| | Speaker | Title | Slides | Recordings |
| 08:30 | Breakfast | | | |
| | SBML I | Chair: Sven Sahle | | |
| 09:00 | Devin Sullivan | High-throughput whole-cell spatial modeling | Slides | <html><a href="/sites/combine/files/combine2014/2014-08-21-sullivan.mov">Video</a></html> |
| 09:30 | Endre T. Somogyi,
Herbert Sauro | Just-in-time compilation and simulation of SBML | Slides | <html><a href="/sites/combine/files/combine2014/2014-08-21-somogyi.mov">Video</a></html> |
| 10:00 | Alex Thomas | JSBML 1.0: Providing a Smorgasbord of Options to Encode Systems Biology Models | Slides | <html><a href="/sites/combine/files/combine2014/2014-08-21-thomas.mov">Video</a></html> |
| 10:30 | Break | | | |
| | SBML II | Chair: Frank Bergmann | | |
| 11:00 | Martin Golebiewski | Data upload into SABIO-RK | Slides | <html><a href="/sites/combine/files/combine2014/2014-08-21-golobiewski.mov">Video</a></html> |
| 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 | <html><a href="/sites/combine/files/combine2014/2014-08-21-tapia.mov">Video</a></html> |
| 12:30 | Lunch | | | |
| 14:00 | Parallel Breakouts | | | |
| | Sarah Keating, Chris Myers | SBML Arrays and other math extensions | Slides | <html><a href="/sites/combine/files/combine2014/2014-08-21-sbml-arrays-math-packages.mov">Video</a></html> |
| | 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 | <html><a href="/sites/combine/files/combine2014/2014-08-21-sbml-dynamic.mov">Video</a></html> |
| | Frank Bergmann | Combine Archive & SED-ML Discussion | n/a | |
| 17:30 | | Breakout report and daily wrap-up | | <html><a href="/sites/combine/files/combine2014/2014-08-21-breakout-recaps.mov">Video</a></html> |
| | Speaker | Title | Slides | Recordings |
| 08:00 | Breakfast | | | |
| | Other Topics | Chair: Pedro Mendes | | |
| 08:30 | Joseph Olufemi Dada | Numerical Markup Language and Data Converter | Slides | <html><a href="/sites/combine/files/combine2014/2014-08-22-dada.mov">Video</a></html> |
| 09:00 | Augustin Luna | PaxtoolsR: An R Package for Pathway Analysis Using Paxtools and Pathway Commons | Slides | <html><a href="/sites/combine/files/combine2014/2014-08-22-luna.mov">Video</a></html> |
| 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 | <html><a href="/sites/combine/files/combine2014/2014-08-22-friedman.mov">Video</a></html> |
| 10:00 | Edwin F. Juárez Rosales | A systems identification-based data pipeline to create digital cell lines from cell culture data | n/a | <html><a href="/sites/combine/files/combine2014/2014-08-22-rosales.mov">Video</a></html> |
| 10:30 | Break | | | |
| 11:00 | Areas of Collaboration and Coordination | Chair: Chris Myers | Slides | <html><a href="/sites/combine/files/combine2014/2014-08-22-myers-areas-of-collaboration.mov">Video</a></html> |
| | | 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 | <html><a href="/sites/combine/files/combine2014/2014-08-22-golebiewski--future-of-combine.mov">Video</a></html> |
| 14:30 | | General discussion about future of COMBINE, liaisons with other networks and outreach | | |
| 15:30 | Falk Schreiber | Announcement for HARMONY 2015 | n/a | <html><a href="/sites/combine/files/combine2014/2014-08-22-falk-harmony2015.mov">Video</a></html> |
| 15:37 | Lucian Smith | The SBOL Story | n/a | <html><a href="/sites/combine/files/combine2014/2014-08-22-lucian.mov">Video</a></html> |
| 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 |
