COMBINE 2015 - Agenda
Agenda
Day 1 (Monday, October 12)
The first day will take place entirely in room 1230 of the Warnock Building on the University of Utah campus.
| Speaker | Title | Slides | Recordings | |
|---|---|---|---|---|
| 8:15am | Chris Myers, Utah | Welcome | Slides | |
| 8:30am - 10:00am | Session 1 Chair: Dagmar Waltemath | Modeling | ||
| 8:30am | Jonathan Karr, Mount Sinai | Toward methods, software, and standards for more comprehensive whole-cell models | Slides | <html><a href="http://old_co.mbine.org/sites/combine/files/combine2015/combine2015-day1-karr.mp3">Audio</a></html> |
| 9:15am | Fred Adler, Utah | Bottoms up! How pointy-headed mathematical biologists approach cell biology and what we could gain from computational biologists | Slides | <html><a href="http://old_co.mbine.org/sites/combine/files/combine2015/combine2015-day1-adler.mp3">Audio</a></html> |
| 10:00am | Break | Catmull Gallery | ||
| 10:30am - noon | Session 2 Chair: Michael Hucka | Visualization | ||
| 10:30am | Huaiyu Mi, USC | An update on Systems Biology Graphical Notation | Slides | <html><a href="http://old_co.mbine.org/sites/combine/files/combine2015/combine2015-day1-mi.mp3">Audio</a></html> |
| 11:15am | Miriah Meyer, Utah | Why an (interactive) visualization is worth a thousand numbers | Slides | <html><a href="http://old_co.mbine.org/sites/combine/files/combine2015/combine2015-day1-meyer.mp3">Audio</a></html> |
| noon | Lunch | Catmull Gallery | ||
| 1:30pm - 3:00pm | Session 3 Chair: David Nickerson | Neuroscience | ||
| 1:30pm | Sharon Crook, ASU | Collaborative Development of Neural Models with NeuroML | Slides | n/a |
| 2:15pm | Richard Normann, Utah | Big Data in Neuroscience, Neural Engineering and Restorative Technologies | n/a | n/a |
| 3:00pm | Break | Catmull Gallery | ||
| 3:30pm - 5:00pm | Session 4 Chair: Chris Myers | Synthetic Biology | ||
| 3:30pm | Anil Wipat, Newcastle | The Synthetic Biology Open Language (SBOL) - recent developments in SBOL tools and repositories | Slides | <html><a href="http://old_co.mbine.org/sites/combine/files/combine2015/combine2015-day1-wipat.mp3">Audio</a></html> |
| 4:15pm | Tara Deans, Utah | Experimental Synthetic Biology: from concept to application | n/a | n/a |
| 5:00pm | Adjourn | |||
| 6:30pm | Banquet | Rice Eccles Stadium Varsity Room |
Day 2 (Tuesday, October 13)
| Speaker | Title | Slides | Recordings | |
|---|---|---|---|---|
| 8:30am - 10:00am | Session 5 Chair: Anil Wipat | SBOL | Slides | |
| 8:30am | Nicholas Roehner, Boston | Multiplicity of Representation in SBOL 2.0 | Slides | <html><a href="http://old_co.mbine.org/sites/combine/files/combine2015/combine2015-day2-roehner.mp3">Audio</a></html> |
| 8:45am | Zhen Zhang, Utah | libSBOLj 2.0: A Java Library to Support SBOL 2.0 | Slides | <html><a href="http://old_co.mbine.org/sites/combine/files/combine2015/combine2015-day2-zhang.mp3">Audio</a></html> |
| 9:00am | Tramy Nguyen, Utah | A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language | Slides | <html><a href="http://old_co.mbine.org/sites/combine/files/combine2015/combine2015-day2-nguyen.mp3">Audio</a></html> |
| 9:15am | Linh Huynh, UCDavis | Data-driven parameter inference for gene circuit modeling | Slides | <html><a href="http://old_co.mbine.org/sites/combine/files/combine2015/combine2015-day2-huynh.mp3">Audio</a></html> |
| 9:30am | Discussion | |||
| 10am | Break/Posters | Catmull Gallery | ||
| 10:30am - noon | Session 6 Chair: Huaiyu Mi | Visualization | ||
| 10:30am | Vasundra Toure, Lyon | STON translator: SBGN to Neo4j graph database | Slides | <html><a href="http://old_co.mbine.org/sites/combine/files/combine2015/combine2015-day2-toure.mp3">Audio</a></html> |
| 10:45am | Andreas Dräger, UC San Diego | New Standard Resources for Systems Biology: BiGG 2 Database and Visual Pathway Editing with Escher | Slides | <html><a href="http://old_co.mbine.org/sites/combine/files/combine2015/combine2015-day2-draeger.mp3">Audio</a></html> |
| 11:00am | Jacob Beal, BBN | SBOL visual: introduction, recent developments, and current challenges | Slides | <html><a href="http://old_co.mbine.org/sites/combine/files/combine2015/combine2015-day2-beal.mp3">Audio</a></html> |
| 11:15am | James Alastair McLaughlin, Newcastle | VisBOL: Web-based tooling for synthetic biology design visualization | Slides | <html><a href="http://old_co.mbine.org/sites/combine/files/combine2015/combine2015-day2-mclaughlin.mp3">Audio</a></html> |
| 11:30am | Discussion | |||
| noon | Lunch | Catmull Gallery | ||
| 1:30pm - 3:00pm | Session 7 | Breakouts | ||
| Leader: David Nickerson | Model versioning | n/a | ||
| Leader: Herbert Sauro | SBOL Community Discussion Room: Eccles Boardroom | n/a | ||
| Leader: Tobias Czauderna | Grouping in SBGN maps Room: WEB 1248 | n/a | ||
| Quiet hacking Room: WEB 1450 | ||||
| 3:00pm | Break/Posters | Catmull Gallery | ||
| 3:30pm - 5:00pm | Session 8 | Breakouts | ||
| Leader: Chris Myers | SBML/SED-ML whole-cell modeling discussion (arrays, distributions, etc.) | Slides | n/a | |
| Leaders: Jake Beal/Augustin Luna | SBOL Visual 2.0/SBGN Discussion Room: Eccles Boardroom | n/a | ||
| Quiet hacking Room: WEB 1248 | ||||
| Quiet hacking Room: WEB 1450 | ||||
| 5:00pm | Wrapup |
Day 3 (Wednesday, October 14)
| Speaker | Title | Slides | Recordings | |
|---|---|---|---|---|
| 8:30am - 10:00am | Session 9 Chair: John Gennari | SBML/SED-ML | ||
| 8:30am | Leandro Watanabe, Utah | Efficient Analysis of SBML Models Using Arrays | Slides | |
| 8:45am | Nikita Mandrik, Russian Academy of Sciences | BioUML IDE | Slides | |
| 9:00am | Ilya Kiselev, Russian Academy of Sciences | Sed-ML as BioUML workflow | Slides | |
| 9:15am | Lucian Smith, Washington | phraSED-ML: a Paraphrased, Human-Readable Adaptation of SED-ML | Slides | |
| 9:30am | Discussion | |||
| 10:00am | Break/Posters | Catmull Gallery | ||
| 10:30am - noon | Session 10 Chair: Sharon Crook | CellML/Annotations | ||
| 10:30am | David Nickerson, Auckland | Managing model complexity using CellML and Physiome Model Repository | Slides | |
| 10:45am | John H. Gennari, Washington | Semantic Annotation with SBML and CellML Models | Slides | |
| 11:00am | Maxwell L. Neal, Washington | Semantics-based composition of CellML and SBML models | Slides | |
| 11:15am | Nick Juty, EMBL-EBI | Identifiers.org Update | Slides | |
| noon | Lunch | Catmull Gallery | ||
| 1:30pm - 3:00pm | Session 11 | Breakouts | ||
| Leader: David Nickerson | Annotation and Semantics | n/a | ||
| Leader: Bryan Bartley | SBOL Extension Discussion Room: Eccles Boardroom | n/a | ||
| Leader: Tobias Czauderna | LibSBGN Room: WEB 1248 | n/a | ||
| Leader: Fengkai Zhang | SBML Multi Package Room: WEB 1450 | Slides | n/a | |
| 3:00pm | Break/Posters | Catmull Gallery | ||
| 3:30pm - 5:00pm | Session 12 | Breakouts | ||
| Leader: Frank Bergmann | Extending SED-ML Data Generators | n/a | ||
| Leader: Raik Gruenberg | SBOL Extension Discussion Room: Eccles Boardroom | n/a | ||
| Leader: Tobias Czauderna | SBGN Spatial Room: WEB 1248 | n/a | ||
| Quiet hacking Room: WEB 1450 | ||||
| 5:00pm | Wrapup |
Day 4 (Thursday, October 15)
| Speaker | Title | Slides | Recordings | |
|---|---|---|---|---|
| 8:30am - 10:00am | Session 13 Chair: Lucian Smith | Modeling | ||
| 8:30am | Paulo Eduardo Pinto Burke, Sao Paulo | The whole-cell network of Mycoplasma genitalium | Slides | |
| 8:45am | Denis Kazakiewicz, Hasselt | A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium | Slides | |
| 9:00am | Jose-Juan Tapia, Pittsburgh | Using Atomizer to analyze and debug reaction network models | Slides | |
| 9:15am | Dagmar Waltemath, Rostock | Identifying pattern in reaction networks of computational models | Slides | |
| 9:30am | Discussion | |||
| 10:00am | Break/Posters | Catmull Gallery | ||
| 10:30am - noon | Session 14 Chair: Pedro Mendes | Standard Resources | ||
| 10:30am | Martin Scharm, Rostock | COMBINE archive meta data | Slides | |
| 10:45am | Augustin Luna, MSKCC | Biological Pathway Exchange (BioPAX) Format and Pathway Commons Update | Slides | |
| 11:00am | Andreas Weidemann, HITS | Reaction kinetics database SABIO-RK | Slides | |
| 11:15am | Martin Golebiewski, HITS | The NormSys registry for modeling standards in systems and synthetic biology | Slides | |
| 11:30am | Discussion | |||
| noon | Lunch | Catmull Gallery | ||
| 1:30pm - 3:00pm | Session 15 | Breakouts | ||
| Leader: Frank Bergmann | SBML Constraint-based modeling and FBC | Slides | n/a | |
| Leader: Chris Myers | SBOL Infrastructure Discussion Room: Eccles Boardroom | Slides | n/a | |
| Leader: Huaiyu Mi | SBGN Stereotypes Room: WEB 1248 | n/a | ||
| Quiet hacking Room: WEB 1450 | ||||
| 3:00pm | Break/Posters | Catmull Gallery | ||
| 3:30pm - 5:00pm | Session 16 Chair: Martin Golebiewski | Community & Interoperability | ||
| 3:30pm | Jacky Snoep, Stellenbocsh | Making modelling standards more attractive to the community | Slides | |
| 3:45pm | Jacob Beal, BBN | Report on iGEM Interlab Study | Slides | |
| 4:00pm | Martin Golebiewski, HITS | General discussion about the COMBINE community and interoperability aspects | Slides | |
| 5:00pm | Lucian Smith, U. Washington | Lucian's song, "Blank Screen" | Slides | Video |
| 5:00pm | Wrapup |
Day 5 (Friday, October 16)
| Speaker | Title | Slides | Recordings | |
|---|---|---|---|---|
| 8:30am - noon | Session 17 Chair: Herbert Sauro | Cellular Modeling | ||
| 8:30am | Fengkai Zhang, NIH | Build and View Rule-Based Models With Simmune Modeler and Network Viewer | Slides | |
| 8:45am | James P. Sluka, Indiana | The Cell Behavior Ontology: describing the biological behaviors of real and simulated cells seen as spatially active agents | Slides | |
| 9:00am | Samuel Friedman, | MultiCellDS: Standardization of cell phenotypic data for data exchange | n/a | |
| 9:15am | Jia Zhao, UNC | A GPU-based 3D Itegrated Complex-fluid Toolbox for Modeling Cellular Dynamics | Slides | |
| 9:30am | Discussion | |||
| 10:00am | Break/Posters | Catmull Gallery | ||
| 10:30am - 11:00am | Session 18 Chair: Nicholas Roehner | Synthetic Biology | ||
| 10:30am | Bryan Der, MIT | Automated design of combinational logic circuits in bacteria | Slides | |
| 10:45am | Ernst Oberortner, DOE JGI | On the Adoption of Standards at the DOE Joint Genome Institute | Slides | |
| 11:00am | Raik Grunberg, Montreal | A field guide to automated cloning | Slides | |
| 11:15am | Jacob Beal, BBN | Development of Standards for Calibrated Flow Cytometry | Slides | |
| 11:30am | Discussion | |||
| noon | Lunch | Catmull Gallery | ||
| 1:30pm - 3:00pm | Session 19 | Breakouts | ||
| Leader: Ally Hume | SBML Dynamic, Multi-cellular Modeling | Slides | n/a | |
| SBOL libSBOL/tool/use case hacking Room: Eccles Boardroom | n/a | |||
| Leader: Huaiyu Mi | SBGN Hybrid maps Room: WEB 1248 | n/a | ||
| Quiet hacking Room: WEB 1450 | ||||
| 3:00pm | Break/Posters | Catmull Gallery | ||
| 3:30pm - 5:00pm | Session 20 | Breakouts | ||
| Leader: Sven Sahle | Using data with SED-ML | n/a | ||
| SBOL libSBOL/tool/use case hacking Room: Eccles Boardroom | n/a | |||
| Leader: Augustin Luna | SBGN Generics Room: WEB 1248 | n/a | ||
| Quiet hacking Room: WEB 1450 | ||||
| 5:00pm | Wrapup |
POSTERS
| Presenter | Title | Poster |
|---|---|---|
| Koray Atalag University of Auckland | Bridging the Computational Modelling and EHR standards using openEHR and Semantic Web Technology | |
| Mohamed Ayoub U. Wisc-Wash County | Theoretical Study for Hydrogen Bonding: A Model for Biological Systems | |
| Kiri Choi Washington | Tellurium: A Python Based Integrated Environment for Simulation | Poster |
| Nick Juty EMBL-EBI | Jummp: a generic and modular model management platform for life sciences | Poster |
| Nick Juty EMBL-EBI | Identifiers.org: cross-referencing and integration of heterogeneous datasets | Poster |
| Nick Juty EMBL-EBI | 10 simples rules for making data web friendly | Poster |
| Ilya Kiselev Russian Academy of Sciences | Improved SBGN (ML) support in BioUML | Poster |
| Koji Kyoda RIKEN | BDML: an open format for representing quantitative biological dynamics data | Poster |
| J Kyle Medley Washington | High Throughput Dynamical Model Simulation Using libRoadRunner | |
| David Nickerson Auckland | Developing the Virtual Physiological Human: tools, techniques, and best practices for data exchange, storage, and publication | |
| Ernst Oberortner DOE JBI | Automated Verification and Modification of DNA Sequences against DNA Synthesis Constraints | Poster |
| Martin Scharm Rostock | Ontology for differences between versions of computational models | |
| James P. Sluka Indiana | Divide and Conquer: Using SBML to represent both the whole body and subcellular scales in a liver-centric multi scale model | Poster |
| Namrata Tomar | Modeling crosstalk: Human mTOR signaling pathway as a center node | |
| Zach Zundel Utah | Analysis of Weaknesses in SBOL/SBML Modeling through Creation of Use Cases |