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 Audio
9:15am Fred Adler, Utah Bottoms up! How pointy-headed mathematical biologists approach cell biology and what we could gain from computational biologists Slides Audio
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 Audio
11:15am Miriah Meyer, Utah Why an (interactive) visualization is worth a thousand numbers Slides Audio
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 Audio
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 Audio
8:45am Zhen Zhang, Utah libSBOLj 2.0: A Java Library to Support SBOL 2.0 Slides Audio
9:00am Tramy Nguyen, Utah A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language Slides Audio
9:15am Linh Huynh, UCDavis Data-driven parameter inference for gene circuit modeling Slides Audio
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 Audio
10:45am Andreas Dräger, UC San Diego New Standard Resources for Systems Biology: BiGG 2 Database and Visual Pathway Editing with Escher Slides Audio
11:00am Jacob Beal, BBN SBOL visual: introduction, recent developments, and current challenges Slides Audio
11:15am James Alastair McLaughlin, Newcastle VisBOL: Web-based tooling for synthetic biology design visualization Slides Audio
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