COMBINE 2018 - Agenda

Agenda

Breakouts and Remote Attendance

The current breakout agenda is available here:

https://docs.google.com/spreadsheets/d/1nab6zictQ6kLa15h498PpmuL3m-_oUvU8DKu9bg-yjA/edit

Feel free to suggest more breakouts by adding them to the schedule.

Remote attendance is available through the following link:

https://auckland.zoom.us/j/769815643

Presentations taking place in the main conference room will be streamed via this link.

Day 1 (Monday, October 8)

The first day will take place entirely in room 101 of the Rajen Kilachand Center for Integrated Life Sciences and Engineering at Boston University.

Speaker Title Slides
8:00am Breakfast Rajen Kilachand Center Lobby
8:30am - 10:00am Session 1
Chair: Nicholas Roehner
Welcome
8:30am Curtis Madsen, Boston University and Nicholas Roehner, Raytheon BBN Technologies Welcome Slides
8:45am COMBINE Coordinators COMBINE and Its Standards BioPAX CellML NeuroML SBGN SBOL SED-ML
10:00am Break Rajen Kilachand Center Lobby
10:30am - noon Session 2
Chair: Curtis Madsen
10:30am Ernest Fraenkel, Massachusetts Institute of Technology Integrating Multi-Omic Data to Understand Neurodegenerative Diseases Slides
11:15am Zhenjun Hu, Boston University MIND-A Dedicated Web Platform to Analyze Microbial Interaction Networks Slides
noon Lunch Rajen Kilachand Center Lobby
1:30pm - 3:00pm Session 3
Chair: Nicholas Roehner
1:30pm Simon Kasif, Boston University Can AI Explain Life: From Discovery of Antibiotics to Network Axis of Wellness and Longevity
2:15pm Babak Momeni, Boston College Mechanistic Modeling of Microbial Interactions: A Simplicity-Realism Trade-off Slides
3:00pm Break Rajen Kilachand Center Lobby
3:30pm - 5:30pm Session 4
Chair: Curtis Madsen
3:30pm Mary Dunlop, Boston University Dynamics, Feedback, and Transient Antibiotic Resistance in Single Cells
4:15pm Calin Belta, Boston University Computational Tools for Pattern Synthesis in Cellular Systems
5:00pm Matthias König, Humboldt University of Berlin Physiological based modeling of liver metabolism and liver function tests using SBML
5:30pm Adjourn

Day 2 (Tuesday, October 9)

Speaker Title Slides
8:00am Breakfast Rajen Kilachand Center Lobby
8:30am - 10:00am Session 5
Chair: Martin Golebiewski
8:30am Discussion COMBINE Becoming a Legal Entity SISO
9:15am Traci Haddock, iGEM Foundation iGEM: Setting Standards in Synthetic Biology Slides
10:00am Break/Posters Rajen Kilachand Center Lobby
10:30am - noon Session 6 Breakouts
noon Lunch Rajen Kilachand Center Lobby
1:30pm - 3:00pm Session 7 Breakouts
3:00pm Break/Posters Rajen Kilachand Center Lobby
3:30pm - 5:00pm Session 8 Breakouts
5:00pm Wrapup
6:00pm Banquet Porto, Ring Rd, Boston, MA 02199

Day 3 (Wednesday, October 10)

Speaker Title Slides
8:00am Breakfast Rajen Kilachand Center Lobby
8:30am - 10:00am Session 9
Chair: Tramy Nguyen
Visualization
8:30am Michael Blinov, University of Connecticut School of Medicine Precise, scalable and compact visualization of rule-based models
8:45am Sunwoo Kang, Stanford University Rendering Complex Genetic Design with DNAplotlib and pySBOL2 Slides
9:00am Andreas Dräger, University of Tübingen Visualizing Metabolic Network Dynamics through Time-Series Metabolomics Data
9:15am Arezoo Sadeghi, Boston University VisBOL enhancements for SBOL 2 Slides
9:30am Discussion
10:00am Break/Posters Rajen Kilachand Center Lobby
10:30am - noon Session 10
Chair: Bryan Bartley
Tools
10:30am J Kyle Medley, University of Washington The Tellurium Notebook Environment for Authoring Reproducible Models and Simulations Slides
10:45am Kieran Alden, University of York A Tool to Link and Establish Confidence in Evidence Used to Construct SBML Models Slides
11:00am Ayush Pandey, California Institute of Technology Sub-SBML : A Subsystem Interaction Modeling Toolbox for SBML Models Slides
11:15am James Alastair Mclaughlin, Newcastle University A Web-based CAD tool for the Synthetic Biology Open Language
11:30am Discussion
noon Lunch Rajen Kilachand Center Lobby
1:30pm - 3:00pm Session 11 Breakouts
3:00pm Break/Posters Rajen Kilachand Center Lobby
3:30pm - 5:00pm Session 12 Breakouts
5:00pm Wrapup

Day 4 (Thursday, October 11)

Speaker Title Slides
8:00am Breakfast Rajen Kilachand Center Lobby
8:30am - 10:00am Session 13
Chair: David Nickerson
Modeling I
8:30am Darex Vera Rodríguez, University of Puerto Rico at Mayagüez Revealing the mode of action of Ras-Raf inhibitors by molecular dynamics simulations
8:45am Andreas Dräger, University of Tübingen Representation of ME-Models in SBML
9:00am Jeanet Mante, University of Cambridge Quantifying Promoter Element Activation in Marchantia polymorpha Gemmae
9:15am Andreas Dräger, University of Tübingen Model-Based Prediction of Yersinia Enterocolitica Infection Outcome
9:30am Discussion
10:00am Break/Posters Rajen Kilachand Center Lobby
10:30am - noon Session 14
Chair: John Gennari
Repositories
10:30am Olga Krebs, Heidelberg Institute for Theoretical Studies FAIRDOMHub: a repository and collaboration environment for sharing systems biology research Slides
10:45am Zach Zundel, University of Utah Sharing COMBINE Archives using SynBioHub
11:00am Michael Zhang, University of Utah SBOLExplorer: Data Infrastructure and Data Mining for Genetic Design Repositories
11:15am Dany Fu, Boston University Software Tools for Next-Gen Genetic Design Slides
11:30am Discussion
noon Lunch Rajen Kilachand Center Lobby
1:30pm - 3:00pm Session 15 Breakouts
3:00pm Break/Posters Rajen Kilachand Center Lobby
3:30pm - 5:00pm Session 16 Breakouts
5:00pm Wrapup

Day 5 (Friday, October 12)

Speaker Title Slides
8:00am Breakfast Rajen Kilachand Center Lobby
8:30am - 10:00am Session 17
Chair: Olga Krebs
Reproducibility
8:30am Ion Moraru, UConn Health The Center for Reproducible Biomedical Modeling
8:45am Martin Golebiewski, Heidelberg Institute for Theoretical Studies FAIR data exchange in the life sciences by standardization of heterogenous data and multicellular models Slides
9:00am John Gennari, University of Washington Harmonizing semantic annotations on computational models in biology Slides
9:15am Graham Kim, University of Washington Availability of Code from Published Computational Physiology Models Slides
9:30am Discussion
10:00am Break/Posters Rajen Kilachand Center Lobby
10:30am - noon Session 18
Chair: Lucian Smith
Modeling II
10:30am Andreas Dräger, University of Tübingen Modeling of Potentially Virulence-Associated Metabolic Pathways in Pseudomonas aeruginosa PA14 Including Experimental Verification
10:45am David Nickerson, University of Auckland Semantics-based model discovery and assembly for renal transport Slides
11:00am Silvia Morini, University of Milano-Bicocca Metabolic Network Reconstruction of Treponema pallidum spp. pallidum Slides
11:15am Lucrezia Patruno, University of Milano-Bicocca cyTRON/JS: A Cytoscape.js based application for the inference of cancer progression models
11:30am Discussion
11:55am Lucian Smith, California Institute of Technology "Tellurium" Video
noon Lunch Rajen Kilachand Center Lobby
1:30pm - 3:00pm Session 19 Breakouts
3:00pm Break/Posters Rajen Kilachand Center Lobby
3:30pm - 5:00pm Session 20 Breakouts
5:00pm Wrapup

POSTERS

Presenter Title Poster
Kieran Alden, University of York A Tool to Link and Establish Confidence in Evidence Used to Construct Computer Simulations Poster
Jacob Barhak Python Based Standardization Tools for ClinicalTrials.Gov Poster
Michael Blinov, University of Connecticut School of Medicine SED-ML extension for parameter fitting and uncertainty estimates
Kiri Choi, University of Washington Tellurium 2.0: An Extensible Python-based Modeling Environment for Systems Biology
Pedro Fontanarrosa, University of Utah An improved model generation method using Cello’s optimized parameters
Samuel Friedman, Opto-Knowledge Systems, Inc. MutliCellDS: Integration with other Standards
Louis Gil, University of Puerto Rico, Río Piedras Campus Do predictions from protein structure improve clinical interpretation of genetic variants?
Vidhyanand Mahase, Howard University Computational analysis of the disease-causing mutations in Phosphodiesterases
Tramy Nguyen, University of Utah Technology Mapping for Asynchronous Genetic Circuit