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 | <html><a href="https://0u812.github.io/combine-2018-slides">Slides</a></html> |
| 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" | <html><a href="https://drive.google.com/open?id=1cRcJOBCD4VXoRb_tMFWaSveA2NUmJzXS">Video</a></html> |
| 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 |