Proceedings
Program
The schedule of abstracts to be presented as talks and posters. Detailed instructions for presenters are below.
Location
The workshop will take place at the Photonics Center, 8 St. Mary's Street, Room 906, Boston, Massachusetts. Directions and a map are here.
Agenda
(Updated on June 10, 2014)
| Wednesday, June 11th | |
|---|---|
| 8:00 - 9:00 | Breakfast and Registration |
| 9:00 - 9:15 | Opening Remarks |
| Talk Session I: Tools | |
| 9:15 - 9:40 | DIVA: More Science, Less DNA construction Joanna Chen, Hector Plahar, Nina Stawski, Garima Goyal, Jay Keasling and Nathan Hillson |
| 9:40 - 10:05 | GenomeCarver: harvesting genetic parts from genomes to support biological design automation Emily Scher, Yisha Luo, Aaron Berliner, Jackie Quinn, Carlos Olguin and Yizhi Cai |
| 10:05 - 10:30 | Automated Selection Finder (ASF) For Directed Evolution Neda Hassanpour, Brad Gaynor, Mona Yousofshahi, Nikhil Nair and Soha Hassoun. |
| 10:30 - 11:00 | Coffee Break |
| Discussion Session I | |
| 11:00 - 12:00 | Topic: Merging experimentalists and computational efforts in BDA |
| Poster Session I | |
| 12:00 - 12:30 | Lunch |
| 12:30 - 13:30 | Poster Session |
| Keynote | |
| 13:30 - 14:30 | Tuval Ben-Yehezkel Advanced DNA Editing Platforms. |
| Talk Session II: Modeling I | |
| 14:30 - 14:55 | Metabolic Constraint-Based Refinement of Transcriptional Regulatory Networks Sriram Chandrasekaran and Nathan Price |
| 14:55 - 15:20 | Integration of Circuit Design Automation and Genome-scale Modeling Linh Huynh, Minseung Kim and Ilias Tagkopoulos |
| 15:20 - 15:45 | Configurable Linear Control of Biochemical Systems Tai-Yin Chiu, Ruei-Yang Huang, Hui-Ju Katherine Chiang, Jie-Hong Roland Jiang and Francois Fages |
| 15:45 - 16:15 | Coffee Break |
| Talk Session III: Modeling II | |
| 16:15 - 16:40 | A hybrid of multi-omics FBA and Bayesian factor modeling to identify pathway crosstalks Claudio Angione, Naruemon Pratanwanich and Pietro Lio |
| 16:40 - 17:05 | Delay modeling in cell signaling and gene regulatory networks Natasa Miskov-Zivanov, Chang Sheng Clement Loh, Peter Wei and James Faeder |
| Evening Activites | |
| 18:00 - 19:00 | Fenway Park Tour |
| 19:00 - 21:00 | Dinner |
| Thursday, June 12th | |
| 8:00 - 9:00 | Breakfast and Registration |
| Talk Session IV: Circuit Design | |
| 9:00 - 9:25 | Precision Design of Expression from RNA Replicons Jacob Beal, Tyler Wagner, Tasuku Kitada, Andrey Krivoy, Odisse Azizgolshani, Jordan Moberg Parker, Douglas Densmore and Ron Weiss |
| 9:25 - 9:50 | Modular design and implementation of eukaryotic synthetic gene circuits Mario Andrea Marchisio |
| 9:50 - 10:15 | Phenotypic Differences Among Seven Synthetic Oscillator Designs Jason Lomnitz and Michael Savageau |
| 10:15 - 10:45 | Coffee Break |
| Discussion Session II | |
| 10:45 - 11:45 | Topic: BDA training and curricula needs in academia and industry |
| Poster Session II | |
| 11:45 - 12:15 | Lunch |
| 12:15 - 13:15 | Poster Session |
| Keynote | |
| 13:15 - 14:15 | Orit Shaer Reality-Based Interaction for Bio- Design. |
| Talk Session V: Automation | |
| 14:15 - 14:40 | Better Scheduling Software and User Interface for Liquid-Handling Robots Benjamin Schreck, Jonathan Babb and Ron Weiss |
| 14:40 - 15:05 | SMT-based Strategies for Biodesign Automation Boyan Yordanov and Andrew Phillips |
| 15:05 - 15:35 | Coffee Break |
| Talk Session VI: Algorithms | |
| 15:35 - 16:00 | Nonlinear Biochemical Signal Processing via Noise Propagation Kyung Kim, Hong Qian and Hebert Sauro |
| 16:00 - 16:25 | An Aspect Oriented Design and Modelling Framework for Synthetic Biology Philipp Boeing, Darren Nesbeth, Anthony Finkelstein and Chris Barnes |
| 16:25 - 16:50 | Towards Rule-based Knowledge-Based Systems for Synthetic Biology Ernst Oberortner, Audrey Lewis and Douglas Densmore |
| Closing remarks | |
| 16:50 - 17:05 | Closing remarks |
Posters
| Boston University Center of Synthetic Biology (CoSBi) ICE Repository Stephanie Paige, Sonya Inverson, Aaron Heuckroth, Swati Carr, Traci Haddock and Douglas Densmore |
| Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language Nicholas Roehner and Chris Myers |
| A top-down approach to genetic circuit synthesis Sune Mølgaard Laursen, Jakob Jakobsen Boysen and Jan Madsen |
| A Distributed and Interconnected Biological Part Registry Hector Plahar, Joanna Chen, Timothy Ham, Jay Keasling and Nathan Hillson |
| Synthetic Biology Open Language Designer Christian Olsen and Kashef Qaadri |
| Incorporating loading effects into the automated design of complex biocircuits Andras Gyorgy and Domitilla Del Vecchio |
| Using the Method of Types to Improve Adjacency Testing for Elementary Flux Mode Computation Ehsan Ullah, Shuchin Aeron and Soha Hassoun |
| Owl: Electronic Datasheet Generator for Synthetic Biology Evan Appleton, Jenhan Tao, Traci Haddock and Douglas Densmore |
| Optimizing Product Yield Through Identifying Gene Expression Fold Changes Sara Amin, Mona Yousofshahi and Soha Hassoun. |
Sponsor Posters
| A New Synthetic Biology Work-Cell for the Automated Preparation and Purification of Nucleic Acids and Proteins Hudson Robotics |
| Twist Bioscience |
Instructions for Oral and Poster Presentations
Oral presentations
Oral presentations will each be 20 minutes + 5 minutes of Q&A.
Poster presentations
Posters should be in a vertical orientation, maximum 4 feet wide by maximum 6 feet tall.