IWBDA 2014: 6th International Workshop on Bio-Design Automation


Link to proceedings pdf.


The schedule of abstracts to be presented as talks and posters. Detailed instructions for presenters are below.


The workshop will take place at the Photonics Center, 8 St. Mary's Street, Room 906, Boston, Massachusetts. Directions and a map are here.


(Updated on June 10, 2014)

Wednesday, June 11th
8:00 - 9:00Breakfast and Registration
9:00 - 9:15Opening 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
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 - 9:00Breakfast 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
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 - 17:05Closing remarks


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.

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.