IWBDA 2015: 7th International Workshop on Bio-Design Automation

7th International Workshop

on Bio-Design Automation


Link to proceedings pdf.


The following is the preliminary schedule, subject to change.
The schedule of abstracts to be presented as talks and posters. Detailed instructions for presenters are below.


(Updated on August 10, 2015)

Wednesday, August 19th
10:00 - 11:00 BDAC Executive Board Meeting (closed)
11:00 - 12:00 BDAC Membership Meeting (open)
12:00 - 13:00 Lunch break (continue BDAC discussion as needed) (open)
13:00 - 13:30 IWBDA/OWBDA 2016 Discussion (open)
13:30 - 17:30 SBOL Community Outreach Meeting (Coffee Break in the middle) (open)
13:30 - 14:00    Introduction to SBOL
14:00 - 15:00    Live demos of SBOL-based tools
15:00 - 15:30    Coffee Break
15:30 - 17:00    Input from the Bench
17:00 - 17:30    Roadmap and integration with other communities and standards
Thursday, August 20th
8:00 - 8:30 Breakfast and Registration
8:30 - 8:40 Opening Remarks
Douglas Densmore, General Chair
Talk Session I: Standards & Data Exchange, Moderator: Aaron Adler
8:40 - 9:00 Progress from the Synthetic Biology Standards Consortium
Matthew Munson, Sarah Munro and Marc Salit
9:00 - 9:20 The Synthetic Biology Open Language 2.0
Bryan Bartley, Jacob Beal, Kevin Clancy, Goksel Misirli, Nicholas Roehner, Matthew Pocock, Tramy Nguyen, Zhen Zhang, Chris Myers, John Gennari, Herbert Sauro, Curtis Madsen, Anil Wipat and Ernst Oberortner
9:20 - 9:40 A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language
Tramy Nguyen and Chris Myers
9:40 - 10:00 SBOL Stack: The One-stop-shop for Storing and Publishing Synthetic Biology Designs
Curtis Madsen, Goksel Misirli, Matthew Pocock, Jennifer Hallinan and Anil Wipat
10:00 - 10:30 Coffee Break
10:30 - 11:30 Eric Klavins, University of Washington Programmable Synthetic Biology.
Abstract: The design-build-test cycle in synthetic biology requires build and test pipelines that are highly reproducible, maximally informative, and scalable. Traditional laboratory practices where a a small team of researchers designs and performs their own experiments in a unstructured lab, in contrast, are difficult to reproduce and scale. In this talk, I will describe recent efforts to standardize how protocols and workflows are specified using formal, executable programming languages. I will argue that treating experimental workflows as code is leading to a revolution in how experimental work is done and offers huge advantages, such as easy integration into upstream design software and easy collaboration. I will focus in particular on my lab's experience with Aquarium, our human-in-the-loop laboratory operating system, that can be used to run experimental workflow programs reliably and reproducibly. I will describe several projects in yeast synthetic biology that Aquarium has enabled, including cell-cell communication with auxin, large CRISPR based gene circuits, and epigenetic memory devices.
Discussion Session I, Leader: Evan Appleton
11:30 - 12:30 Topic: Cloud Labs vs. Desktop Robots: Can there be only one?
12:30 - 13:00 Lunch
Poster Session and Demos
13:00 - 14:30 Poster Session
Talk Session II: Pathway and Oligo Design, Moderator: Natasa Miskov-Zivanov
14:30 - 14:50 Stoichiometrically Minimal Source Pathways via Model Checking
Matthew Fong and Sanjit Seshia
14:50 - 15:10 Double Dutch: A Tool for Designing Libraries of Variant Metabolic Pathways
Nicholas Roehner and Douglas Densmore
15:10 - 15:30 Millstone: Software for iterative genome engineering
Gleb Kuznetsov, Daniel B. Goodman, Marc J. Lajoie, George M. Church, Kevin Y. Chen, Changping Chen, Michael G. Napolitano and Brian W. Ahern
15:30 - 16:00 Coffee Break
Lab Tour
16:00 - 17:00 Klavins lab tour
Evening Activites
17:00 - 21:00 Dinner at UW Club
Friday, August 21st
8:00 - 8:30Breakfast and Registration
Talk Session III: Process Management, Moderator: Nic Roehner
8:30 - 8:50 MERLIN: a DNA Design Tool for Large-Scale Genome Engineering
Michael Quintin, Aaron Lewis, Natalie Ma, Douglas Densmore and Farren Isaacs
8:50 - 9:10 Software for Engineering Biology in a Multi-Purpose Foundry
Benjie Chen, Dan Cahoon, Barry Canton and Austin Che
9:10 - 9:30 YeastFabCAM: Computer Assisted Manufacturing for constructing large-scale genetic parts registries
Yisha Luo, Yue Shen, Emily Scher, Junbiao Dai and Yizhi Cai
9:30 - 9:50 Successful Failure: Best Practices for Quality Control of Large-scale DNA Assembly
Bryan Bartley, Michal Galdzicki, John Gennari and Herbert Sauro
9:50 - 10:20 Coffee Break
Industry Showcase, Moderator: Jake Beal
10:20 - 10:40 Realizing the dream of clean, structured data: Bringing manufacturing-grade quality to R&D
Timothy Gardner, Riffyn
10:40 - 11:00 TBD
Chris Grant, Synthace
11:00 - 12:00 Miriah Meyer, University of Utah Why an (interactive) visualization is worth a thousand numbers.
Astract: The advancement of techniques and methods for collecting data has fundamentally changed how we study life and all of its complexities. But generating data is only the first step --- developing methods to make sense of vast collections of information is now widely considered the major challenge. A key component of addressing this challenge is visualization, which supports sense-making by representing data as pictures and supporting exploration through human-computer interactions. In this talk I'll discuss how we design interactive visualizations and how scientists use these tools to glean insight from complex data.
12:00 - 13:30 Lunch
Discussion Session II, Leader: Doug Densmore
13:30 - 14:30 Topic: BDA Commercialization Business Models
Talk Session IV: Genetic Circuits I, Moderator: Traci Haddock
14:30 - 14:50 Automated design of genetic logic circuits
Bryan Der, Douglas Densmore and Christopher Voigt
14:50 - 15:10 Parameter inference for gene circuit models
Linh Huynh and Ilias Tagkopoulos
15:10 - 15:30 Design of Biological Circuits Using Signal-to-Noise Ratio
Jacob Beal
15:30 - 16:00 Coffee Break
Talk Session V: Genetic Circuits II, Moderator: Kevin LeShane
16:00 - 16:20 SynBad: An SVP Design Framework
Owen Gilfellon, Goksel Misirli, Curtis Madsen, Jennifer Hallinan, Paolo Zuliani and Anil Wipat
16:20 - 16:40 D-VASim: Dynamic Virtual Analyzer and Simulator for Genetic Circuits
Hasan Baig and Jan Madsen
16:40 - 17:00 Fluigi: An Automated Framework for Creating Bioelectronic Devices
Haiyao Huang, Aaron Heuckroth, Ryan J. Silva and Douglas Densmore
Closing remarks
17:00 - 17:15 Closing remarks
Douglas Densmore


* Adaptive imaging cytometry to estimate parameters of gene networks models in systems and synthetic biology
David Ball, Matthew Lux, Neil Adames, and Jean Peccoud
archiYEAST: a command-line synthetic yeast architect
Laura Adam and Eric Klavins
Big Mechanism Design and Analysis Automation
Anuva Kulkarni, Cheryl Telmer, and Natasa Miskov-Zivanov
On the complexity of codon context optimization
Dimitris Papamichail, Hongmei Liu, and Georgios Papamichail
Context Aware Pipetting
Charles Fracchia, Joseph Jacobson, and George Church
CRISPR and TAL Search and Design Tools for Cell Engineering
Daniel Williams, Sridhar Ranganathan, and Joel Brockman
Design and Characterization of Genetic Circuits using Multiplex DNA Synthesis
Daniel Goodman, Casper Enghuus, and George Church
* Design framework to program prokaryotic cell with diversified digital operations
Adison Wong, Chueh Loo Poh, and Richard Kitney
Design optimizations of precise synthetic genome targeting and editing small molecules for diverse disease loci
Faisal Reza and Peter M. Glazer
A Detailed, flexible standard for sharing DNA concepts
Barbara Frewen, Jed Dean, and Aaron Kimball
Efficient Analysis of SBML Models Using Arrays
Leandro Watanabe and Chris Myers
Extending the features and improving the performance of gro simulator: new bacterial conjugation and gene expression modules
Martín Gutiérrez, Paula Gregorio-Godoy, Guillermo Pérez Del Pulgar, and Alfonso Rodríguez-Patón
* GenoLIB: a database of biological parts derived from a library of common plasmid features
Neil R. Adames, Mandy L. Wilson, Gang Fang, Matthew W Lux, Benjamin Glick, and Jean Peccoud
Phagebook: A Software Environment for Social Synthetic Biology
Kathleen Lewis, Inna Turshudzhyan, Kara Le Fort, Nicholas Musella, Nicholas Roehner, Prashant Vaidyanathan, and Douglas Densmore
Phoenix: An automated design-build-test tool
Evan Appleton, Yash Agarwal, Zachary Chapasko, Ernst Oberortner, Alan Pacheco, Prashant Vaidyanathan, Nicholas Roehner, and Douglas Densmore
Pooled, in situ assembly of complex genomic libraries using sorter-assisted genome engineering
Robert Egbert, Eric Yu, and Adam Arkin
Scylax™ - Automated design of cell factories incorporating synthetic enzymes
Michal Galdzicki, Kyle Medley, Rudesh D Toofanny, Stanley Gu, Yih-En Andrew Ban, Herbert M Sauro, and Alexandre Zanghellini
Towards Semi-Automated Experimental Design Using Model Inference in Synthetic Biology
Tileli Amimeur, Eric Klavins
Towards a sequence-level DNA design specification language
Nicholas Bolten and Eric Klavins
* = Previously published work, not included in proceedings


Instructions for Oral and Poster Presentations

Oral presentations

Oral presentations will each be 15 minutes + 5 minutes of Q&A.

Poster presentations

Posters should be in a horizontal orientation, 40 inches wide by 30 inches tall.