Proceedings
Program
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.
Agenda
(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 |
| Keynote | |
| 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? |
| Lunch | |
| 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 - 8:30 | Breakfast 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 |
| Keynote | |
| 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. |
| Lunch | |
| 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 |
Posters
| * 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 |
Sponsor Posters
| Autodesk |
| SynBERC |
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.