IWBDA 2017: 9th International Workshop on Bio-Design Automation, Pittsburgh, PA, USA

9th 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 July 26, 2017)

Tuesday, August 8th
08:00 - 07:30 (August 9th) 2nd BDAthlon programming contest
Wednesday, August 9th
8:00 - 8:35 Arrival, Breakfast, and Registration
8:35 - 8:50 Opening Remarks
Natasa Miskov-Zivanov, General Chair
Talk Session I: Experiment-Machine Interfaces, Moderator: Evan Appleton
8:50 - 9:10 Visual Expression of Experimental Protocols
James Scott-Brown and Antonis Papachristodoulou
9:10 - 9:30 Automating Robots with Genetically Engineered Cells
Keith Heyde, John Lake and Warren Ruder
9:30 - 9:40 Short Break
Keynote I
9:40 - 10:40 Dr. Caroline Ajo-Franklin Engineering Microorganisms that Create and Communicate with Materials
Abstract: My research group uses biophysics and synthetic biology to engineer and explore the nanoscale interface between living microbes and inorganic materials. We are particularly interested in the basic mechanisms underlying charge transfer and assembly of materials at this living/non-living interface. In the first part of my talk, I will describe how we have engineered bi-directional electronic communication between living microbes and non-living systems using synthetic biology. By transplanting extracellular electron transfer pathways into the industrial organism Escherichia coli, we can confer upon these cells a molecularly-defined route to both accept and donate electrons to electrodes. Both current production and current consumption shift the metabolism of E. coli in well-defined ways, demonstrating that this electronic interface can control intracellular state. In the second part of my talk, I will describe how we have used surface-layer (S-layer) proteins as a programmable material. S-layer proteins form a highly ordered crystalline, yet porous, layer on the outermost cell surface of most species of bacteria and archaea. By engineering S-layers on the surface of different microorganisms, we can create arrays that modulate both the binding and mineralization of inorganic materials.
10:40 - 11:10 Coffee Break
Talk Session II: Design Automation, Moderator: Nicholas Roehner
11:10 - 11:30 A Top-down Approach to Genetic Circuit Synthesis and Optimized Technology Mapping
Hasan Baig and Jan Madsen
11:30 - 11:50 Heterologous Pathway Optimization using the Pathway Map Calculator
Sean Halper and Howard Salis
11:50 - 12:10 Function-driven, Graphical Design Tool for Microfluidic Chips: 3DuF
Joshua Lippai, Radhakrishna Sanka, Ali Lashkaripour, and Douglas Densmore
12:10 - 12:20 Short Break
Poster Pitches I
12:20 - 12:30 Poster Pitches: 1 minute per poster
12:30 - 12:35 Announcements
12:35 - 13:30 Lunch
Poster Session and Demos I
13:30 - 14:30 Poster Session
Keynote II
14:30 - 15:30 Randy Rettberg Title TBD
Abstract TBD
15:30 - 16:00 Coffee Break
Talk Session III: Genetic Design Spaces, Moderator: Khaled Sayed
16:00 - 16:20 Mapping Genetic Design Space with Phylosemantics
Bryan A Bartley, Michal Galdzicki, Robert Sidney Cox, and Herbert M Sauro
16:20 - 16:40 Large-Scale Genetic Design: Moving From Designs to Design Spaces
Nicholas Roehner and Douglas Densmore
16:40 - 17:00 Modeling the Structural Determinants of mRNA Stability for Operon Design
Daniel Cetnar and Howard Salis
17:00 - 17:05 Announcements
Evening Activities
18:00 - 21:00 Conference Dinner at The Porch at Schenley Plaza.
Thursday, August 10th
8:00 - 8:30Arrival, Breakfast, and Registration
Talk Session IV: Modeling, Moderator: Curtis Madsen
8:30 - 8:50 iBioSim 3: A Tool for Model-Based Genetic Circuit Design
Leandro Watanabe, Tramy Nguyen, Michael Zhang, Chris Myers, Curtis Madsen, and Nicholas Roehner
8:50 - 9:10 Standard Enabled Model Generator for Genetic Circuit Design
Göksel Misirli, Tramy Nguyen, James McLaughlin, Chris Myers, and Anil Wipat.
9:10 - 9:30 Test-SFM: An automated model test system for systematic development of sequence-to-function models
Alexander Reis and Howard Salis
9:30 - 9:40 Short Break
Keynote III
9:40 - 10:40 Prof. James Faeder Rule-based modeling of cellular processes
Abstract: In this talk I will discuss challenges faced in developing detailed models of biochemical networks, that encompass large numbers of interacting components. Many of these same challenges arise iin synthetic biology. Although simpler coarse-grained models are often useful for gaining insight into biological mechanisms, detailed models are often necessary to understand how molecular components work in the network context and essential to developing the ability to manipulate such networks for practical benefits. The rule-based modeling (RBM) approach, in which biological molecules can be represented as structured objects whose interactions are governed by rules that describe their biochemical interactions, is the basis for addressing multiple scaling issues that arise in the development of large scale models. Currently available software tools for RBM, such as BioNetGen, Kappa, and Simmune, enable the specification and simulation of large scale models, and these tools are in widespread use by the modeling community. I will review some of the developments that gave rise to those capabilities and describe our current efforts broaden the appeal of these tools as well as to better enable collaborative development of models through re-use of existing models and improving visual representations of models. It is expected that a number of these advances will also be useful in synthetic biology.
10:40 - 11:10 Coffee Break
Talk Session V: Standards and Domain Specific Languages, Moderator: Bryan Bartley
11:10 - 11:30 A Test Suite for Compliance Testing of Software Support for the Synthetic Biology Open Language
Meher Samineni and Chris Myers
11:30 - 11:50 Toward Quantitative Comparison of Fluorescent Protein Expression Levels via Fluorescent Beads
Jacob Beal, Nicholas Delateur, Brian Teague, Ron Weiss, John Sexton, Sebastian Castillo-Hair, and Jeffrey J. Tabor
11:50 - 12:10 mLSI Design with MINT
Radhakrishna Sanka, Joshua Lippai, and Douglas Densmore
Poster Pitches II
12:10 - 12:20 Poster Pitches: 1 minute per poster
12:20 - 12:25 Announcements
12:25 - 13:30 Lunch
Poster Session and Demos II
13:30 - 14:30 Poster Session
Talk Session VI: Machine Learning, Moderator: Adam Butchy
14:30 - 14:50 From machine reading to discrete models of cellular signaling
Khaled Sayed, Cheryl Telmer, and Natasa Miskov-Zivanov
14:50 - 15:10 Garuda: A Synthetic Biology Platform that Learns from Data
Rizki Mardian, Manuel Gimenez, Marcia Sahaya Louis, Radhakrishna Sanka, and Douglas Densmore
15:10 - 15:30 Forward Engineering of Optimal CRISPR Guide RNA Sequences via Machine Learning
Riley Doyle, Mark Dunne, Neil Humphryes-Kirilov, and Leigh Brody
15:30 - 16:00 Coffee Break
Discussion Session, Leader: TBD
16:00 - 17:00 Discussion Topic: TBA
Closing Remarks and Awards
17:00 - 17:15 Closing remarks
Natasa Miskov-Zivanov, General Chair
Friday, August 11th
09:00 - 17:00 2nd Annual Introductory SBOL Workshop (agenda)


Poster Session and Demos I
An automated cell-free method for the measurement of mammalian gene-expression
Margarita Kopniczky, Kirsten Jensen, David McClymont, and Paul Freemont
Automated creation of temporal properties from protein interaction data
Emilee Holtzapple, Cheryl Telmer, and Natasa Miskov-Zivanov
Fluigi Cloud - A Cloud CAD Platform for Microfluidics
Kestutis Subacius, Priya Kapadia, Radhakrishna Sanka, Shane McCormack, Anish Asthana, and Douglas Densmore
Phoenix: A Systems Engineering Approach to Spatial and Temporal Pattern Synthesis in Genetic Systems
Curtis Madsen, Evan Appleton, Prashant Vaidyanathan, Rizki Mardian, Cristian-Ioan Vasile, Katherine Elkind, Alexander Bennett, Fan Cao, Masakazu Nagata, Calin Belta, and Douglas Densmore
Re-wiring plant regulatory networks to enhance stress tolerance
Iulia Gherman
Software and Automation Enabled NGS Pipelines at Ginkgo Bioworks
Yaoyu Yang, Dawn Thompson, Teryn Citino, Zach Neuschaefer, Lina Faller, Chris Mitchell, Benjie Chen, Jamie Cho, Kristen Tran, Elaine Shapland, and Barry Canton
A Novel Flexible Library for Representation of ‎the Biological Systems in Computer Algorithms *
Mehrshad Khosraviani and Sepehr Najjarpour
* Included in proceedings, but authors unable to attend
Poster Session and Demos II
Algorithms for selecting fluorescent reporters
Evan Appleton, Prashant Vaidyanathan, David Tran, Alex Vahid, George Church, and Douglas Densmore
Automated Portable Microfluidic Bioreactor for Synthetic Biology
John Lake, Keith Heyde and Warren Ruder
Design Automation based on Fluid Dynamics
Ali Lashkaripour, Radhakrishna Sanka, Joshua Lippai, and Douglas Densmore
Discrete Modeling of the JAK2/STAT5 Signaling pathway to Determine Important Negative Feedback Mechanisms
Adam Butchy, Alexandre Terrier, Cheryl Telmer, and Natasa Miskov-Zivanov
Examining the thermodynamic basis of differential gene expression in vitro
Grace Vezeau and Howard Salis
Poly-omic statistical methods describe cyanobacterial metabolic adaptation to fluctuating environments *
Supreeta Vijayakumar and Claudio Angione
* Included in proceedings, but authors unable to attend
Towards Computer-Assisted Genetic Design
Yury Ivanov and Douglas Densmore

Twist Bioscience

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.