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 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 |
| Lunch | |
| 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 website |
| 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 - 8:30 | Arrival, 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 |
| Lunch | |
| 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) |
Posters
| 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 | |
Sponsor Exhibition
| 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.