Proceedings
Link to proceedings supplemental pdf.
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 7, 2016)
| Monday, August 15th | |
|---|---|
| 09:00 - 18:30 | 15th SBOL Workshop Prior to IWBDA, there will be a one-day SBOL workshop on August 15th, 2016 at Newcastle University, Newcastle upon Tyne, UK. The workshop is aimed for software developers, and will include demos and tutorials. Although there is no registration fee for the SBOL workshop, participants should still register. For details about this workshop and the registration please click here: http://sbolstandard.org/1226-2/. |
| Tuesday, August 16th | |
| 08:00 - 00:00 (August 17th) | 1st BDAthlon programming contest |
| Wednesday, August 17th | |
| 8:00 - 8:30 | Arrival, Breakfast, and Registration |
| 8:30 - 8:40 | Opening Remarks Anil Wipat and Pietro Lio', Co-General Chairs |
| Talk Session I: Logic, Moderator: Nic Roehner | |
| 8:40 - 9:00 | Design for Improved Repression in RNA Replicons Jacob Beal and Ron Weiss |
| 9:00 - 9:20 | Noise Tolerance Analysis for Reliable Analog Computation in Living Cells Ramez Danial |
| 9:20 - 9:40 | Utilizing Signal Temporal Logic to Characterize and Compose Modules in Synthetic Biology Curtis Madsen, Prashant Vaidyanathan, Cristian-Ioan Vasile, Rachael Ivison, Junmin Wang, Calin Belta, and Douglas Densmore |
| 9:40 - 10:00 | Single Cell Analysis of RNA-engineered Logic Gates Christopher Schneider, Jascha Diemer, Leo Bronstein, Heinz Koeppl, and Beatrix Suess |
| 10:00 - 10:30 | Coffee Break |
| Keynote I | |
| 10:30 - 11:30 | Dr. Amoolya Singh
Automating Design at an Industrial Biotech Abstract: Amyris has developed a high-throughput genetic engineering platform for designing and building custom microbes to serve as living factories. Using an industrial scale fermentation process, our microbes convert cheap sugars into a wide variety of high value target molecules, including medicines, commodity and specialty chemicals. Our end products provide low cost, high quality malaria medication and renewable substitutes for fuels and chemicals. Amyris' R&D efforts span rational & random design and construction of microbial strains, high-throughput screening and analytical chemistry, fermentation at multiple scales, and genotype/phenotype data mining. Every aspect of this work is facilitated and accelerated by quantitative science and software & hardware automation. In this talk, I will outline the computational challenges inherent in automating the design of microbial strains. To meet these challenges, we use a range of innovations including genotype specification languages and high-level functional ontologies of parts and pathways; metabolic and statistical models; literature mining algorithms; and design of experiments approaches. |
| Talk Session II: Tools I, Moderator: Traci Haddock | |
| 11:30 - 11:50 | BioBlocks: A Web-Based Visual Environment for Programming Experimental Protocols in Biological Sciences Vishal Gupta, Jesús Irimia, Iván Pau, and Alfonso Rodríguez-Patón |
| 11:50 - 12:10 | An Environment for Augmented Biodesign Using Integrated Data Resources James McLaughlin, Goksel Misirli, Matthew Pocock, and Anil Wipat |
| Poster Pitches | |
| 12:10 - 12:30 | Poster Pitches: 1 minute per poster |
| Lunch | |
| 12:30 - 12:40 | Announcements |
| 12:40 - 13:10 | Lunch |
| Poster Session and Demos | |
| 13:10 - 14:10 | Poster Session |
| Talk Session III: Pathways, Moderator: Evan Appleton | |
| 14:10 - 14:30 | extFogLight: Using Weighted Metabolic AND/OR Graph to Find Stoichiometric Balanced Pathways Mehrshad Khosraviani and Morteza Saheb Zamani |
| 14:30 - 14:50 | PathwayGenie - Pathway Design from Selection to Plasmid Neil Swainston, Pablo Carbonell, Adrian Jervis, Christopher Robinson, Mark Dunstan, and Jean-Loup Faulon |
| 14:50 - 15:10 | Integrated Predictive Genome-Scale Models to Improve the Metabolic Re-Engineering Efficiency Vishwesh Kulkarni, Lina El Menjra, Pablo Carbonell, and Jean-Loup Faulon |
| 15:10 - 15:30 | SBCDOE: a Design of Experiments-based Part Planner for Synthetic Biology Production of Chemicals Mark Dunstan, Adrian Jervis, Christopher Robinson, Neil Swainston, Jean-Loup Faulon, and Pablo Carbonell |
| 15:30 - 15:40 | Coffee Break |
| Evening Activities | |
| 15:40 - 15:45 | Coaches leave at Centre for Life |
| 17:00 - 18:00 | Durham Castle tour |
| 18:00 - 19:00 | Durham Cathedral tour |
| 19:30 - 22:30 | Conference Dinner at the Durham Castle. Coaches depart at 10:30 PM. |
| Thursday, August 18th | |
| 8:00 - 8:30 | Arrival, Breakfast, and Registration |
| Talk Session IV: Tools II, Moderator: Jacob Beal | |
| 8:30 - 8:50 | A Web-Based Validator and Validation API for the Synthetic Biology Open Language Zach Zundel, Meher Samineni, Zhen Zhang, and Chris Myers |
| 8:50 - 9:10 | SBOLDesigner 2.0 Michael Zhang and Chris Myers |
| 9:10 - 9:30 | Bioform: an in-silico 3D Physical Modelling Platform for the Design and Analysis of Bacterial Populations Jonathan Naylor, Harold Fellermann, Waleed Mohammed, Nick Jakubovics, Joy Mukherjee, Catherine Biggs, Phillip Wright, and Natalio Krasnogor |
| 9:30 - 9:50 | TEBio - Tools for Engineering Biology James Scott-Brown, Thomas Prescott, and Antonis Papachristodoulou |
| 9:50 - 10:20 | Coffee Break |
| Keynote II | |
| 10:20 - 11:20 | Prof. Natalio Krasnogor
Accelerating Synthetic Biology via Software and Hardware Advances Abstract: In this talk I will discuss recent work done in my lab that contributes towards accelerating the specify -> design -> model -> build -> test & iterate biological engineering cycle. This will describe advances in biological programming languages for specifying combinatorial DNA libraries, the utilisation of off-the-shelf microfluidic devices to build the DNA libraries as well as data analysis techniques to accelerate computational simulations. |
| Talk Session V: Standards, Moderator: Harold Fellermann | |
| 11:20 - 11:40 | ShortBOL: A shorthand for SBOL Matthew Pocock, Chris Taylor, Goksel Misirli, James McLaughlin, and Anil Wipat |
| 11:40 - 12:00 | A Data Model for the Description of Bioparts Iñaki Sainz de Murieta, Matthieu Bultelle, and Richard I. Kitney |
| Lunch | |
| 12:00 - 13:30 | Lunch |
| Talk Session VI: Automation, Moderator: Luis Ortiz | |
| 13:30 - 13:50 | Design and Automated Inference of Design Principles in Gene Regulatory Networks: a Multiobjective Optimization Approach Irene Otero-Muras and Julio R. Banga |
| 13:50 - 14:10 | How to Remember and Revisit Many Genetic Design Variants Automatically Nicholas Roehner and Douglas Densmore |
| 14:10 - 14:30 | Towards Automated Biosecurity: Screening of Synthetic Biology Constructs Benjamin Apra, Arthur Vigil, and James Diggans |
| Discussion Session, Leader: Doug Densmore | |
| 14:30 - 15:30 | Discussion Topic: BDA Hackathons and Community Engagement |
| 15:30 - 16:00 | Coffee Break |
| Talk Session VII: Circuits, Moderator: Goksel Misirli | |
| 16:00 - 16:20 | Realization of Large Logic Circuits with Long-Term Memory Using CRISPR/Cas9 Systems Tai-Yin Chiu, Cheng-Han Hsieh and Jie-Hong Roland Jiang |
| 16:20 - 16:40 | 3D Printing of Microbes for Material Production Benjamin Lehner and Anne S. Meyer |
| 16:40 - 17:00 | MakerFluidics: Microfluidics for the Masses Ryan Silva, Radhakrishna Sanka, and Douglas Densmore |
| Closing Remarks and Awards | |
| 17:00 - 17:15 | Closing remarks Anil Wipat and Pietro Lio', Co-General Chairs |
Posters
| Bacterial Detoxification of Martian Soil Coupled to Oxygen Production Valentijn Broeken and Lisanne van Oosterhoud |
| Business Process Management of Synthetic Biology Workflows Christopher Reynolds, Jocelyne Holdbrook, Kealan Exley, and Richard Kitney |
| CVLTool: Oligonucleotide Design Software for Assembly of Orthogonal Codon Variant Gene Libraries Surya Teja Chinta and Dimitris Papamichail |
| Genetic Systems Engineering Prashant Vaidyanathan, Evan Appleton, Curtis Madsen, Cristian-Ioan Vasile, Alan Pacheco, Iman Haghighi, Nicholas Roehner, Rachael Ivison, Junmin Wang, Yash Agarwal, Zachary Chapasko, Calin Belta, and Douglas Densmore |
| Improving Controllability of Biosynthesis of Gold Nanoparticles by Shewanella oneidensis through Genetic Manipulation Juliano Bertozzi Silva, Gregory Fowler, and Phillip Wright |
| Load Capacity Improvements in Transcriptional Systems Using Discrete-Time L1-Adaptive Control Hamidreza Jafarnejadsani, Jongmin Kim, Naira Hovakimyan, and Vishwesh Kulkarni |
| Logic and Timing Analysis of Genetic Logic Circuits using D-VASim Hasan Baig and Jan Madsen |
| MINT - A MIcrofluidic NetlisT Format Radhakrishna Sanka, Haiyao Huang, Ryan Silva, and Douglas Densmore |
| Modular Assembly of an Electronically Integrated Genetic Circuit Library Luis Ortiz, Thomas Costa, and Douglas Densmore |
| Modular Composition of Synthetic Biology Designs using Rule-Based Models Goksel Misirli, William Waites, Matteo Cavaliere, Paolo Zuliani, Vincent Danos, Anil Wipat, and Ricardo Honorato-Zimmer |
| Owl v2.0: A Web-Application Workspace for Synthetic Biology Yury Ivanov, Prashant Vaidyanathan, Evan Appleton, Zach Chapasko, Arash Khospavar, and Douglas Densmore |
| Phagebook Alpha: A Software Environment for Social Synthetic Biology Johan Ospina, Inna Turshudzhyan, Allison Durkan, Kristel Tan, Anna Goncharova, Prashant Vaidyanathan, Nicholas Roehner, and Douglas Densmore |
| A Powerful, Open Source, Extensible, Cloud Tool to Drive Biological Design and Construction Edinburgh Genome Foundry, Autodesk Bionano Research, and Eli Groban |
| A Statistical Approach Reveals Designs for the Most Robust Stochastic Gene Oscillators Mae Woods, Miriam Leon, Ruben Perez-Carrasco, and Chris Barnes |
| SynBIS – The Synthetic Biology Information System Matthieu Bultelle, Iñaki Sainz de Murieta, and Richard Kitney |
Sponsor Posters
| 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.