IWBDA 2016: 8th International Workshop on Bio-Design Automation, Newcastle University, Newcastle upon Tyne, UK

8th International Workshop on Bio-Design Automation


Link to proceedings pdf.

Link to proceedings supplemental 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 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
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 - 8:30Arrival, 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
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


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

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.