SB5.0: THE FIFTH INTERNATIONAL MEETING ON SYNTHETIC BIOLOGY

JUNE 15-17, 2011

STANFORD UNIVERSITY

The BioBricks Foundation is pleased to present 6 workshops taking place during the SB5.0 Meeting, led by and featuring members of the global synthetic biology community, and organized around topics of interest to the community. Sign up to reserve your free spot in the SB5.0 Workshops. There are 2 concurrent workshops on each day of the meeting.

• MAKE SURE YOU ARE SIGNING UP FOR ONLY 1 WORKSHOP PER DAY.
• ONLY REGISTERED ATTENDESS OF THE SB5.0 MEETING CAN SIGN UP FOR THE WORKSHOPS. IF YOU DO NOT HOLD A CONFIRMED REGISTRATION TO THE SB5.0 MEETING, YOU WILL NOT BE ALLOWED INTO THE WORKSHOPS.

DAY 1 Concurrent Workshops

SIGN UP FOR WORKSHOP 1A -OR- 1B

WORKSHOP 1A: DNA ASEMBLY METHODS

Wed, June 15: 12:00-2:00

Location:  Dinkelspiel Auditorium

Workshop Lead:  Nathan Hillson, Joint BioEnergy Instittute

This workshop will provide brief presentations on chip-based DNA synthesis technology and its applications (Siyuan Chen), DNA assembly methodologies (Dan Gibson), and a hands-on tutorial of DNA assembly design automation software tools (Nathan Hillson). Registrants interested in participating in the hands-on software tutorial are encouraged to register for a user account (http://jbei-exwebapp.lbl.gov/j5) prior to the workshop.

Workshop Presenters: Daniel Gibson (J. Craig Venter Institute), Nathan Hillson (Joint BioEnergy Institute), Siyuan Chen (Agilent Technologies)

WORKSHOP 1B: NEXT GENERATION SEQUENCING

Wed, June 15: 12:00-2:00

Location:  Old Union Ballroom

Workshop Lead: Cole Trapnell, Broad Institute

The idea behind this workshop is to introduce you to the power and flexibility of next generation sequencing, and provide a hands-on guide to applying this technology in your research. Far from just being a high-throughput DNA sequencing technology, next generation sequencing is now widely being used to do things like find sites for DNA/RNA binding proteins, quantify gene expression via transcript abundance, find where polymerase and ribosomes are sitting in the cell and even measuring RNA structures. What's even better is that next generation sequencing experiments are getting easier and easier to perform with well established kits available, and the costs of runs are dropping dramatically.

In this workshop you will learn the basics behind next generation sequencing technology, how to make a sequencing library, and how to analyze next generation sequencing data. After an introduction to the technology, I will describe -some of the many interesting and creative ways that people are applying the technology in assays such as genome sequencing, protein binding site identification (CHiP-Seq), ribosome location mapping (Ribo-Seq), and measuring transcript abundance (RNA-Seq). I'll then go through an in-depth demo on analyzing RNA-Seq data to measure differences in gene expression on a yeast data set. After this, I'll highlight a creative new way to use next generation sequencing to probe RNA structure called SHAPE-Seq, and finish off with describing resources to kits, protocols, and data analysis tools so that you can start using next generation sequencing in your research when you get home from SB5!

Check out the other posts in the Workshop Forum for things you can do before the workshop, and to post any questions you may have.

Workshop Presenters: Cole Trapnell (Broad Institute)

DAY 2 Concurrent Workshops

SIGN UP FOR WORKSHOP 2A -OR- 2B

WORKSHOP 2A: WHAT DO WE NEED FROM SYNTHETIC BIOLOGY?

Thur, June 16: 12:00-2:00

Location:  Dinkelspiel Auditorium

Workshop Lead: Kevin Costa, SynBERC

The panel discussion will bring together various representatives from government and private agencies as well as the biotechnology industry to answer the question "What do we need from synthetic biology?". For the field of synthetic biology to mature at an increasing rate, we need a strong dialogue between public sector representatives and the practitioners of synthetic biology. In other words, this workshop will people who need results from this field a chance to speak directly with those who are doing the work. Some sample topics:

• What areas are currently being overlooked in synthetic biology?
• What benchmarks do we need to meet in the coming years?
• What killer apps are we missing?
• Has progress since SB1.0 been what we needed?
• What is the role of manufacturing facilities (e.g., BioFabs) in filling our needs?
• How do public and private sectors come together to advocate for increased research funding?

Workshop Presenters:  Linda Chrisey (U.S. Office of Naval Research), Theresa Good (U.S. National Science Foundation), Alicia Jackson (U.S. DARPA), Jack Newman (Amyris), Todd Peterson (Life Technologies)

WORKSHOP 2B: AVENUES FOR EDUCATION ABOUT SYNTHETIC BIOLOGY

Thur, June 16: 12:00-2:00

Location:  Old Union Ballroom

Workshop Lead: Natalie Kuldell, MIT

Synthetic biology provides many educational opportunities: bridging science and engineering in the classroom, engendering critical and creative thinking in students, and attracting public interest in the goals and outcomes of the field. To date, however, there have been few opportunities to anticipate the educational needs in synthetic biology and to coordinate our efforts. This workshop will include a short panel discussion with researchers, educators and public outreach professionals who will sketch some educational strategies. Participants in this workshop will break into small groups to identify key endeavors in synthetic biology that would benefit from a coordinated educational strategy over the next 1, 5, and 10 years and explore a range of mechanisms to realize these educational goals. A good outcome from this workshop will be a prioritized list of educational gaps (emerging or existing) and some strategies for developing educational materials around them. A great outcome from this workshop will be partnerships between formal, informal and public communication professionals to address the needs we identify.

Workshop Panelists:  Darlene Cavalier (Discover Magazine), King Lau Chow (Hong Kong University of Science and Technology), Jonathan Eisen (UC David and PLoS Biology), Ellen Jorgenson (Genspace NYC), Natalie Kuldell (MIT), Ilona Miko (Nature Education), Judy Scotchmoor (UC Berkeley).

DAY 3 Concurrent Workshops

SIGN UP FOR WORKSHOP 3A -OR- 3B

WORKSHOP 3A: WETWARE TOOLS FOR SYNTHETIC BIOLOGY

Fri, June 17: 12:00-2:00

Location: Dinkelspiel Auditorium

Workshop Lead: Reshma Shetty, Ginkgo Bioworks

Vivek Mutalik and Guillaume Cambray from the BioFAB will discuss the design, construction and validation of a set of reusable genetic parts for gene expression in E. coli.  Zach Serber from Amyris will discuss Automated Strain Engineering. Finally Mark Fischer from Duane Morris will outline the contribution and use of BioBrick parts via the BioBricks Foundation's BioBrick Public Agreements.

Workshop Presenters:  Guillaume Cambray (BIOFAB), Mark Fischer (Duane Morris LLP), Vivek Mutalik (BIOFAB), and Zach Serber (Amyris)

WORKSHOP 3B: SOFTWARE TOOLS FOR SYNTHETIC BIOLOGY

Fri, June 17: 12:00-2:00

Location: Old Union Ballroom

Workshop Lead: Austin Che, Ginkgo Bioworks

The goal of this workshop will be to brief participants on the software tools available to enable the engineering of biology.  Doug Densmore from Boston University will give an overview of design automation tools for synthetic biology.  Peter Karp will discuss EcoCyc and MetaCyc.

Workshop Presenters:  Douglas Densmore (SBOL) and Peter Karp (SRI)