TX-TL Workshop, Jun 2014

As part of the DARPA Living Foundries program, Caltech will be hosting a hands-on workshop on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 23-26 Jun 2014. This workshop is by invitation only.

Workshop goals

The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

• Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
• Assemble and test genetic circuits using linear DNA assembly in a single day
• Implement and test a novel 3-6 promoter circuit in E. coli within a single week
• Create enough TX-TL extract and buffer for 300+ reactions, shipped to your home institution

Summary Schedule

The schedule below gives an overview of the activities during the workshop.

Monday morning Optional tutorials (details below): Lab basics - meet in 111 Keck at 9 am MATLAB basics - meet in 111 Keck at 9 am	Tuesday morning Meet in 111 Keck at 9 am Analyzing TX-TL results (from overnight run) TX-TL using linear DNA	Wednesday morning Meet in 111 Keck at 9 am Analyze data from previous evening Plan and set up characterization experiments	Thursday morning Meet in 111 Keck at 9 am Analyze data from previous evening Plan and set up final characterization experiments Prepare presentation of characterization data
Monday afternoon Continued tutorials Lab basics (con't) Geneious - meet in 114 Steele at 3:30 pm Main workshop starts at 4 pm in 111 Keck Overview of workshop and TX-TL system Set up and run first TX-TL reactions	Tuesday afternoon TX-TL modeling toolbox Characterization project discussions and initial experiments	Wednesday afternoon Set up characterization runs Vesicles and ALL demonstrations (optional)	Thursday afternoon Group presentations of characterization data Adjourn by 4 pm
Monday evening Group dinner on South Lake Avenue Lab session: 8-10 pm	Tuesday evening Dinner on your own Lab session: 8-10 pm	Wednesday evening Group dinner in Old Pasadena

Travel arrangements

The workshop will begin at ~3:30 pm on 23 Jun (Mon) and will finish by 4 pm on 26 Jun (Thu). Participants are responsible for making their own travel arrangements:

• For those who are flying in to LAX, it takes 40-60 minutes to get from LAX to Caltech by taxi. If you are flying into Burbank (BUR), it takes 20-30 minutes.
• A set of optional tutorials will take place on 23 June 8:30 am to 3:30 pm for participants who do not have experience in either laboratory techniques, sequence analysis software (aPe, Geneious, etc), or MATLAB programming. While not required, these tutorials may be helpful for some participants to get more out the workshop.
• Directions and lodging - Saga Motor Hotel is 15 minute walk to campus; Hilton is 15-20 minutes.
• All meetings and lectures will take place in 114 Steele Lab (building 81 on campus map); lab activities will take place in 136 Keck (building 78)
• Participants will be working in the lab, so must have closed shoes and covered legs (no shorts).
• If possible, please bring a laptop with Excel (or equivalent) installed. Other useful software is listed below.

Read-ahead material

We will assume everyone has watched the following 15 minute video before attending the workshop:

• Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology. Journal. of Visualized Experiments (JoVE), e50762, doi:10.3791/50762 (2013).

  Note: this paper has not yet been released; workshop participants will receive a preprint link via e-mail)

If you have time, we also encourage you to take a look at the following material before arriving:

• J. Shin and V. Noireaux, An E. coli cell-free expression toolbox: application to synthetic gene circuits and artificial cells. ACS Synthetic Biology, 1(1):29–41, 2012.
• Biomolecular Breadboards pages on OpenWetWare
  • Modeling overview - setting up simulations using MATLAB-based TX-TL toolbox
  • Preliminary data - includes linear DNA protection, protein degradation
  • More info - additional references and presentations on TX-TL

Software

We will make use of the following software as part of the workshop:

• Microsoft Excel (or Numbers)
• ApE (free), Geneious (free trial)
• MATLAB, Simbiology
• TX-TL modeling toolbox (requires MATLAB 2010+ and SimBiology]

Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.