View source for 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. __NOTOC__

=== 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

=== Summary Schedule ===

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

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==== Monday morning ====
Optional tutorials (details below):
* Lab basics - meet in 111 Keck at 9 am
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==== Tuesday morning ====
Meet in 111 Keck at 9 am
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
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* Group lunch at Caltech faculty club
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==== Wednesday morning ====
Meet in 111 Keck at 9 am
* Analyze data from previous evening
* Plan and set up characterization experiments

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==== 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

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==== Monday afternoon ====
Continued tutorials
* MATLAB basics - meet in 114 Steele Lab at 1 pm

'''Main workshop starts at 4 pm''' in 111 Keck
* Overview of workshop and TX-TL system
* Lab safety briefing
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==== Tuesday afternoon ====
* TX-TL modeling toolbox
* Characterization project discussions and initial experiments

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==== Wednesday afternoon ====
* Set up characterization runs
* Vesicles and ALL demonstrations (optional)

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==== Thursday afternoon ====
* Group presentations of characterization data

Adjourn by 4 pm
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==== Monday evening ====
Group dinner on South Lake Avenue

Lab session: 8-10 pm
* Set up and run first TX-TL reactions

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==== Tuesday evening ====
Dinner on your own

Lab session: 8-10 pm
* Set up TX-TL runs

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==== Wednesday evening ====
Group dinner in Old Pasadena

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Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab.  You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels.  If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program.  You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.  

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious).  You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== 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|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 111 Keck Lab (building 78 on {{campus map|campus map}}); lab activities will take place in 136 Keck.
* 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, [http://www.jove.com/video/50762 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).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells].  ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system].  ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox 
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info 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)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ 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.