Synthetic Biology:Polka Dots

As there still seems to be web hits on this page, the important contents of this page have been reformatted a bit and put up here for historical reference. In 2004, this Synthetic Biology class was taught at MIT during the month of January.

Synthetic Biology Lab: Engineered Genetic Polka Dots
The course web site is at https://stellar.mit.edu/S/project/iap/ia04/synthetic-biology-lab/index.html.

How to Apply
Please send an email to (no longer functional email address) that includes the following information:
 * 1) Name
 * 2) School
 * 3) Expected year of graduation (if appropriate)
 * 4) Major (if decided)
 * 5) The lab will run from Monday January 5 to Thursday January 29.  Are you able to spend 2 hours per day in class/discussion and 1 to 6 hours per day working on your project? Yes/no?

Instructors & Contact Information

 * Drew Endy, Fellow, MIT Biology & Biological Engineering
 * Tom Knight, Senior Research Scientist, MIT AI Lab & EECS
 * Randy Rettberg, Distinguished Engineer, Sun, Apple & BBN (retired)
 * Gerald J. Sussman, Matsushita Professor of Electrical Engineering (on leave IAP 2004)
 * Very Special Guests, TBA

Information for Prospective Students
We appreciate your interest in MIT's 2004 IAP Synthetic Biology Lab. The theme this year is to design genetically encoded systems that make use of cell-cell signaling and cell-based logic to create polka-dot (or other) patterns  in bacterial lawns. The course has no pre-requisites but requires "heavy-lifting" from all participants. Work includes, but is not limited to, literature scouring, database querying, DNA editing, and genetic device and system design, modeling, and simulation. The work is performed in groups; last-year's groups contained a good-mix of expertise (i.e., no one person had to learn/do everything). Enrollment is limited as it is the second time the course has been taught and we have finite resources for system fabrication and assembly. To apply please send a brief email to the instructors. There are no prerequisites or requirements; last year's participants ranged from first-year undergraduates to postdoctoral researchers. We expect to notify participants by December 8, 2003.

Frequently Asked Questions

 * 1) I won't be here &lt;any random day/week&gt; in January, can I still take the class? It depends. A random day here/there shouldn't be a problem (but you will need to coordinate with your group once the course starts).
 * 2) Can I sit in on the lectures? No, we do not allow  for listeners (space, et cetera).
 * 3) How much time will the course require? ~2 hours per weekday for   lecture and group discussions (lunch is provided). You should plan to spend an additional 1-6 hours per day to work on your project.
 * 4) Will I be doing experiments? Will I gain &quot;wet-lab&quot; experience? What will I be doing? The course is purposefully designed to avoid requiring any wet-lab experiments. Instead students (and instructors) first work to specify DNA encoding genetic devices. Once the newly specified DNA has been ordered the class shifts gears to work on the conception, design and specification of integrated biological systems. By analogy, the designer of a complex integrated electronic circuit does not typically also build the silicon chip. However, if you are a class participant and have extra time each morning, we  may be able to arrange  an  experience &quot;bashing&quot; DNA (please indicate such an interest in your application).
 * 5) You made &quot;blinkers&quot; last IAP, did anything blink? Short answer: we are still building the systems but are closing in on completion. Long answer (copied from a report): During January, 2003 we conducted a four-week long experimental course in which 16 students were asked to design genetically-encoded oscillators using protein-DNA logic (PDL); students were given a 20,000 base pair DNA synthesis budget. In addition, students were asked to design their systems using standard biological parts such that the resulting parts could be used in more than one system (i.e, parts were shared across the class). The course workflow was:  (i) model-based system design, (ii) model-driven simulation, (iii) layout,  documentation, and plan of characterization, (iv) parts ordering via commercial  suppliers, and (v) parts return and system assembly. Design, simulation, layout  and documentation took one month. Editing the student-specified parts and placing  the parts synthesis order took two months. Parts synthesis required another one to five months. System assembly from standard parts is taking an additional four months, for a total elapsed time of one year. Current estimates are that the 2004 course will run to completion in five months and that, given current technology, three months start-finish will be realized.

Expected Schedule
(DRAFT v0.1, 11/15/03. Content & structure subject to radical change until further notice.)

Scheduled class time: Noon-2p, M-F (lunch provided or BYO) Additional unstructured time to work on projects: whenever, ~1-6hr/day

Monday 1/5/04	Introduction, biological engineering theory, pattern formation intro. Tuesday 1/6/04	Cell-cell signaling in bacteria Wednesday 1/7/04	Standard biological parts Thursday 1/8/04	Channels and gates -- device design and specification Friday 1/9/04	Channels and gates -- device design and specification

Monday 1/12/04	Channels and gates -- device design and specification Tuesday 1/13/04	Channels and gates -- device design and specification Wednesday 1/14/04	Channels and gates -- device model and parameterization Thursday 1/15/04	Channels and gates -- device model and parameterization Friday 1/16/04	Channels and gates -- handoff of final device specifications

Monday 1/19/04	Amorphous computing -- languages and patterns; engineering biology and society Tuesday 1/20/04	System design -- brainstorm I Wednesday 1/21/04	System design -- brainstorm II Thursday 1/22/04	System design -- system specification I Friday 1/23/04	System design -- system specification II

Monday 1/26/04 	System design -- reduce to practice I Tuesday 1/27/04	System design -- reduce to practice II Wednesday 1/28/04	System design -- reduce to practice III Thursday 1/29/04	System design -- group presentations and wrap Friday 1/30/04	NO CLASS -- ski, snowboard, make snowfolks, sleep

Sponsors (i.e., much thanks to)

 * MIT Computer Science &amp; Artificial Intelligence Lab.
 * MIT Biology Department
 * MIT Biological Engineering Division
 * MIT Computational & Systems Biology Initiative
 * MIT Electrical Engineering & Computer Science Department
 * MIT Synthetic Biology Working Group
 * Defense Advanced Research Projects Agency
 * Hewlett-Packard Life Sciences
 * DNA synthesis by Blue Heron Biotechnology

Reading
Articles


 * 1) 1 pmid=12949263
 * 2) 2 pmid=14500902
 * 3) 3 pmid=12736688
 * 4) 4 pmid=12451174
 * 5) 5 pmid=10659856

Misc

"Amorphous computing"

Books (in you want to learn some basic biology re: gene expression regulation )

A Genetic Switch by Mark Ptashne (introductory) The lac Operon by Benno Muller-Hill (more advanced/subtle)