Transcript Cambridge Presentation July 2010 - Registry part

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iGEM,
The Registry of Standard Biological Parts,
And Synthetic Biology
Cambridge, UK
July 5, 2010
Randy Rettberg
[email protected]
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Synthetic Biology Question
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Can simple biological systems be
built from standard, interchangeable
parts and operated in living cells?
Or, is biology so complex that each
case is unique?
Education Driving Research
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Device-Level System Diagram 2003
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Parts- and Device-Level System Diagram
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iGEM Philosophy
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iGEM Philosophy: Get and Give
Teams are expected to use the parts, ideas, and
experience of teams in previous years.
Teams are expected to contribute their parts,
ideas, and experiences.
iGEM 2004 (SBC 04)
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iGEM 2005
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iGEM 2005
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iGEM 2006
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iGEM 2007
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iGEM 2008
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iGEM 2009
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iGEM 2010 Teams - 2
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iGEM AND High School Teams
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 Advisor:
 Advisor:
 Advisor:
Wendell Lim
Orion Weiner
James Onuffer
 Teacher at Lincoln High School: George Cachianes
 Teacher at Lincoln High School: Julie Reis
Plus 10 “Buddies”
Is iGEM Safe?
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Is iGEM Secure?
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iGEM Growth and Scale
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iGEM Scale and Growth
Year
Teams Jamboree Total
IAP
4
20
20
2004
5
70
70
2005
13
120
150
2006
32
360
400
2007
54
570
750
2008
84
825
1180
2009
112
1100
1650
2010
130
1300
1950
2011
180
1800
2700
2012
250
2500
3700
Or Not !
iGEM 2010 and Beyond
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− 2010 130 Teams, Jamboree at MIT November 68
− 2011 180 (?) Teams,
– Regional Jamborees in October
– World Championship at MIT (Nov. 5-7)
– Regional iGEM Headquarters
− iGEM Labs and Courses
– Sign up at ung.igem.org
− iGEM Society, Institution, Foundation
− iGEM Alumni Association
New Synthetic Biologists
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Registry Labs
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Synthetic Biology Courses
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iGEM Community Now
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•
•
•
•
7,041
6,513
1,782
920
•
•
•
•
•
12,327
5,166
2,328
1,691
795
user accounts
unique emails
users have logged in since Feb 2010
have entered parts
parts entered
DNA samples at the Registry
reported to work
parts sent by last year’s teams
sequence confirmed parts
The Registry: Quality Not Quantity
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Parts in the Registry are believed to be of low quality.
1. The DNA Sample does not match the part sequence or
cannot be transformed.
2. The Part is not well documented in the Registry.
3. The Part has not been measured.
4. Interchangeable parts are not possible.
5. Lots of parts are junk.
Part Quality
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Parts in the Registry are believed to be of low quality.
1. The DNA Sample does not match the part sequence or
cannot be transformed.
–
DNA Quality Control Program
2. The Part is not well documented in the Registry.
–
Curation, Ratings, Judges, Filtering
3. The Part has not been measured.
–
BioFab, Jason’s measurement program, Devices
4. Interchangeable parts are not possible.
–
BioLint
5. Lots of parts are junk
–
Delete, clean up, hide
BBa_K274002 - email
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BBa_K274002 – Main Page
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BBa_K274002 – Get This Part
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BBa_K274002 - Show 2 other locations
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Extra PstI Site - email
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DNA Samples: Quality Control Program
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Sample QC: Digest Gel
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Sample QC: Antibiotic Test Plate
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Sample QC: Sequence Analysis
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Sample QC: Sample Provenance
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The Registry – Pace of Change
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May 2003
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partsregistry.org
Example Part
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Parameters, Categories, . . .
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Catalog Style 2009
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Plasmids/Assembly
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2010 DNA Distribution
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2010 Kit Plates 1-3
3A Assembly
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Sample QC: Shipping Changes
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1. Compatible with RFC10 (no EcoRI, XbaI,SpeI, PstI)
2. In pSB1C3 if possible, contact [email protected] if not
3. Enter sequencing information
4. Use shipping form
Part Documentation – Not Good
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Part Documentation – Vanillin p. 1
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Part Documentation – Vanillin p. 2
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Part Documentation – E0040 p. 1
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Part Documentation – E0040 p. 2
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Part Documentation – Why a Wiki
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Part Documentation – Why a Wiki
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Part Documentation – Why a Wiki
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Part Documentation – Why a Wiki
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Devices: A ‘Black Box’
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Devices: Interfaces
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Primary Interfaces
The intended functions of this device.
Secondary Interfaces
Materials required for the proper operation of this part
or expected to be generated by this part. E.g. energy,
waste
Tertiary Interfaces
Possible but unexpected interactions with the
environment.
Devices: Main Page
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This device takes inputs and makes outputs
according the proof of Fremat’s Last Theorem
described in our team’s wiki. We ran out of
time to complete the proof, but it is obvious to
any capable undergraduate.
Other applications of this device include
universal cryptography, X-ray vision processing,
and world peace.
Pin
Name
I/O
Type
Subtype
A
Gate
Input
PoPS
URL:alllsdf.asdf.
B
Number
Input
PoPS
URL:allsdf.asfd
C
Ready
Input
IPTG
URL:rsbp.42356
D
Reset
Input
Heat
URL:rsbp.5900
E
Result
Outpur
PoPS
URL:alilsdf.asdf
Devices: Design
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This device consists of 3 different parts to compute magic numberskj kjlaalklkjf jaksalskdfj df f f as df f a
sd f asd fad f asd f a sdf a df a sd f asd fad sf asdf asdf as df asdf as dfa dsf a sdf as dfas
dfaksdjfklkrtf wt 5givi g hio ytf jopuiguyf iuhjii y uuhjoo jo hygyhijk oh ugy t rt y ii I I yt tg h jk I iuy f
g hj k I y e 3 4 u jm k hf gh j
Devices: Other Interfaces
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− Examples include proteins used internal to the function of the
part.
− Sensitivities to DNA binding proteins
− Required use of energy molecules
Devices: DNA Implementation
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DNA Segments
A
C
B
D
Devices: Representations
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SBML Model
<kjdfjl>lksdjflL<
<Lkjflds>
<PART>klsdjflak
Clotho
Lkjfaiovunenzvncvnnn.vzvrvb cwkernfc
fyhnkufhabcbxteqwxmc,vgbl,ih0upyt;lfdsnzgoi
Empty
Empty
Devices: Measurement
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−
−
−
−
−
−
Measurement values
Units (URI)
Measurement Protocol (URI)
Group (URI)
Measurement Batch ID (URI)
Comments
Devices: References
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− References
More Registries – A Web of Registries
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SynBERC
iGEM in Europe
iGEM in Asia
MIT
SB Corp
ASM
Registry Version 4
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Tools
Hard Information
Objects
mySQL
Users
Wiki
MediaWiki
Engine
mySQL
A 21st Century Registry Design
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Viewer
Tool
Viewer
Tool
Tool
Viewer
Tool
Tool
Syn-Bio-Co 1
Syn-Bio-Co 2
Public Data
School 1
Lab 1
How can the interfaces be developed?
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External Tools
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ERC Meeting
SynBERC Introduction
Key Issues
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− Getting Synthetic Biologists to add parts
− Quality of the collection
− Intellectual Property
− Thousands of users – live
− Timing
− Integration with bioinformatics tools
− Secrecy and limited access ?
Some Issues
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−
−
−
−
−
−
−
−
How will the interfaces be developed?
Who gets to edit what?
Are there groups, user accounts, a user community?
Where does the software run? in the user’s PC, in the lab
server, at a central site, in the “cloud” (at Google or
Amazon)
How will pre-publication be handled?
Why will anyone share anything?
Will the core be a community or centralized development?
How will free-form content be supported?
Status of Synthetic Biology - 2010
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− Science, Engineering, and Industry
– Cultures and Values
− Arguments by analogy fail four times, why bother?
− Failure to execute vs Failure to imagine
− Representation in a young field
− Community
− 1850 vs 2010:
– Resistors, Capacitors, Inductors, Current Sources, Voltage
Sources, Diodes, Transistors, Meters, Shielding, Ground Planes
− Support
− Centers for Systems and Synthetic Biology
Engineering Products
– Apple Quadra 840AV
“Ahead of its time, the
840AV and its relative, the
Centris/Quadra 660AV, were
the first Macintoshes to
include 16-bit 48KHz stereo
audio recording capability,
as well as S-Video and
Composite video input and
output. They were also the
first personal computers that
supported speech
recognition (PlainTalk) outof-the-box.”
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Voltmeter - Electronic
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Voltmeter - Microbiology
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Biologists Use - Jello ?
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Good News - Soldering ~ Assembly
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BioBrick Standard Assembly - TK
Good News – Modularity Exists
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CI
LacI
OLac
RBS
434 cI
CI
LacI
T
Biological Insulation ?
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Apple QuickTake – too early
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Apple QuickTake 100 introduced
February 16, 1994, the Apple QuickTake 100
was one of the first consumer digital
cameras. It came with a heafty price tag of
$749 for a single focal length, fixed focus
camera with maximum 640 x 480 resolution.
Adjusted for inflation the price was nearly
$1,100 in 2006 dollars. Shutter sppeds were
1/30 to 1/175 second. The QuickTake 100
could only be used directly with an Apple
Mac. The later Quicktake 150, introduced
May 1995, could also be used with a
Windows PC. Both had only 1mb internal
storage and no external storage. They could
hold about 16 images before you had to
download the images to the computer.
Connection to the computer was with a
round Apple serial cord. The QuickTake 100
and 150 were made by Kodak.
iPad 1992 - way too early
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Apple PenLite (ATG 1992)
iGEM 2009
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iGEM Growth and Scale
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iGEM Scale and Growth
Year
Teams Jamboree Total
IAP
4
20
20
2004
5
70
70
2005
13
120
150
2006
32
360
400
2007
54
570
750
2008
84
825
1180
2009
112
1100
1650
2010
130
1300
1950
2011
180
1800
2700
2012
250
2500
3700
Or Not !
Heidelberg 2008
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