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igem.org iGEM, The Registry of Standard Biological Parts, And Synthetic Biology Cambridge, UK July 5, 2010 Randy Rettberg [email protected] igem.org Synthetic Biology Question igem.org 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 igem.org Device-Level System Diagram 2003 igem.org Parts- and Device-Level System Diagram igem.org iGEM Philosophy igem.org 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) igem.org iGEM 2005 igem.org iGEM 2005 igem.org iGEM 2006 igem.org iGEM 2007 igem.org iGEM 2008 igem.org iGEM 2009 igem.org igem.org iGEM 2010 Teams - 2 igem.org iGEM AND High School Teams igem.org 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? igem.org Is iGEM Secure? igem.org iGEM Growth and Scale igem.org 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 igem.org − 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 igem.org Registry Labs igem.org Synthetic Biology Courses igem.org iGEM Community Now igem.org • • • • 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 igem.org 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 igem.org 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 igem.org BBa_K274002 – Main Page igem.org BBa_K274002 – Get This Part igem.org BBa_K274002 - Show 2 other locations igem.org Extra PstI Site - email igem.org DNA Samples: Quality Control Program igem.org Sample QC: Digest Gel igem.org Sample QC: Antibiotic Test Plate igem.org Sample QC: Sequence Analysis igem.org Sample QC: Sample Provenance igem.org The Registry – Pace of Change igem.org igem.org May 2003 igem.org igem.org igem.org igem.org igem.org igem.org partsregistry.org Example Part igem.org Parameters, Categories, . . . igem.org Catalog Style 2009 igem.org Plasmids/Assembly igem.org 2010 DNA Distribution igem.org 2010 Kit Plates 1-3 3A Assembly igem.org Sample QC: Shipping Changes igem.org 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 igem.org Part Documentation – Vanillin p. 1 igem.org Part Documentation – Vanillin p. 2 igem.org Part Documentation – E0040 p. 1 igem.org Part Documentation – E0040 p. 2 igem.org Part Documentation – Why a Wiki igem.org Part Documentation – Why a Wiki igem.org Part Documentation – Why a Wiki igem.org Part Documentation – Why a Wiki igem.org Devices: A ‘Black Box’ igem.org Devices: Interfaces igem.org 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 igem.org 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 igem.org 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 igem.org − Examples include proteins used internal to the function of the part. − Sensitivities to DNA binding proteins − Required use of energy molecules Devices: DNA Implementation igem.org DNA Segments A C B D Devices: Representations igem.org SBML Model <kjdfjl>lksdjflL< <Lkjflds> <PART>klsdjflak Clotho Lkjfaiovunenzvncvnnn.vzvrvb cwkernfc fyhnkufhabcbxteqwxmc,vgbl,ih0upyt;lfdsnzgoi Empty Empty Devices: Measurement igem.org − − − − − − Measurement values Units (URI) Measurement Protocol (URI) Group (URI) Measurement Batch ID (URI) Comments Devices: References igem.org − References More Registries – A Web of Registries igem.org SynBERC iGEM in Europe iGEM in Asia MIT SB Corp ASM Registry Version 4 igem.org Tools Hard Information Objects mySQL Users Wiki MediaWiki Engine mySQL A 21st Century Registry Design igem.org 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? igem.org External Tools igem.org ERC Meeting SynBERC Introduction Key Issues igem.org − 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 igem.org − − − − − − − − 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 igem.org − 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.” igem.org Voltmeter - Electronic igem.org Voltmeter - Microbiology igem.org Biologists Use - Jello ? igem.org Good News - Soldering ~ Assembly igem.org BioBrick Standard Assembly - TK Good News – Modularity Exists igem.org CI LacI OLac RBS 434 cI CI LacI T Biological Insulation ? igem.org Apple QuickTake – too early igem.org 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 igem.org Apple PenLite (ATG 1992) iGEM 2009 igem.org iGEM Growth and Scale igem.org 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 igem.org