Podcasts

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=iGEM Explainer Vodcasts=
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<html><a rel="enclosure" href="http://blip.tv/file/get/IgemLabs-iGEMExplainer01DrewEndyDefiningSyntheticBiology399.flv" onclick="window.popup_player_258600 = window.open('http://blip.tv/file/254077/?skin=popup&file_type=flv','post_258600','toolbar=no,scrollbars=no,directories=no,resizable=yes,width=360,height=305,top=20,left=20,location=no,menubar=no,status=yes,'); return false;"><img src="http://blip.tv/file/get/IgemLabs-iGEMExplainer01DrewEndyDefiningSyntheticBiology399.flv.jpg" height="100px" width"133px" /></a></html>
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| colspan="3" style="font-family: Verdana, sans-serif; font-size: 1.3em; font-weight: bold;" | <html><a rel="enclosure" href="http://blip.tv/file/get/IgemLabs-iGEMExplainer01DrewEndyDefiningSyntheticBiology399.flv" onclick="window.popup_player_258600 = window.open('http://blip.tv/file/254077/?skin=popup&file_type=flv','post_258600','toolbar=no,scrollbars=no,directories=no,resizable=yes,width=360,height=305,top=20,left=20,location=no,menubar=no,status=yes,'); return false;" style="color: black;">Drew Endy: Defining Synthetic Biology</a></html>
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| colspan="3"| "Make it easier to build things. Define the things you are building with by using standards. Hide biological complexity with abstraction."  Drew explains Synthetic Biology from the ground up; from the foundations of genetic engineering laid in the 1970's. <span id="Vod1Shower" class="_toggler_show-Vod1Details _toggler_hide--Vod1Shower" style="font-size: 0.8em; color: #9fcc52;"> more...</span> <div class="Vod1Details" style="display: none;">
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Synthetic Biology is an approach to engineering biology. That means it's not metabolic engineering, it's not bioprocess engineering, it's not cancer cell engineering; It means it's an approach to making those sorts of things. It's not the particular application, it's the approach you use to realize that particular application. To say that differently, Synthetic Biology isn't making a specific thing, it's how you make something.
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What is biotechnology? As a process it depends on 1. Recombinant DNA, 2. Polymerase Chain Reaction (PCR), and 3. Automated Sequencing. The last 30 years of biotech depend on these three technologies, which define the process for writing DNA (Recombinant DNA and PCR) and reading it out (Automated Sequencing). This is genetic engineering. So people ask, How is anything you do different than genetic engineering? For it to be different than genetic engineering, there have to be more things on this list.
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The first new thing on this list is 4. Automated Construction of DNA. Instead of using PCR and Recombinant DNA to make DNA (analogous to cutting and pasting an essay together), you can just pay someone to print it directly for you. You can be the expert designer of DNA and someone else can be the expert constructor of DNA.
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<h3><a rel="enclosure" href="http://blip.tv/file/get/IgemLabs-iGEMExplainer01DrewEndyDefiningSyntheticBiology399.flv" onclick="window.popup_player_258600 = window.open('http://blip.tv/file/254077/?skin=popup&file_type=flv','post_258600','toolbar=no,scrollbars=no,directories=no,resizable=yes,width=360,height=305,top=20,left=20,location=no,menubar=no,status=yes,'); return false;">
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Drew Endy: Defining Synthetic Biology
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<a rel="enclosure" href="http://blip.tv/file/get/IgemLabs-iGEMExplainer01DrewEndyDefiningSyntheticBiology399.flv" onclick="window.popup_player_258600 = window.open('http://blip.tv/file/254077/?skin=popup&file_type=flv','post_258600','toolbar=no,scrollbars=no,directories=no,resizable=yes,width=360,height=305,top=20,left=20,location=no,menubar=no,status=yes,'); return false;">
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"Make it easier to build things. Define the things you are building with by using standards. Hide biological complexity with abstraction." </div>
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5. Standards: What are we going to make? Maybe I want to make a lot of things quickly, so I need some way of defining how to put things together - that's New!
 
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6. The last thing is Abstraction. Everybody talks about how complicated biology is, and when we engineer DNA today we usually memorize specific DNA sequences and program at the level of nucleotides, like TAATAA - that would be like programming computers with raw binary by hand, manipulating individual bits like 0101110.
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<h3><a rel="enclosure" href="http://blip.tv/file/get/IgemLabs-iGEMExplainer02DrewEndyBelieveInSyntheticBiology355.flv" onclick="window.popup_player_258502 = window.open('http://blip.tv/file/253979/?skin=popup&file_type=flv','post_258502','toolbar=no,scrollbars=no,directories=no,resizable=yes,width=360,height=305,top=20,left=20,location=no,menubar=no,status=yes,'); return false;">
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Drew Endy: Believe in Synthetic Biology
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"Why should you consider changing how you engineer biological systems from doing ad-hoc research to something that's a more scalable engineering framework?" </div>
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What is Synthetic Biology? It builds on genetic engineering - Recombinant DNA, PCR, and Automated Sequencing - by adding three new foundational technologies - Automated Construction, Standards, and Abstraction - these are each as important as the first three, and taken together define a new process for engineering biological systems.
 
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This is called Synthetic Biology. It's a means to an end. Make it easier to build things. Define the things you are building with using standards. Hide biological complexity with abstraction. <span class="_toggler_hide-Vod1Details _toggler_show--Vod1Shower" style="font-size: 0.8em; color: #9fcc52;"> ...hide</span></div>
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<h3><a rel="enclosure" href="http://blip.tv/file/get/IgemLabs-iGEMExplainer03DrewEndyWhatIsAStandardBiologicalPart197.flv" onclick="window.popup_player_258904 = window.open('http://blip.tv/file/254379/?skin=popup&file_type=flv','post_258904','toolbar=no,scrollbars=no,directories=no,resizable=yes,width=360,height=305,top=20,left=20,location=no,menubar=no,status=yes,'); return false;">
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Drew Endy: What is a Standard Biological Part?
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| style="word-spacing: 1em;" | <html><a href="http://igem.blip.tv/file/get/IgemLabs-iGEMExplainer01DrewEndyDefiningSyntheticBiology399.mov" title="Download large quicktime file (640x480px)" style="color: #9fcc52;">screen</a> <a href="http://igem.blip.tv/file/get/IgemLabs-iGEMExplainer01DrewEndyDefiningSyntheticBiology948.mp4" title="formatted for iPods (320x240px h.264 quicktime)" style="color: #9fcc52;">ipod</a></html>
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| style="font-size: 1.8em; text-align: right; padding-right: 0.2em;" | [5:00]
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<a rel="enclosure" href="http://blip.tv/file/get/IgemLabs-iGEMExplainer03DrewEndyWhatIsAStandardBiologicalPart197.flv" onclick="window.popup_player_258904 = window.open('http://blip.tv/file/254379/?skin=popup&file_type=flv','post_258904','toolbar=no,scrollbars=no,directories=no,resizable=yes,width=360,height=305,top=20,left=20,location=no,menubar=no,status=yes,'); return false;">
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"What does it mean to have a Standard Biological Part - for example, a BioBrick-standard biological part? Well, why would something like that be important?" </div>
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<h3><a rel="enclosure" href="http://blip.tv/file/get/IgemLabs-Tutorial41AddingAndDocumentingABasicPart403.flv" onclick="window.popup_player_269439 = window.open('http://blip.tv/file/264878/?skin=popup&file_type=flv','post_269439','toolbar=no,scrollbars=no,directories=no,resizable=yes,width=360,height=305,top=20,left=20,location=no,menubar=no,status=yes,'); return false;">
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4.1 - Adding and Documenting a Basic Part
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<a rel="enclosure" href="http://blip.tv/file/get/IgemLabs-Tutorial41AddingAndDocumentingABasicPart403.flv" onclick="window.popup_player_269439 = window.open('http://blip.tv/file/264878/?skin=popup&file_type=flv','post_269439','toolbar=no,scrollbars=no,directories=no,resizable=yes,width=360,height=305,top=20,left=20,location=no,menubar=no,status=yes,'); return false;">
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<img src="https://static.igem.org/mediawiki/2007/9/95/Vodcasts_Tutorial-4-basicpart1.jpg" width="133" height="100" alt="" />
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In this screencast Reshma Shetty adds a basic part to the registry. Follow along at <a href="http://partsregistry.org/Help:Team_experience_tutorial#Make_a_part">section 4.1 of the team experience tutorial</a>.</div>
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<h3><a rel="enclosure" href="http://blip.tv/file/get/IgemLabs-Tutorial42EnteringPartSequenceAndFeatures835.flv" onclick="window.popup_player_269484 = window.open('http://blip.tv/file/264923/?skin=popup&file_type=flv','post_269484','toolbar=no,scrollbars=no,directories=no,resizable=yes,width=360,height=305,top=20,left=20,location=no,menubar=no,status=yes,'); return false;">
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4.2 - Entering Part Sequence and Features
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<html> <a rel="enclosure" href="http://blip.tv/file/get/IgemLabs-iGEMExplainer02DrewEndyBelieveInSyntheticBiology355.flv" onclick="window.popup_player_258502 = window.open('http://blip.tv/file/253979/?skin=popup&file_type=flv','post_258502','toolbar=no,scrollbars=no,directories=no,resizable=yes,width=360,height=305,top=20,left=20,location=no,menubar=no,status=yes,'); return false;"><img src="http://blip.tv/file/get/IgemLabs-iGEMExplainer02DrewEndyBelieveInSyntheticBiology355.flv.jpg" height="100px" width"133px" /></a></html>
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</a></h3>
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| colspan="3" style="font-family: Verdana, sans-serif; font-size: 1.3em; font-weight: bold;" | <html> <a rel="enclosure" href="http://blip.tv/file/get/IgemLabs-iGEMExplainer02DrewEndyBelieveInSyntheticBiology355.flv" onclick="window.popup_player_258502 = window.open('http://blip.tv/file/253979/?skin=popup&file_type=flv','post_258502','toolbar=no,scrollbars=no,directories=no,resizable=yes,width=360,height=305,top=20,left=20,location=no,menubar=no,status=yes,'); return false;" style="color: black;">Drew Endy: Believe in Synthetic Biology</a></html>
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| colspan="3"| So what's the point of all this? Why should you care about automated construction of DNA and standards and abstraction? Why should you consider changing how you engineer biological systems from doing ad-hoc research to something that's a more scalable engineering framework? <span id="Vod2Shower" class="_toggler_show-Vod2Details _toggler_hide--Vod2Shower" style="font-size: 0.8em; color: #9fcc52;">more...</span> <div class="Vod2Details" style="display: none;">
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<img src="https://static.igem.org/mediawiki/2007/5/52/Vodcasts_Tutorial-4-basicpart2.jpg" width="133" height="100" alt="" />
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But does it work? Why don't you look at some of the projects - look at some of the projects that are working - looking at the MIT project from last year: they got a genetically encoded inverter off the shelf and because it was a standard inverter they could put it together easily with other parts, they didn't have to memorize the DNA sequences of all the different devices they used... [and successfully engineered two novel reporter devices that produces bannana and wintergreen scents]!
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<a href="http://blip.tv/file/get/IgemLabs-Tutorial42EnteringPartSequenceAndFeatures343.mp4">ipod</a>
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Add the sequence and annotate several features,to finish entering the basic part in the registry. Follow along at <a href="http://partsregistry.org/Help:Team_experience_tutorial#Make_a_part">tutorial 4.2</a>.</div>
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So basically, what these new technologies get you, automated construction, standards, and abstraction, is a more powerful approach to engineering biology! <span class="_toggler_hide-Vod2Details _toggler_show--Vod2Shower" style="font-size: 0.8em; color: #9fcc52;"> ...hide</span></div>
 
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| width="55" style="font-size: 1.5em; text-align: left; padding-left: 2px;" |  Save:
 
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| style="word-spacing: 1em;" | <html><a href="http://blip.tv/file/get/IgemLabs-iGEMExplainer02DrewEndyBelieveInSyntheticBiology355.mov" title="Download large quicktime file (640x480px)" style="color: #9fcc52;">screen</a> <a href="http://blip.tv/file/get/IgemLabs-iGEMExplainer02DrewEndyBelieveInSyntheticBiology361.mp4" title="formatted for iPods (320x240px h.264 quicktime)" style="color: #9fcc52;">ipod</a></html>
 
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| style="font-size: 1.8em; text-align: right; padding-right: 0.2em;" | [1:41]
 
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<h3><a rel="enclosure" href="http://blip.tv/file/get/IgemLabs-tutorial43ReviewingYourPart564.flv" onclick="window.popup_player_269487 = window.open('http://blip.tv/file/264926/?skin=popup&file_type=flv','post_269487','toolbar=no,scrollbars=no,directories=no,resizable=yes,width=360,height=305,top=20,left=20,location=no,menubar=no,status=yes,'); return false;">
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4.3 - Reviewing Your Part
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<html> <a rel="enclosure" href="http://blip.tv/file/get/IgemLabs-iGEMExplainer03DrewEndyWhatIsAStandardBiologicalPart197.flv" onclick="window.popup_player_258904 = window.open('http://blip.tv/file/254379/?skin=popup&file_type=flv','post_258904','toolbar=no,scrollbars=no,directories=no,resizable=yes,width=360,height=305,top=20,left=20,location=no,menubar=no,status=yes,'); return false;"><img src="http://blip.tv/file/get/IgemLabs-iGEMExplainer03DrewEndyWhatIsAStandardBiologicalPart197.flv.jpg" height="100px" width"133px"/></a></html>
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| colspan="3" style="font-family: Verdana, sans-serif; font-size: 1.3em; font-weight: bold;" | <html> <a rel="enclosure" href="http://blip.tv/file/get/IgemLabs-iGEMExplainer03DrewEndyWhatIsAStandardBiologicalPart197.flv" onclick="window.popup_player_258904 = window.open('http://blip.tv/file/254379/?skin=popup&file_type=flv','post_258904','toolbar=no,scrollbars=no,directories=no,resizable=yes,width=360,height=305,top=20,left=20,location=no,menubar=no,status=yes,'); return false;" style="color: black;">Drew Endy: What is a Standard Biological Part</a></html>
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<a rel="enclosure" href="http://blip.tv/file/get/IgemLabs-tutorial43ReviewingYourPart564.flv" onclick="window.popup_player_269487 = window.open('http://blip.tv/file/264926/?skin=popup&file_type=flv','post_269487','toolbar=no,scrollbars=no,directories=no,resizable=yes,width=360,height=305,top=20,left=20,location=no,menubar=no,status=yes,'); return false;">
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| colspan="3"| "What does it mean to have a Standard Biological Part - for example, a BioBrick-standard biological part? Well, why would something like that be important? A good question. It's interesting that a lot of the iGEM teams show up and say they are using BioBricks, right, BioBricks-this, BioBricks-that, Standard biological parts this-that-and-the-other-thing; It's pretty weird, because it turns out not everyone is using BioBricks."3 <span id="Vod3Shower" class="_toggler_show-Vod3Details _toggler_hide--Vod3Shower" style="font-size: 0.8em; color: #9fcc52;">more...</span> <div class="Vod3Details" style="display: none;">
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So what is a standard biological part, and more specifically what is a Biobrick-standard biological part, and more importantly, why should you care? Well, there are a couple of issues here. What is a part, first off? A part is a level in an Abstraction Hierarchy. A part is defined as a basic biological function that can be encoded as genetic material. So a ribosome binding site (RBS), that's a function; it initiates protein synthesis; you could define the sequence of RNA that defines a ribosome binding site. Ok - basic biological function encoded in genetic material: that's a part.
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What's a Standard Part? A Standard Part would be something whose properties had been limited in such a way that the standard might support something, for instance, reliable physical and function composition. So a Standard Biological Part is not the latest bit of sequencing information you just discovered in nature and sequenced; it's not the parts list that the genomicist will get you. Rather, a Standard Biological Part is a part that has been refined and engineered to support... something - and I think the most important thing it could support would be reliable physical and functional composition, just like this nut and bolt. <span class="_toggler_hide-Vod3Details _toggler_show--Vod3Shower" style="font-size: 0.8em; color: #9fcc52;"> ...hide</span></div>
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Learn how to locate and review a part you (or any other team) has designed on the Registry. Follow along at <a href="http://partsregistry.org/Help:Team_experience_tutorial#Make_a_part">tutorial 4.3</a>.</div>
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Latest revision as of 03:21, 21 June 2007

Drew Endy: Defining Synthetic Biology

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"Make it easier to build things. Define the things you are building with by using standards. Hide biological complexity with abstraction."

Drew Endy: Believe in Synthetic Biology

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"Why should you consider changing how you engineer biological systems from doing ad-hoc research to something that's a more scalable engineering framework?"

Drew Endy: What is a Standard Biological Part?

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"What does it mean to have a Standard Biological Part - for example, a BioBrick-standard biological part? Well, why would something like that be important?"

4.1 - Adding and Documenting a Basic Part

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In this screencast Reshma Shetty adds a basic part to the registry. Follow along at section 4.1 of the team experience tutorial.

4.2 - Entering Part Sequence and Features

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Add the sequence and annotate several features,to finish entering the basic part in the registry. Follow along at tutorial 4.2.

4.3 - Reviewing Your Part

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Learn how to locate and review a part you (or any other team) has designed on the Registry. Follow along at tutorial 4.3.

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