Team:Genspace/Project

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<h2>What is the Open Lab?</h2>
<h2>What is the Open Lab?</h2>
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<p>Genspace has a unique opportunity to expand its impact beyond its physical presence in New York and bring hands-on involvement with synthetic biology to schools and communities around the world. The Open Lab is the key step towards this vision; it is the complete set of knowledge, tools, and resources required to successfully develop a thriving community biolab, all created following open source principles. Enthusiast communities and organizations around the world can partner with the Open Lab to fill in key gaps in knowledge, tools, or resources to launch their own community biolabs.</p>
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<p>Genspace has a unique opportunity to expand its impact beyond its physical presence in New York and bring hands-on involvement with synthetic biology to schools and communities around the world. The Open Lab is the key step towards this vision; it is the complete set of knowledge, tools, and resources required to successfully develop a thriving community biolab, all created following open source principles. Enthusiast communities and organizations around the world can use the Open Lab to fill in key gaps in knowledge, tools, or resources to launch their own community biolabs.</p>
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<h2>What is currently being developed for the Open Lab?</h2>
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<p>Genspace is currently focusing on two essentials projects that will form the core of the knowledge and tool components for the Open Lab.</p>
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<p><strong>1. Open Lab Blueprint</strong> – visit <a alt="Open Lab Blueprint" href="http://www.OpenLab-Blueprint.org" target="_blank">OpenLab-Blueprint.org</a> to view.
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<p class="textcenter"><strong>Open Lab Blueprint Screenshot</strong><br /><a href="https://static.igem.org/mediawiki/2014/6/6b/Main-page.jpg" target="_blank"><img src="https://static.igem.org/mediawiki/2014/2/2e/Project-overview.jpg" alt="Project Overview" class="aligncenter" /></a></p>
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<p>The Open Lab Blueprint is an easy-to-follow guide to launch and develop a sustainable community biolab. The website is a work in progress and is hosting at <a alt="Open Lab Blueprint" href="http://www.OpenLab-Blueprint.org" target="_blank">OpenLab-Blueprint.org</a>. This Blueprint is a holistic view of the community biolab and includes the following components:</p>
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<ul>
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<li>Starting up a lab, including identifying the right space, acquisition of key equipment, and efficiently implementing safety standards and best practices.</li>
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<li>Developing a community, including building awareness, developing programs of engagement for students, the amateur scientists, and the general public, and collaborating with the broader scientific and educational communities.</li>
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<li>Creating unique content, including educational resources, using the Genspace curriculum and engaging activities, focused on tailored, site-specific explorations and experiments.</li>
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<li>Operating a biolab, including a resource base of protocols for standard genetic engineering activities, geared towards a budget-constrained lab, operational best-practices ranging from procurement of reagents to proper storage of experiments, and financial sustainability models.</li>
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<a href="https://static.igem.org/mediawiki/2014/7/78/Project-overview-2-lg.jpg" target="_blank"><img src="https://static.igem.org/mediawiki/2014/2/2e/Project-overview-2.jpg" alt="Project Overview 2" class="aligncenter" /></a>
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<p> <a href="https://2014.igem.org/Team:Genspace/Pilot/FamiLAB">Pilot</a>
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<p><strong>2. Open Plasmid</strong> - The Open Plasmid is a key tool for the community biolab. Genspace has partnered with Cathal Garvey, founder of Indie Biotech, to design an open source and IP-free plasmid for the community biolab. The Open Plasmid is a core platform on which many experiments in a community biolab can be built on, essentially the equivalent of an Arduino for the citizen science community. The plasmid is designed to be easily modifiable, and therefore approachable to everyone from weekend researcher to curious high school student. The plasmid is also designed to be easy to cultivate with minimal resources. Unlike most plasmids, it does not need to be grown with antibiotics, significantly increasing accessibility to budget-constrained organizations, and having less negative environmental impact.</p>
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<p>As a first step, we have cloned the IP-free fluorescent protein genes. These are meant to be used together with the Open Plasmid. Each gene codes for a differently fluorescent protein: cyan, green, and red. These sequences can be used as teaching tools for classes or workshops or as molecular tools by independent researchers who are part of the community.</p>
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<p><strong>3. BioGlyphics</strong> - BioGlyphics is a platform for creating visual lab protocols. It is designed so people can create a lab protocol using a simple drag and drop web app. BioGlyphics is still in an early development phase. But, the final version of the app will automatically generate code for lab automation software for each visual lab protocol. We also envision building a online community that will allow biomakers, teachers, and community labs to share and comment on each protocol - a sort of github/thingiverse for lab protocols.</p>
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<iframe src="//www.slideshare.net/slideshow/embed_code/40335249" width="700" height="500" frameborder="0" marginwidth="0" marginheight="0" scrolling="no" style="border:1px solid #CCC; border-width:1px; margin-bottom:5px; max-width: 100%;" allowfullscreen> </iframe> <div style="margin-bottom:5px"> <strong> <a href="https://www.slideshare.net/efern211/bioglyphics-a-2014-genspace-igem-team-project" title="BIOGLYPHICS: A 2014 GENSPACE IGEM TEAM PROJECT" target="_blank">BIOGLYPHICS: A 2014 GENSPACE IGEM TEAM PROJECT</a> </strong> from <strong><a href="http://www.slideshare.net/efern211" target="_blank">Eric Fernandez</a></strong> </div>
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<iframe src="//player.vimeo.com/video/109102631" width="500" height="281" frameborder="0" webkitallowfullscreen mozallowfullscreen allowfullscreen></iframe> <p><a href="http://vimeo.com/109102631">BioGlyphics visual lab protocols. This video shows an early prototype of the protocol creation web app.</a> from <a href="http://vimeo.com/user33388903">Eric Fernandez</a> on <a href="https://vimeo.com">Vimeo</a>.</p>
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<p> <b>The idea for BioGlyphics was born out of a beginner's frustration with your standard text based lab protocols.</b></>
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<a href="http://imgur.com/QlV0YDO"><img src="http://i.imgur.com/QlV0YDO.png" title="source: imgur.com" /></a>
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<p><b>We saw 4 main problems with text protocols.</b></p>
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<p> <b>1. Poor Consistency</b>
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Each person writing a protocol phrases things a bit differently and focuses on different content. For a beginner in the lab this can be confusing.
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“Spin down” vs. “Centrifuge” </p>
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<p> <b>2. Poor Visualization</b>
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It can be hard for a beginner in a lab to connect the text of a protocol with clear actions they need to perform. </p>
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<p> <b>3. Low Efficiency</b>
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Writing text protocols is not very time efficient. You need to spend time deciding word choice and what level of detail to cover. </p>
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<p> <b>4. Machine Illegible</b>
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Because the text of protocols is not consistent in language or formatting, computer programs that run lab automation software are not able to use it.
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</p>
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<p> We started wishing that we had something new. Something more visual and easy to quickly grasp. What if instead of inconsistent confusing text we had something for lab protocols that more resembled IKEA instructions? </p>
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<a href="http://imgur.com/HAi1tmd"><img src="http://i.imgur.com/HAi1tmd.png" title="source: imgur.com" /></a>
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<p> Our next step was to get the community involved. On 7/7/14 we hosted a public event - The BioGlyphics Iconathon. We brought together
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graphic designers and artists from all over the NYC metro area and invited them to design BioGlyphics at a event hosted in a Brooklyn community work space.</p>
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<a href="http://imgur.com/QL5fIaD"><img src="http://i.imgur.com/QL5fIaD.png" title="source: imgur.com" /></a>
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<p> We then created an early prototype of what a BioGlyphics protocol would look like. We created the complete IGEM transformation protocol in BioGlyphics.</p>
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<a href="http://imgur.com/pKgpOBo"><img src="http://i.imgur.com/pKgpOBo.png" title="source: imgur.com" /></a>
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<p><b>We really liked the result for the following reasons:</b></p>
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<p><b>1. 100% consistent.</b>
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Each protocol follows the same logical format. </p>
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<p><b> 2. Easy to understand and visualize. </b> 
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Materials and Procedures are visually defined just like IKEA instructions. </p>
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<p> <b> 3. Fast & easy to create. </b>
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Simple drag and drop web/android/iOS app interface. </p>
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<p><b>4. Will be 100% machine readable for lab automation software. </b>
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Making a protocol in this format will automatically build machine code behind the scenes. </p>
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<p><b>Where are we now? BioGlyphics in currently in the first stage of a 3 step process of development.</b></p>
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<p><b>Stage 1.</b> Proof of concept and basic early prototype. Initial development of Bioglyphic icons and exploration into lab automation programming. (We are here.) </p>
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<p><b>Stage 2.</b> Raise funding and find dedicated volunteers for the full development of the web application and online community. 2015-2016. </p>
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<p><b>Stage 3.</b> Spread BioGlyphics to other community labs, teachers, and bio makers across the country. Late 2016. </p>
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<a href="http://imgur.com/yqH7MFy"><img src="http://i.imgur.com/yqH7MFy.png" title="source: imgur.com" /></a>
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<li><a href="https://2014.igem.org/Team:Genspace/Project/Open-Lab-Blueprint">Open Lab Blueprint</a></li>
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<li><a href="https://2014.igem.org/Team:Genspace/Project/Opentrons-Robot">OpenTrons Robot</a></li>
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<li><a href="https://2014.igem.org/Team:Genspace/Project/IP-Free Genes">IP-Free Genes</a></li>
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<li><a href="https://2014.igem.org/Team:Genspace/Project/Bioglyphics">BioGlyphics</a></li>
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Latest revision as of 02:32, 18 October 2014

Project

What is the Open Lab?

Genspace has a unique opportunity to expand its impact beyond its physical presence in New York and bring hands-on involvement with synthetic biology to schools and communities around the world. The Open Lab is the key step towards this vision; it is the complete set of knowledge, tools, and resources required to successfully develop a thriving community biolab, all created following open source principles. Enthusiast communities and organizations around the world can use the Open Lab to fill in key gaps in knowledge, tools, or resources to launch their own community biolabs.

  1. Open Lab Blueprint
  2. OpenTrons Robot
  3. IP-Free Genes
  4. BioGlyphics

Retrieved from "http://2014.igem.org/Team:Genspace/Project"