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| - | <title>BostonU iGEM Team: Welcome</title> | + | <h1>Puppeteer Notebook</h1> |
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| - | </head>
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| - | <body class="basiclayout">
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| - | <div id="bu-wellesley_wiki_content">
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| - | <div id="igemlogo">
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| - | <a href="https://2013.igem.org/Main_Page"><img src="https://static.igem.org/mediawiki/2012/1/13/Igemwhite_back.png" alt="iGEM 2012 main page" style="position: absolute; top: 10px; left: 10px;"width="90"></a>
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| - | </div>
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| - | <p style="text-align:center;"><a href="https://2013.igem.org/Team:BostonU"><img src="https://static.igem.org/mediawiki/2013/2/2c/Marsh.png" width="800px" length="200px"></a></p>
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| - | <ul id="nav">
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| - | <li><a href="#">Our Team</a>
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| - | <ul>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/Team">Team</a></li>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/Social">Summer Fun</a></li>
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| - | </ul>
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| - | </li>
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| - | <li><a href="#">Project</a>
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| - | <ul>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/Project_Overview">Project Overview and Abstract</a></li>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/MoCloChara">Introduction to MoClo and Characterization</a></li>
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| - | <ul>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/QS">Quorum Sensing</a></li>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/HK">Histidine Kinase</a></li>
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| - | </ul>
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| - | </li>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/DataSheet">Data Sheet App</a></li>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/Methodology ">Methodology Overview</a></li>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/Results ">Results Summary</a></li>
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| - | </ul>
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| - | </li>
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| - | <li><a href="#">Achievements</a>
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| - | <ul>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/Data">Data Collected</a></li>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/Parts">Parts Submitted</a></li>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/MoClo">MoClo Kit</a></li>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/Gold">Medal Fulfillment</a></li>
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| - | </ul>
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| - | </li>
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| - | <li><a href="#">Notebook</a>
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| - | <ul>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/Protocols">Protocols</a></li>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/NotebookML">Characterization Notebook</a></li>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/NotebookQS">Quorum Sensing Notebook</a></li>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/NotebookHK">Histidine Kinase Notebook</a></li>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/Clotho">Clotho Notebook</a></li>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/PUP">Puppeteer Notebook</a></li>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/TroubleShooting">Troubleshooting</a></li>
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| - | </ul>
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| - | </li>
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| - | <li><a href="#">Considerations</a>
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| - | <ul>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/NEGEM">New England iGEM Regional Meeting</a></li>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/Human Practices">Human Practices</a></li>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/Safety">Safety</a></li>
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| - | </ul>
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| - | <li><a href="#">Acknowledgements</a>
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| - | <ul>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/Collaborations">Collaborations</a></li>
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| - | <li><a href="https://2013.igem.org/Team:BostonU/Acknowledgements">Acknowledgements</a></li>
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| - | </ul>
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| - | </li>
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| - | </head>
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| - | <br><br>
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| - | <b>June 5, 2013</b><br>
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| - | Design to Direction<br>
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| - | compare contrast doing things via puppeteer vs. human (~100-200 parts in two weeks?)
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| - | <br> hope to reduce error and
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| - | <br> could use tecan to switch out backbone.
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| - | <br>maybe create basic moclo XFP transcription units
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| - | <br>Robot does:
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| - | <br>Moclo rxn
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| - | <br>Transformation
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| - | <br>Ligation
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| - | <br>Restriction Digest
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| - | <br>resource tracking, when to replace
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| - | <br><br>
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| - | Come up with hypothesis of human vs. machine
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| - | <br> Efficiency of Robot? Puppeteer speed up planning for robot? Error of human and reaction failure?
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| - | <br>For human error - have a partner checking for errors
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| - | <br><br>
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| - | Human errors
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| - | <br>- setting plates up wrong(have partners)
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| - | <br>- make sure dilutions are right (excel errors? have partners do excel together)
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| - | <br>- just always have partners.
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| - | <br>- don’t rush
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| - | <br><br>
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| - | Protocols must be adapted to go with puppeteer/robot. Testing to optimize.
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| - | <br>Aiming to test by making ten devices in duplicate
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| - | <br><br>
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| - | <i>Target for Tuesday June 11</i>
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| - | <br>figure out steps of protocol for robot in excel sheet with exact buffer/enz/etc.
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| - | <br>10 devices
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| - | <br>
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| - | ADD WHITEBOARD PICTURE FROM DROPBOX FOLDER
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| - | <br><br><br>
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| - | <b>June 11, 2013</b>
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| - | <br>See picture for parts that need to be made * 4
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| - | <br>dilute to 25 fmol
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| - | <br>
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| - | <br>Janoo sent working csv files for Raven
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| - | <br><br>
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| - | ADD WHITEBOARD PICTURE FROM DROPBOX FOLDER
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| - | <br><br><br>
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| - | <b>June 18, 2013</b>
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| - | <br>download arcs file from Raven.
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| - | <br>Arcs = raven to puppeteer
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| - | <br>upload arc file into puppeteer
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| - | <br>In puppeteer, select arc file, and personnel involved.
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| - | <br>→ then assembly graph and protocol graph generated
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| - | <br>*went over process in the assembly graph.
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| - | <br>
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| - | <br><i>next step: know details of the protocols themselves</i>
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| - | <br>require the specific instruction of the protocol. more detailed than excel sheets and how to allocate resources. <br>how much and what resources are needed to go from 1 rxn to 10 rxn etc
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| - | <br><br>
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| - | Want higher level details--> pick up this tube, etc
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| - | <br><br>
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| - | labels are 8 letter labels. generated in raven/puppeteer that needs to be written on the container. (randomly generated), doesn’t tell us about the contents of the sample
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| - | <br><br>
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| - | Showed current naming protocol for L1
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| - | <br>*brain storming about labeling*
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| - | <br>maybe send out a survey to wetlab about labeling
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