Difference between revisions of "Team:Northeastern Boston/notebook"

 
(72 intermediate revisions by 2 users not shown)
Line 7: Line 7:
 
<div class='wrapper'>
 
<div class='wrapper'>
 
  <div id='sidebar'>
 
  <div id='sidebar'>
−
    <div id='bar_title' class='title'>
+
    <div id='bar_title' class='title'><a href="https://2015.igem.org/Team:Northeastern_Boston">
−
      Menu
+
      Northeastern</a>
 
    </div>
 
    </div>
 
    <ul class='nav'>
 
    <ul class='nav'>
 
      <li>
 
      <li>
−
        <a>Home</a>
+
        <a id='a-home' href="https://2015.igem.org/Team:Northeastern_Boston">Home</a>
 
      </li>
 
      </li>
 
      <li>
 
      <li>
−
        <a href="https://2015.igem.org/Team:Northeastern_Boston/team">Team</a>
+
      <a id='a-team' href="https://2015.igem.org/Team:Northeastern_Boston/Attributions">Team</a>
 
      </li>
 
      </li>
 
      <li>
 
      <li>
−
        <a>Project</a>
+
        <a id='a-project' href="https://2015.igem.org/Team:Northeastern_Boston/Description">Project</a>
 
      </li>
 
      </li>
 +
      <div class='sub-nav__container'>
 +
      <li id='a-parts' class='sub-nav__parent'>
 +
        <a>
 +
        Parts
 +
        <div class='nav-container__arrow'></div>
 +
        </a>
 +
      </li>
 +
      <div class='sub-nav__children hidden'>
 +
      <li class='sub-nav__child'>
 +
        <a href="https://2015.igem.org/Team:Northeastern_Boston/BasicParts">Basic & Composite</a>
 +
      </li>
 +
      <li class='sub-nav__child'>
 +
        <a href="https://2015.igem.org/Team:Northeastern_Boston/Design">Expression Plasmid</a>
 +
      </li>
 +
      </div>
 +
    </div>
 +
      <div class='sub-nav__container'>
 +
      <li id='a-notebook' class='sub-nav__parent'>
 +
        <a>
 +
        Notebook
 +
        <div class='nav-container__arrow flip-vertical'></div>
 +
        </a>
 +
      </li>
 +
      <div class='sub-nav__children'>
 +
      <li class='sub-nav__child'>
 +
        <a class='active'>Protocols</a>
 +
      </li>
 +
      <li class='sub-nav__child'>
 +
        <a href="https://2015.igem.org/Team:Northeastern_Boston/Workflow">Workflow</a>
 +
      </li>
 +
      </div>
 +
    </div>
 +
            <div class='sub-nav__container'>
 +
      <li id='a-humanpractices' class='sub-nav__parent'>
 +
        <a>
 +
        Human Practices
 +
        <div class='nav-container__arrow'></div>
 +
        </a>
 +
      </li>
 +
      <div class='sub-nav__children hidden'>
 +
      <li class='sub-nav__child'>
 +
        <a href="https://2015.igem.org/Team:Northeastern_Boston/Collaborations">Collaborations</a>
 +
      </li>
 +
      <li class='sub-nav__child'>
 +
        <a href="https://2015.igem.org/Team:Northeastern_Boston/Practices">Outreach</a>
 +
      </li>
 +
      <li class='sub-nav__child'>
 +
        <a href="https://2015.igem.org/Team:Northeastern_Boston/Written_Investigation">Written Investigation</a>
 +
      </li>
 +
      </div>
 +
    </div>
 
      <li>
 
      <li>
−
        <a>Parts</a>
+
      <a id="a-safety" href="https://2015.igem.org/Team:Northeastern_Boston/safety">Safety</a>
 
      </li>
 
      </li>
 +
     
 
      <li>
 
      <li>
−
        <a class='active' href="https://2015.igem.org/Team:Northeastern_Boston/notebook">Notebook</a>
+
      <a id="a-measurement" href="https://2015.igem.org/Team:Northeastern_Boston/measurement">Interlab</a>
−
      </li>
+
−
      <li>
+
−
        <a>Attributions</a>
+
−
      </li>
+
−
      <li>
+
−
        <a>Collaborations</a>
+
−
      </li>
+
−
      <li>
+
−
        <a>Human Practices</a>
+
−
      </li>
+
−
      <li>
+
−
      <a>Safety</a>
+
−
      </li>
+
−
      <li>
+
−
      <a>Modeling</a>
+
−
      </li>
+
−
      <li>
+
−
      <a href="https://2015.igem.org/Team:Northeastern_Boston/measurement">Measurement</a>
+
−
      </li>
+
−
      <li>
+
−
      <a>Software</a>
+
 
      </li>
 
      </li>
 +
     
 
    </ul>
 
    </ul>
 
  </div>
 
  </div>
 
  <div class='content'>
 
  <div class='content'>
−
  <div id="project_description" class='article'>
+
  <div id='page-header__protocols' class='page-header'>
 +
  <h1 class="page-header__title" align="left" style="border-width:0">PROTOCOLS</h1>
 +
  </div>
 +
  <div class="Notebook">
  
−
    <h1 id="project_header">Notebook</h1>
+
     
  
−
    <div class='tab-container tab-hide'>
+
 
 +
<h2>DNA</h2>
 +
 
 +
<div class='tab-container tab-hide'>
 
<span class='tab-container__title'>HiFi DNA Assembly</span>
 
<span class='tab-container__title'>HiFi DNA Assembly</span>
 
<div class='tab-container__arrow down-arrow'></div>
 
<div class='tab-container__arrow down-arrow'></div>
−
<iframe seamless src="https://www.protocols.io/widgets/protocol/HiFi-DNA-Assembly-NEB-dn85hv" style="width: 850px; height: 1100px; border: 1px solid transparent;"></iframe>
+
<iframe src="https://www.protocols.io/widgets/protocol/HiFi-DNA-Assembly-NEB-dn85hv" style="width: 850px; height: 1100px; border: 1px solid transparent;"></iframe>
 
</div>
 
</div>
 +
 
<div class='tab-container tab-hide'>
 
<div class='tab-container tab-hide'>
−
<span class='tab-container__title'>HiFi DNA Assembly</span>
+
<span class='tab-container__title'>Plasmid Miniprep</span>
 +
<div class='tab-container__arrow down-arrow'></div>
 +
<iframe seamless src="https://www.protocols.io/widgets/protocol/Plasmid-Miniprep-dp95r5" style="width: 850px; height: 1100px; border: 1px solid transparent;"></iframe>
 +
</div>
  
 +
<div class='tab-container tab-hide'>
 +
<span class='tab-container__title'>Gel Electrophoresis</span>
 +
<div class='tab-container__arrow down-arrow'></div>
 +
<iframe seamless src="https://www.protocols.io/widgets/protocol/Gel-Electrophoresis-dqa5sd" style="width: 850px; height: 1100px; border: 1px solid transparent;"></iframe>
 +
</div>
 +
 +
<div class='tab-container tab-hide'>
 +
<span class='tab-container__title'>PCR with Phusion</span>
 +
<div class='tab-container__arrow down-arrow'></div>
 +
<iframe seamless src="https://www.protocols.io/widgets/protocol/PCR-with-Phusion-dqb5sm" style="width: 850px; height: 1100px; border: 1px solid transparent;"></iframe>
 +
</div>
 +
 +
<div class='tab-container tab-hide'>
 +
<span class='tab-container__title'>Gel DNA Recovery</span>
 +
<div class='tab-container__arrow down-arrow'></div>
 +
<iframe seamless src="https://www.protocols.io/widgets/protocol/Gel-DNA-Recovery-dqc5sv" style="width: 850px; height: 1100px; border: 1px solid transparent;"></iframe>
 +
</div>
 +
 +
<div class='tab-container tab-hide'>
 +
<span class='tab-container__title'>T4 Ligation</span>
 +
<div class='tab-container__arrow down-arrow'></div>
 +
<iframe seamless src="https://www.protocols.io/widgets/protocol/Ligation-of-Sticky-Ends-with-T4-dqd5s5" style="width: 850px; height: 1100px; border: 1px solid transparent;"></iframe>
 +
</div>
 +
 +
<div class='tab-container tab-hide'>
 +
<span class='tab-container__title'>Restriction Digest</span>
 
<div class='tab-container__arrow down-arrow'></div>
 
<div class='tab-container__arrow down-arrow'></div>
−
<iframe src="https://www.protocols.io/widgets/protocol/LB-Agar-Plates-dp85rv" style="width: 850px; height: 1100px; border: 1px solid transparent;"></iframe>
+
<iframe seamless src="https://www.protocols.io/widgets/protocol/Restriction-Digest-of-DNA-dqf5tm" style="width: 850px; height: 1100px; border: 1px solid transparent;"></iframe>
 
</div>
 
</div>
  
 +
<h2><i>Escherichia coli</i></h2>
 +
 +
<div class='tab-container tab-hide'>
 +
<span class='tab-container__title'>LB Agar Plates</span>
 +
<div class='tab-container__arrow down-arrow'></div>
 +
<iframe src="https://www.protocols.io/widgets/protocol/LB-Agar-Plates-dp85rv" style="width: 850px; height: 1100px; border: 1px solid transparent;"></iframe>
 +
</div>
 +
 +
<div class='tab-container tab-hide'>
 +
<span class='tab-container__title'>E. coli Heat Shock</span>
 +
<div class='tab-container__arrow down-arrow'></div>
 +
<iframe seamless src="https://www.protocols.io/widgets/protocol/Transformation-of-E-coli-with-Heat-Shock-dqe5td" style="width: 850px; height: 1100px; border: 1px solid transparent;"></iframe>
 +
</div>
 +
 +
 +
<h2><i>Chlamydomonas reinhardtii</i></h2>
 +
 +
<div class='tab-container tab-hide'>
 +
<span class='tab-container__title'>TAP Agar Plates</span>
 +
<div class='tab-container__arrow down-arrow'></div>
 +
<iframe seamless src="https://www.protocols.io/widgets/protocol/TAP-Agar-Plates-dtq6mv" style="width: 850px; height: 1100px; border: 1px solid transparent;"></iframe>
 +
</div>
 +
   
 +
<div class='tab-container tab-hide'>
 +
<span class='tab-container__title'>Glass Bead Transformation</span>
 +
<div class='tab-container__arrow down-arrow'></div>
 +
<iframe seamless src="https://www.protocols.io/widgets/protocol/Glass-Bead-Transformation-of-Chlamydomonas-dtn6md" style="width: 850px; height: 1100px; border: 1px solid transparent;"></iframe>
 +
</div>
 +
<p> </p>
 +
<p> </p>
 +
<div class="minimal-dropdown__container">
 +
      <div class="minimal-dropdown__header">
 +
      <h2 class="minimal-dropdown__title">Protocols.io</h2>
 +
      <a class='minimal-dropdown__arrow'></a>
 +
      </div>
 +
      <div class="minimal-dropdown__content hidden">
 +
 +
<p>Northeastern 2015 has decided to use <a href="https://www.protocols.io/" target="_blank">Protocols.io</a>to host all of its iGEM protocols. Protocols.io is an online open source wet lab protocol repository. Researchers can upload their experimental protocol, share it others, build in functionality (like timers), and "fork" other researchers' protocols (adapting them for their particular situation).</p>
 +
 +
<p>We think this is worth breaking the <a href="https://2015.igem.org/Wiki_Requirements" target="_blank">"No iFrames"</a> rule. The benefit of teams being able to create an easily referenced and modifiable protocol, outweigh the potential "cheating" from iGEM teams altering the externally hosted content (in part because altering lab protocols is relatively benign). Other teams could, with the Protocols.io app, exactly replicate the protocol that we followed, for example, when we transformed <a href="https://www.protocols.io/view/Glass-Bead-Transformation-of-Chlamydomonas-dtn6md" target="_blank"><i>C. reinhardtii.</i></a></p>
 +
 +
<p>Reproducibility is the existential crisis that plagues science; when results in one lab are completely unrepeatable elsewhere, the value of science plummets. Protocols.io could be one potential solution. We enjoyed using it, forking protocols, and making our own. We encourage other teams to try it as well. Protocols don't need to be hidden in transgenerational, witchcraft-ready tomes, or lab-protected Dropboxes. Instead, these methods should be as easy to access as possible.</p>
 +
      </div>
 +
      </div>
 
    </div>
 
    </div>
 
  </div>
 
  </div>

Latest revision as of 22:30, 18 September 2015

PROTOCOLS

DNA

HiFi DNA Assembly
Plasmid Miniprep
Gel Electrophoresis
PCR with Phusion
Gel DNA Recovery
T4 Ligation
Restriction Digest

Escherichia coli

LB Agar Plates
E. coli Heat Shock

Chlamydomonas reinhardtii

TAP Agar Plates
Glass Bead Transformation

Protocols.io