Difference between revisions of "Team:BostonU HW/Notebook"

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{{BostonU_HW}}
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<head>
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<meta charset="utf-8" />
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<link rel="apple-touch-icon" sizes="76x76" href="assets/img/apple-icon.png">
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<link rel="icon" type="image/png" href="assets/img/favicon.png">
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<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1" />
  
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<title>Attributions</title>
  
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<div class="column full_size">
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<meta content='width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=0' name='viewport' />
  
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<h1>Notebook</h1>
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<!-- EXTRA STYLING -->
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<p> Document the dates you worked on your project. This should be a detailed account of the work done each day for your project.</p>
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<style>
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#Title{
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color: red;
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}
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#page_background{
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background-image: url("https://static.igem.org/mediawiki/2017/0/04/MARS_General_Background.png");
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}
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#BACKGROUND{
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width: 100%;
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position: absolute;
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}
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#MARS{
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width: 15%;
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position: absolute;
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margin-top: 8%;
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margin-left: 5%;
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}
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#TITLE{
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position: absolute;
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width: 40%;
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margin-left: 22%;
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margin-top: 11%;
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}
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.main{
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margin-top: 2%;
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#Header_Pic{
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height: 60%;
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#Paragraph{
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text-align: center;
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}
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</style>
  
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</head>
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<div class="clear"></div>
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<!-- *************THIS IS WHERE PAGE STARTS************* -->
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<body>
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<div class="landing-page">
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<div class="wrapper" id="page_background">
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<div class="header" id="Header_Pic">
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<img src="https://static.igem.org/mediawiki/2017/0/02/MARSbackground.png" id="BACKGROUND">
 +
<img src="https://static.igem.org/mediawiki/2017/2/22/MARSLogo2.png" id="MARS">
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<img src="https://static.igem.org/mediawiki/2017/5/50/MARS_Timeline.png" id="TITLE">
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</div>
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<div class="main main-raised" id="uF_101">
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<div class="container">
 +
<div class="text" style="margin-bottom:3%;">
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<h1><u>May</u></h1>
 +
<ul>
 +
<li>The BU Wetlab and Hardware iGEM teams participated in joint Wetlab safety and protocol training</li>
 +
<li>The team performed an initial literature review in order to learn more about the types of microfluidic devices being design</li>
 +
<li>
 +
The team was given a software overview/explanation of the three CIDAR lab microfluidic design tools: 3Duf, Fluigi, and Neptune
 +
</li>
 +
<li>The team was given an overview/explanation of the CIDAR lab microfluidic design manufacturing process: Makerfluidics</li>
 +
</ul>
 +
</div>
 +
</div>
 +
</div>
  
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<div class="column half_size">
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<div class="main main-raised" style="margin-top:5%" id="uF_101">
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<h5>What should this page have?</h5>
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<div class="container">
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<ul>
+
<div class="text" style="margin-bottom:3%;">
−
<li>Chronological notes of what your team is doing.</li>
+
<h1>June</h1>
−
<li> Brief descriptions of daily important events.</li>
+
<ul>
−
<li>Pictures of your progress. </li>
+
<li>From the  literature review, each member chose one chip of interest to replicate and test</li>
−
<li>Mention who participated in what task.</li>
+
<ol>
−
</ul>
+
<li>LAMP Chip
 +
<ul>
 +
<li>3 iterations designed in Fluigi</li>
 +
<li>5 iterations designed in 3Duf and tested</li>
 +
</ul>
 +
</li>
 +
<li>Multiplex Drug Testing Chip</li>
 +
<ul>
 +
<li>2 iterations designed in 3Duf and tested</li>
 +
<li>1 iteration designed in Fluigi</li>
 +
</ul>
 +
<li>Magnetic Mixer Chip</li>
 +
<ul>
 +
<li></li>
 +
<li></li>
 +
</ul>
 +
</ol>
 +
<li>BU Wetlab iGEM Team Collaboration began</li>
 +
<ul>
 +
<li>At the initial meeting BU Weltab provided BU Hardware with a protocol they thought could be performed in a microfluidic device</li>
 +
<li>6 potential chips designed for Wetlab collaboration</li>
 +
</ul>
 +
<li>Submitted Microfluidics iGEM Poll to the iGEM collaborations page</li>
 +
<li>Volume Dispensing Chips
 +
<ul>
 +
<li>3 iterations desgined in 3Duf and tested</li>
 +
</ul>
 +
</li>
 +
<li>Alternative Tree Primitive Designs
 +
<ul>
 +
<li>
 +
Given repeat difficulties faced while using trees in designs, alternative designs were tested to determine if there was a better design
 +
</li>
 +
<li>3 iterations designed in 3Duf and tested</li>
 +
</ul>
 +
</li>
 +
<li>Transformation Chip
 +
<ul>
 +
<li>6 Iterations designed in Fluigi</li>
 +
<li>2 Iterations designed in 3Duf and tested</li>
 +
</ul>
 +
</li>
 +
<li>Magnetic Mixer Chip
 +
<ul>
 +
<li>5 Iterations milled and tested</li>
 +
<li>Magnetic particles introduced into chip</li>
 +
<li>Experimented with different protocols</li>
 +
</ul>
 +
</li>
 +
<li>Cell Sorting
 +
<ul>
 +
<li>1 iteration milled and tested </li>
 +
<li>Magnetic particles run through chip</li>
 +
</ul>
 +
</li>
 +
<li>Attended Northeastern iGEM practice conference (NEGEM) at BU
 +
<ul>
 +
<li>Received feedback on iGEM narrative</li>
 +
<li>Developed project ideas based off of feedback</li>
 +
</ul>
 +
</li>
 +
<li>MARS Repository begins to form after talking with researchers from CILSE’s Biological Design Center </li>
 +
</ul>
 +
</div>
 +
</div>
 +
</div>
  
−
</div>
+
<div class="main main-raised" style="margin-top:5%" id ="Chip_Repo">
 +
<div class="container">
 +
<h1>July</h1>
 +
<div class="text" style="margin-bottom:3%;">
 +
<ul>
 +
<li>Alternative Tree Primitive Designs
 +
<ul>
 +
<li>1 iteration designed in 3Duf and tested</li>
 +
<li>1This design was markedly better at dispensing liquid equally, therefore it was used in later designs</li>
 +
</ul>
 +
</li>
 +
<li>Cell Lysis Chip
 +
<ul>
 +
<li>3 iterations designed in 3Duf and tested</li>
 +
<li>Changes made to fix issues with fluid input and mixing </li>
 +
<li>Initial draft of protocol written</li>
 +
</ul>
 +
</li>
 +
<li>Wetlab Collaboration Chip
 +
<ul>
 +
<li>4 iterations milled</li>
 +
<li>Sealing issues improved upon</li>
 +
<li>Testing done with shared liquid input</li>
 +
</ul>
 +
</li>
 +
<li>DNA Digestion Chip
 +
<ul>
 +
<li>4 iterations milled </li>
 +
<li>Iterations made to better replicate protocol on a chip </li>
 +
<li>Pipetting chamber designed and optimized for chip</li>
 +
</ul>
 +
</li>
 +
<li>BU Hardware visits BosLab during monthly showcase
 +
<ul>
 +
<li>Provided insight into what small scale biohacker space is like, and what synthetic biology community is looking for in microfluidics</li>
 +
</ul>
 +
</li>
 +
<li>Fluid Functionality begins to be developed
 +
<ul>
 +
<li>Idea of primitive level analysis developed along with some qualitative failures</li>
 +
</ul>
 +
</li>
 +
<li>Worked with Neptune (2016 BU Hardware Team) automated syringe pumps tried to increase accuracy and improve function</li>
 +
<li>MARS Repository chips began to be placed in subsections of isolation, modification, and quantification</li>
 +
<li>Transformation Chip
 +
<ul>
 +
<li>2 iterations designed in Fluigi</li>
 +
<li>8 iterations designed in 3Duf and tested</li>
 +
<li>Changes made to overall design as well as valve sizes</li>
 +
</ul>
 +
</li>
 +
<li>Summer Pathways
 +
<ul>
 +
<li>Participated in Summer Pathways alongside the BU Wetlab Team</li>
 +
<li>Created an interactive microfluidics design activity for the attending high school students</li>
 +
<li>Engaged with students to design microfluidic devices based on synbio protocols </li>
 +
</ul>
 +
</li>
 +
<li>Harvard iGEM Team Collaboration
 +
<ul>
 +
<li>Initial meetings to discuss plans </li>
 +
</ul>
 +
</li>
 +
<li>WPI iGEM Team Collaboration
 +
<ul>
 +
<li>During the initial Skype call we discussed the nature of their lead assay and how it might be moved onto a microfluidic</li>
 +
<li>Their team visited our lab and performed verified their assay’s functionality on the BU spectrometer</li>
 +
</ul>
 +
</li>
 +
<li>Tutorial Videos
 +
<ul>
 +
<li>PDMS video filmed</li>
 +
</ul>
 +
</li>
 +
<li>Peristaltic Pump Chip
 +
<ul>
 +
<li>Design inspired by another paper with different geometries</li>
 +
<li>4 iterations designed in 3Duf and tested</li>
 +
</ul>
 +
</li>
 +
<li>Metering Primitive
 +
<ul>
 +
<li>In order to allow for accurate volume dispension on a microfluidic device, a metering primitive inspired by the peristaltic pump was designed</li>
 +
<li>2 iterations designed in 3Duf and tested</li>
 +
</ul>
 +
</li>
 +
</ul>
 +
</div>
 +
</div>
  
−
<div class="column half_size">
+
</div>
−
<h5>Inspiration</h5>
+
−
<p>You can see what others teams have done to organize their notes:</p>
+
  
−
<ul>  
+
<div class="main main-raised" style="margin-top:5%" id="FF">
−
<li><a href="https://2014.igem.org/Team:ATOMS-Turkiye/Notebook">2014 ATOMS-Turkiye</a></li>
+
<div class="container">
−
<li><a href="https://2014.igem.org/Team:Tec-Monterrey/ITESM14_project.html#tab_notebook">2014 Tec Monterrey</a></li>
+
<h1>August</h1>
−
<li><a href="https://2014.igem.org/Team:Kyoto/Notebook/Magnetosome_Formation#title">2014 Kyoto</a></li>
+
<div class="text" style="margin-bottom:3%;">
−
<li><a href="https://2014.igem.org/Team:Cornell/notebook">2014 Cornell</a></li>
+
<ul>
−
</ul>
+
<li>Transformation Chip
 +
<ul>
 +
<li>13 iterations designed in 3Duf and tested</li>
 +
<li>Different valve dimensions tested</li>
 +
</ul>
 +
</li>
 +
<li>Ligation Chip
 +
<ul>
 +
<li>2 iterations designed in 3Duf</li>
 +
</ul>
 +
</li>
 +
<li>Tutorial Videos
 +
<ul>
 +
<li>PDMS Video finalized</li>
 +
<li>Milling Video recording and scripting completed</li>
 +
</ul>
 +
</li>
 +
<li>DNA Digestion
 +
<ul>
 +
<li>2 iterations milled and tested</li>
 +
</ul>
 +
</li>
 +
<li>Wetlab Collaboration Chip
 +
<ul>
 +
<li>1 iteration milled and tested</li>
 +
</ul>
 +
</li>
 +
<li>Cell Lysis Chip
 +
<ul>
 +
<li>Design finalized </li>
 +
<li>Testing with magnetic particles in chamber</li>
 +
</ul>
 +
</li>
 +
<li>Cell Culturing
 +
<ul>
 +
<li>Initial CAD model designed and tested</li>
 +
<li>Spin coated PDMS </li>
 +
<li>Second and final CAD model designed and tested </li>
 +
</ul>
 +
</li>
 +
<li>Wiki
 +
<ul>
 +
<li>Initial pages started to be constructed </li>
 +
<li>Wiki architecture organized</li>
 +
</ul>
 +
</li>
 +
<li>Fluid Functionality
 +
<ul>
 +
<li>Quantitative tests begin to be developed</li>
 +
</ul>
 +
</li>
 +
 
 +
</ul>
 +
</div>
 +
</div>
 +
 
 +
</div>
 +
 
 +
<div class="main main-raised" id="uF_101">
 +
<div class="container">
 +
<h1>September</h1>
 +
<div class="text" style="margin-bottom:3%;">
 +
<ul>
 +
<li>Transformation Chip
 +
<ul>
 +
<li>1 iteration designed in 3Duf and tested</li>
 +
<li>Different valve dimension tested</li>
 +
</ul>
 +
</li>
 +
<li>Tutorial Videos
 +
<ul>
 +
<li>Milling video finalized</li>
 +
<li>Assembly video filmed and scripted</li>
 +
<li>Cleaning video filmed and audio recorded</li>
 +
</ul>
 +
</li>
 +
<li>Fluid Functionality
 +
<ul>
 +
<li>Channels quantitative tests finalized</li>
 +
</ul>
 +
</li>
 +
<li>Antibiotic Resistance*FOOTNOTE*
 +
<ul>
 +
<li>Initial design developed</li>
 +
</ul>
 +
</li>
 +
<li>Wetlab Collaboration Chip
 +
<ul>
 +
<li>2 Iterations milled and tested </li>
 +
<li>Protocol and design finalized </li>
 +
<li>Chip tested by Wetlab </li>
 +
</ul>
 +
</li>
 +
</ul>
 +
</div>
 +
</div>
 +
 
 +
</div>
 +
 
 +
<div class="main main-raised" id="uF_101" style="margin-bottom:3%">
 +
<div class="container">
 +
<h1>October</h1>
 +
<div class="text" style="margin-bottom:3%;">
 +
<ul>
 +
<li>Transformation Chip
 +
<ul>
 +
<li>4 iterations designed in 3Duf and tested</li>
 +
<li>Different metering scales tested</li>
 +
</ul>
 +
</li>
 +
<li>PCR Chip
 +
<ul>
 +
<li>4 iterations designed in 3Duf and tested</li>
 +
</ul>
 +
</li>
 +
<li>Cell Sorting
 +
<ul>
 +
<li>2 iterations milled and tested </li>
 +
<li>Protocol finalized and documented</li>
 +
</ul>
 +
</li>
 +
<li>Ligation Chip
 +
<ul>
 +
<li>1 iteration designed in 3Duf</li>
 +
</ul>
 +
</li>
 +
<li>Video tutorials
 +
<ul>
 +
<li>Assembly video finalized</li>
 +
<li>Cleaning video finalized</li>
 +
</ul>
 +
</li>
 +
<li>WPI iGEM Team Collaboration chip design documented finalized</li>
 +
<li>Attended Northeastern iGEM practice conference #2 (NEGEM) at MIT
 +
<ul>
 +
<li>Received feedback on iGEM presentation</li>
 +
<li>Incorpated feedback for final presentation</li>
 +
</ul>
 +
</li>
 +
<li>Fluid Functionality
 +
<ul>
 +
<li>Valve quantitative test finalized </li>
 +
<li>Mixer quantitative test finalized </li>
 +
</ul>
 +
</li>
 +
<li>Antibiotic Resistance
 +
<ul>
 +
<li>Design finalized using 3Duf</li>
 +
<li>Milled and documented</li>
 +
</ul>
 +
</li>
 +
 
 +
<li>Harvard iGEM Collaboration
 +
<ul>
 +
<li>Validated Harvard optical density sensor</li>
 +
</ul>
 +
</li>
 +
 
 +
</ul>
 +
</div>
 +
</div>
 +
 
 +
</div>
 +
 
 +
  </div>
  
 
</div>
 
</div>
 +
</body>
 +
 
</html>
 
</html>
 +
 +
{{Team:BostonU_Hardware/Javascript}}

Revision as of 21:25, 28 October 2017

BostonU_HW

Attributions

May

  • The BU Wetlab and Hardware iGEM teams participated in joint Wetlab safety and protocol training
  • The team performed an initial literature review in order to learn more about the types of microfluidic devices being design
  • The team was given a software overview/explanation of the three CIDAR lab microfluidic design tools: 3Duf, Fluigi, and Neptune
  • The team was given an overview/explanation of the CIDAR lab microfluidic design manufacturing process: Makerfluidics

June

  • From the literature review, each member chose one chip of interest to replicate and test
    1. LAMP Chip
      • 3 iterations designed in Fluigi
      • 5 iterations designed in 3Duf and tested
    2. Multiplex Drug Testing Chip
      • 2 iterations designed in 3Duf and tested
      • 1 iteration designed in Fluigi
    3. Magnetic Mixer Chip
  • BU Wetlab iGEM Team Collaboration began
    • At the initial meeting BU Weltab provided BU Hardware with a protocol they thought could be performed in a microfluidic device
    • 6 potential chips designed for Wetlab collaboration
  • Submitted Microfluidics iGEM Poll to the iGEM collaborations page
  • Volume Dispensing Chips
    • 3 iterations desgined in 3Duf and tested
  • Alternative Tree Primitive Designs
    • Given repeat difficulties faced while using trees in designs, alternative designs were tested to determine if there was a better design
    • 3 iterations designed in 3Duf and tested
  • Transformation Chip
    • 6 Iterations designed in Fluigi
    • 2 Iterations designed in 3Duf and tested
  • Magnetic Mixer Chip
    • 5 Iterations milled and tested
    • Magnetic particles introduced into chip
    • Experimented with different protocols
  • Cell Sorting
    • 1 iteration milled and tested
    • Magnetic particles run through chip
  • Attended Northeastern iGEM practice conference (NEGEM) at BU
    • Received feedback on iGEM narrative
    • Developed project ideas based off of feedback
  • MARS Repository begins to form after talking with researchers from CILSE’s Biological Design Center

July

  • Alternative Tree Primitive Designs
    • 1 iteration designed in 3Duf and tested
    • 1This design was markedly better at dispensing liquid equally, therefore it was used in later designs
  • Cell Lysis Chip
    • 3 iterations designed in 3Duf and tested
    • Changes made to fix issues with fluid input and mixing
    • Initial draft of protocol written
  • Wetlab Collaboration Chip
    • 4 iterations milled
    • Sealing issues improved upon
    • Testing done with shared liquid input
  • DNA Digestion Chip
    • 4 iterations milled
    • Iterations made to better replicate protocol on a chip
    • Pipetting chamber designed and optimized for chip
  • BU Hardware visits BosLab during monthly showcase
    • Provided insight into what small scale biohacker space is like, and what synthetic biology community is looking for in microfluidics
  • Fluid Functionality begins to be developed
    • Idea of primitive level analysis developed along with some qualitative failures
  • Worked with Neptune (2016 BU Hardware Team) automated syringe pumps tried to increase accuracy and improve function
  • MARS Repository chips began to be placed in subsections of isolation, modification, and quantification
  • Transformation Chip
    • 2 iterations designed in Fluigi
    • 8 iterations designed in 3Duf and tested
    • Changes made to overall design as well as valve sizes
  • Summer Pathways
    • Participated in Summer Pathways alongside the BU Wetlab Team
    • Created an interactive microfluidics design activity for the attending high school students
    • Engaged with students to design microfluidic devices based on synbio protocols
  • Harvard iGEM Team Collaboration
    • Initial meetings to discuss plans
  • WPI iGEM Team Collaboration
    • During the initial Skype call we discussed the nature of their lead assay and how it might be moved onto a microfluidic
    • Their team visited our lab and performed verified their assay’s functionality on the BU spectrometer
  • Tutorial Videos
    • PDMS video filmed
  • Peristaltic Pump Chip
    • Design inspired by another paper with different geometries
    • 4 iterations designed in 3Duf and tested
  • Metering Primitive
    • In order to allow for accurate volume dispension on a microfluidic device, a metering primitive inspired by the peristaltic pump was designed
    • 2 iterations designed in 3Duf and tested

August

  • Transformation Chip
    • 13 iterations designed in 3Duf and tested
    • Different valve dimensions tested
  • Ligation Chip
    • 2 iterations designed in 3Duf
  • Tutorial Videos
    • PDMS Video finalized
    • Milling Video recording and scripting completed
  • DNA Digestion
    • 2 iterations milled and tested
  • Wetlab Collaboration Chip
    • 1 iteration milled and tested
  • Cell Lysis Chip
    • Design finalized
    • Testing with magnetic particles in chamber
  • Cell Culturing
    • Initial CAD model designed and tested
    • Spin coated PDMS
    • Second and final CAD model designed and tested
  • Wiki
    • Initial pages started to be constructed
    • Wiki architecture organized
  • Fluid Functionality
    • Quantitative tests begin to be developed

September

  • Transformation Chip
    • 1 iteration designed in 3Duf and tested
    • Different valve dimension tested
  • Tutorial Videos
    • Milling video finalized
    • Assembly video filmed and scripted
    • Cleaning video filmed and audio recorded
  • Fluid Functionality
    • Channels quantitative tests finalized
  • Antibiotic Resistance*FOOTNOTE*
    • Initial design developed
  • Wetlab Collaboration Chip
    • 2 Iterations milled and tested
    • Protocol and design finalized
    • Chip tested by Wetlab

October

  • Transformation Chip
    • 4 iterations designed in 3Duf and tested
    • Different metering scales tested
  • PCR Chip
    • 4 iterations designed in 3Duf and tested
  • Cell Sorting
    • 2 iterations milled and tested
    • Protocol finalized and documented
  • Ligation Chip
    • 1 iteration designed in 3Duf
  • Video tutorials
    • Assembly video finalized
    • Cleaning video finalized
  • WPI iGEM Team Collaboration chip design documented finalized
  • Attended Northeastern iGEM practice conference #2 (NEGEM) at MIT
    • Received feedback on iGEM presentation
    • Incorpated feedback for final presentation
  • Fluid Functionality
    • Valve quantitative test finalized
    • Mixer quantitative test finalized
  • Antibiotic Resistance
    • Design finalized using 3Duf
    • Milled and documented
  • Harvard iGEM Collaboration
    • Validated Harvard optical density sensor