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

 
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background-image: url("https://static.igem.org/mediawiki/2017/0/04/MARS_General_Background.png");
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background-image: url("https://static.igem.org/mediawiki/2017/9/94/LARGE_background_MARS.png");
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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">
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<img src="https://static.igem.org/mediawiki/2017/9/94/LARGE_background_MARS.png" id="BACKGROUND">
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<img src="https://static.igem.org/mediawiki/2017/2/22/MARSLogo2.png" id="MARS">
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<div class="container" margin-top:"2%;">
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<img src="https://static.igem.org/mediawiki/2017/5/50/MARS_Timeline.png" id="TITLE">
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<div class="col-md-3">
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<img src="https://static.igem.org/mediawiki/2017/2/22/MARSLogo2.png" width="100%" style="margin-top:-37%;">
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</div>
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<div class="col-md-9" style="color:#eef1f5; font-size:100px; font-family:Arial,Gadget,sans-serif; margin-top:1%;">
 +
Notebook
 +
</div>
 +
</div>
 
</div>
 
</div>
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<div class="main main-raised" id="uF_101">
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<div class="main main-raised" style="margin-top:2%;">
 
<div class="container">
 
<div class="container">
 
<div class="text" style="margin-bottom:3%;">
 
<div class="text" style="margin-bottom:3%;">
−
<h1><u>May</u></h1>
+
<h1>May</h1>
 
<ul>
 
<ul>
−
<li>The BU Wetlab and Hardware iGEM teams participated in joint Wetlab safety and protocol training</li>
+
<li>The BostonU 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 performed an initial literature review in order to learn more about the types of microfluidic devices being design</li>
 
<li>
 
<li>
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<li>From the  literature review, each member chose one chip of interest to replicate and test</li>
 
<li>From the  literature review, each member chose one chip of interest to replicate and test</li>
 
<ol>
 
<ol>
−
<li>LAMP Chip
+
<li>LAMP Chip<sup>[1]</sup>
 
<ul>
 
<ul>
 
<li>3 iterations designed in Fluigi</li>
 
<li>3 iterations designed in Fluigi</li>
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</ul>
 
</ul>
 
</li>
 
</li>
−
<li>Multiplex Drug Testing Chip</li>
+
<li>Multiplex Drug Testing Chip<sup>[2]</sup></li>
 
<ul>
 
<ul>
 
<li>2 iterations designed in 3Duf and tested</li>
 
<li>2 iterations designed in 3Duf and tested</li>
 
<li>1 iteration designed in Fluigi</li>
 
<li>1 iteration designed in Fluigi</li>
 
</ul>
 
</ul>
−
<li>Magnetic Mixer Chip</li>
+
<li>Magnetic Mixer Chip<sup>[3]</sup></li>
 
<ul>
 
<ul>
−
<li></li>
+
<li>5 Iterations milled and tested</li>
−
<li></li>
+
<li>Magnetic particles introduced into chip</li>
 +
<li>Experimented with different protocols</li>
 
</ul>
 
</ul>
 
</ol>
 
</ol>
−
<li>BU Wetlab iGEM Team Collaboration began</li>
+
<li>BostonU Wetlab iGEM Team Collaboration began</li>
 
<ul>
 
<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>At the initial meeting BostonU Wetlab provided BostonU Hardware with a protocol they thought could be performed in a microfluidic device</li>
 
<li>6 potential chips designed for Wetlab collaboration</li>
 
<li>6 potential chips designed for Wetlab collaboration</li>
 
</ul>
 
</ul>
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<li>Volume Dispensing Chips
 
<li>Volume Dispensing Chips
 
<ul>
 
<ul>
−
<li>3 iterations desgined in 3Duf and tested</li>
+
<li>3 iterations designed in 3Duf and tested</li>
 
</ul>
 
</ul>
 
</li>
 
</li>
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<li>6 Iterations designed in Fluigi</li>
 
<li>6 Iterations designed in Fluigi</li>
 
<li>2 Iterations designed in 3Duf and tested</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>
 
</ul>
 
</li>
 
</li>
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</ul>
 
</ul>
 
</li>
 
</li>
−
<li>BU Hardware visits BosLab during monthly showcase
+
<li>BostonU Hardware visits BosLab during monthly showcase
 
<ul>
 
<ul>
 
<li>Provided insight into what small scale biohacker space is like, and what synthetic biology community is looking for in microfluidics</li>
 
<li>Provided insight into what small scale biohacker space is like, and what synthetic biology community is looking for in microfluidics</li>
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</ul>
 
</ul>
 
</li>
 
</li>
−
<li>Worked with Neptune (2016 BU Hardware Team) automated syringe pumps tried to increase accuracy and improve function</li>
+
<li>Worked with Neptune (2016 BostonU 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>MARS Repository chips began to be placed in subsections of isolation, modification, and quantification</li>
 
<li>Transformation Chip
 
<li>Transformation Chip
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<li>Summer Pathways
 
<li>Summer Pathways
 
<ul>
 
<ul>
−
<li>Participated in Summer Pathways alongside the BU Wetlab Team</li>
+
<li>Participated in Summer Pathways alongside the BostonU Wetlab Team</li>
 
<li>Created an interactive microfluidics design activity for the attending high school students</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>
 
<li>Engaged with students to design microfluidic devices based on synbio protocols </li>
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</ul>
 
</ul>
 
</li>
 
</li>
−
<li>Peristaltic Pump Chip
+
<li>Peristaltic Pump Chip<sup>[4]</sup>
 
<ul>
 
<ul>
 
<li>Design inspired by another paper with different geometries</li>
 
<li>Design inspired by another paper with different geometries</li>
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<li>Metering Primitive
 
<li>Metering Primitive
 
<ul>
 
<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>In order to allow for accurate volume dispensing on a microfluidic device, a metering primitive inspired by the peristaltic pump was designed</li>
 
<li>2 iterations designed in 3Duf and tested</li>
 
<li>2 iterations designed in 3Duf and tested</li>
 
</ul>
 
</ul>
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</ul>
 
</ul>
 
</li>
 
</li>
−
<li>Cell Culturing
+
<li>Cell Culturing<sup>[6]</sup>
 
<ul>
 
<ul>
 
<li>Initial CAD model designed and tested</li>
 
<li>Initial CAD model designed and tested</li>
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</div>
 
</div>
  
−
<div class="main main-raised" id="uF_101">
+
<div class="main main-raised" style="margin-top:5%;" id="uF_101">
 
<div class="container">
 
<div class="container">
 
<h1>September</h1>
 
<h1>September</h1>
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</ul>
 
</ul>
 
</li>
 
</li>
−
<li>Antibiotic Resistance*FOOTNOTE*
+
<li>Antibiotic Resistance<sup>[5]</sup>
 
<ul>
 
<ul>
 
<li>Initial design developed</li>
 
<li>Initial design developed</li>
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</div>
 
</div>
  
−
<div class="main main-raised" id="uF_101" style="margin-bottom:3%">
+
<div class="main main-raised" id="uF_101" style="margin-top:5%;">
 
<div class="container">
 
<div class="container">
 
<h1>October</h1>
 
<h1>October</h1>
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<ul>
 
<ul>
 
<li>Received feedback on iGEM presentation</li>
 
<li>Received feedback on iGEM presentation</li>
−
<li>Incorpated feedback for final presentation</li>
+
<li>Incorporated feedback for final presentation</li>
 
</ul>
 
</ul>
 
</li>
 
</li>
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</div>
 
</div>
 +
<div class="main main-raised" style="margin-top:5%;" id="uF_101">
 +
<div class="container">
 +
<div class="text" style="margin-bottom:3%;">
 +
<h1>Citations</h1>
 +
<ol>
 +
<li>Tourlousse, D. M., Ahmad, F., Stedtfeld, R. D., Seyrig, G., Tiedje, J. M., & Hashsham, S. A. (2012). A polymer microfluidic chip for quantitative detection of multiple water- and foodborne pathogens using real-time fluorogenic loop-mediated isothermal amplification. Biomedical Microdevices, 14(4), 769–778. <a href = "https://doi.org/10.1007/s10544-012-9658-3">https://doi.org/10.1007/s10544-012-9658-3</a>
 +
</li>
 +
<li>Mohan, R., Mukherjee, A., Sevgen, S. E., Sanpitakseree, C., Lee, J., Schroeder, C. M., & Kenis, P. J. A. (2013). A multiplexed microfluidic platform for rapid antibiotic susceptibility testing. Biosensors and Bioelectronics, 49, 118–125. <a href = "https://doi.org/10.1016/j.bios.2013.04.046">https://doi.org/10.1016/j.bios.2013.04.046</a>
 +
</li>
 +
<li>Liang-Hsuan Lu, Kee Suk Ryu, & Chang Liu. (2002). A magnetic microstirrer and array for microfluidic mixing. Journal of Microelectromechanical Systems, 11(5), 462–469. <a href = "https://doi.org/10.1109/jmems.2002.802899">https://doi.org/10.1109/jmems.2002.802899</a>
 +
 +
</li><li>Nguyen, T. V., Duncan, P. N., Ahrar, S., & Hui, E. E. (2012). Semi-autonomous liquid handling via on-chip pneumatic digital logic. Lab on a Chip, 12(20), 3991. <a href = "https://doi.org/10.1039/c2lc40466d">https://doi.org/10.1039/c2lc40466d</a></li>
 +
<li>Hou, H. W., Bhagat, A. A. S., Lin Chong, A. G., Mao, P., Wei Tan, K. S., Han, J., & Lim, C. T. (2010). Deformability based cell margination—A simple microfluidic design for malaria-infected erythrocyte separation. Lab on a Chip, 10(19), 2605. <a href = "https://doi.org/10.1039/c003873c">https://doi.org/10.1039/c003873c</a></li>
 +
                                        <li>Lee KS, Boccazzi P, Sinskey AJ, Ram RJ. Microfluidic chemostat and turbidostat with flow rate, oxygen, and temperature control for dynamic continuous culture. Lab Chip. 2011;11(10):1730-9.<a href = "https://doi.org/10.1039/c1lc20019d">https://doi.org/10.1039/c1lc20019d</a>
 +
</li>
 +
</ol>
 +
</div>
 +
</div>
 +
</div>
  
 
   </div>
 
   </div>
 +
 +
<!-- THIS IS FOOTER -->
 +
<div class="wrapper" style="background:#1c1f1f; margin-top:0px;margin-right:0px !important; margin-left:0px !important;" id="Footer">
 +
  <div class="container" style="text-align:center !important">
 +
 +
    <div class="col-md-2" style="color:white; margin-bottom:30px; margin-top:5px;">
 +
      <h3>CONTACT US</h3>
 +
    <div style="text-align:center;">
 +
      <a href="mailto:igembuhw@gmail.com">
 +
      <img src="https://static.igem.org/mediawiki/2017/7/74/MARS_WHITEEmail.png" style="height:60px; margin-top:20px;">
 +
      </a>
 +
        <a href="https://www.instagram.com/buigemhardware/?hl=en">
 +
        <img src="https://static.igem.org/mediawiki/2017/9/93/MARS_Final_insta.png" style="height:60px; margin-top:20px;">
 +
      </a>
 +
          <a href="https://twitter.com/igemhwbu">
 +
          <img src="https://static.igem.org/mediawiki/2017/b/b6/MARS_Twitter_White.png" style="height:60px; margin-top:20px;">
 +
          </a>
 +
      </div>
 +
      </div>
 +
      <div class="col-md-10" style="margin-bottom:30px;">
 +
        <img src="https://static.igem.org/mediawiki/2017/0/0e/MARS_SponsorsFinal.png" style="width:100%; margin-top:30px;" usemap="#image-map">
 +
    </div>
 +
</div>
 +
 +
</div>
 +
 +
  
 
</div>
 
</div>

Latest revision as of 02:22, 1 November 2017

BostonU_HW

Attributions
Notebook

May

  • The BostonU 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[1]
      • 3 iterations designed in Fluigi
      • 5 iterations designed in 3Duf and tested
    2. Multiplex Drug Testing Chip[2]
      • 2 iterations designed in 3Duf and tested
      • 1 iteration designed in Fluigi
    3. Magnetic Mixer Chip[3]
      • 5 Iterations milled and tested
      • Magnetic particles introduced into chip
      • Experimented with different protocols
  • BostonU Wetlab iGEM Team Collaboration began
    • At the initial meeting BostonU Wetlab provided BostonU 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 designed 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
  • 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
  • BostonU 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 BostonU 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 BostonU 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[4]
    • Design inspired by another paper with different geometries
    • 4 iterations designed in 3Duf and tested
  • Metering Primitive
    • In order to allow for accurate volume dispensing 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[6]
    • 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[5]
    • 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
    • Incorporated 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

Citations

  1. Tourlousse, D. M., Ahmad, F., Stedtfeld, R. D., Seyrig, G., Tiedje, J. M., & Hashsham, S. A. (2012). A polymer microfluidic chip for quantitative detection of multiple water- and foodborne pathogens using real-time fluorogenic loop-mediated isothermal amplification. Biomedical Microdevices, 14(4), 769–778. https://doi.org/10.1007/s10544-012-9658-3
  2. Mohan, R., Mukherjee, A., Sevgen, S. E., Sanpitakseree, C., Lee, J., Schroeder, C. M., & Kenis, P. J. A. (2013). A multiplexed microfluidic platform for rapid antibiotic susceptibility testing. Biosensors and Bioelectronics, 49, 118–125. https://doi.org/10.1016/j.bios.2013.04.046
  3. Liang-Hsuan Lu, Kee Suk Ryu, & Chang Liu. (2002). A magnetic microstirrer and array for microfluidic mixing. Journal of Microelectromechanical Systems, 11(5), 462–469. https://doi.org/10.1109/jmems.2002.802899
  4. Nguyen, T. V., Duncan, P. N., Ahrar, S., & Hui, E. E. (2012). Semi-autonomous liquid handling via on-chip pneumatic digital logic. Lab on a Chip, 12(20), 3991. https://doi.org/10.1039/c2lc40466d
  5. Hou, H. W., Bhagat, A. A. S., Lin Chong, A. G., Mao, P., Wei Tan, K. S., Han, J., & Lim, C. T. (2010). Deformability based cell margination—A simple microfluidic design for malaria-infected erythrocyte separation. Lab on a Chip, 10(19), 2605. https://doi.org/10.1039/c003873c
  6. Lee KS, Boccazzi P, Sinskey AJ, Ram RJ. Microfluidic chemostat and turbidostat with flow rate, oxygen, and temperature control for dynamic continuous culture. Lab Chip. 2011;11(10):1730-9.https://doi.org/10.1039/c1lc20019d