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

 
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<body>
 
<body>
  
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<div class="services bg-primary">
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<header id="top" class="header">
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<div class="row text-center">
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        <div class="col-lg-10 col-lg-offset-1">
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        <div class="text-vertical-center" style="color: white;">
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            <h1>Results</h1>
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</div>
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</div>
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</div>
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</div>
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<br><br/>
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        <span class="icon-bar"></span>
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        <span class="icon-bar"></span>
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      <a class="navbar-brand" href="https://2016.igem.org/Team:BostonU_HW"><img src="https://static.igem.org/mediawiki/2016/9/97/T--BostonU_HW--NeptuneLogo_rcwolf.png" height="38" width="55" style="display: inline-block; padding-right: 17px; ">BU HW 2016</a>
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    </div>
  
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Hi there
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        <li class="sliding-middle-out dropdown">
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</div>
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            <a href="#" class="dropbtn">TEAM </a>
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                  <a href="https://2016.igem.org/Team:BostonU_HW/Team">Meet the Team </a>
 +
                  <a href="https://2016.igem.org/Team:BostonU_HW/Attributions">Attributions</a>
 +
                  <a href="https://2016.igem.org/Team:BostonU_HW/Collaborations">Collaborations</a>
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            <a href="#" class="dropbtn">PROJECT</a>
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            <img src="https://static.igem.org/mediawiki/2016/5/58/T--BostonU_HW--indexTriangle_rcwolf.png" width="36" height="18" style="margin-bottom: 0 !important; margin-top: 0; padding-bottom: 0 !important; border: none; display: block; margin: 0 auto;">
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            <div class="dropdown-content">
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                  <a href="https://2016.igem.org/Team:BostonU_HW/Results">Results</a>
 +
                  <a href="https://2016.igem.org/Team:BostonU_HW/Demonstrate">Demonstration</a>
 +
                  <a href="https://2016.igem.org/Team:BostonU_HW/Proof">Proof</a>
 +
                  <a href="https://2016.igem.org/Team:BostonU_HW/Design">Design</a>
 +
                  <a href="https://2016.igem.org/Team:BostonU_HW/Parts">Parts</a>
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            </div>
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        </li>
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        <li class="sliding-middle-out dropdown">
 +
            <a href="#" class="dropbtn">NOTEBOOK</a>
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            <div class="dropdown-content">
 +
                  <a href="https://2016.igem.org/Team:BostonU_HW/Notebook">Timeline</a>
 +
                  <a href="https://2016.igem.org/Team:BostonU_HW/Experiments">Experiments</a>
 +
                  <a href="https://2016.igem.org/Team:BostonU_HW/Safety">Safety</a>
 +
            </div>
 +
        </li>
 +
        <li class="sliding-middle-out dropdown">
 +
            <a href="https://2016.igem.org/Team:BostonU_HW/Human_Practices" class="dropbtn">HUMAN PRACTICES</a>
 +
            <div class="dropdown-content">
 +
                  <a href="https://2016.igem.org/Team:BostonU_HW/HP/Silver">Silver</a>
 +
                  <a href="https://2016.igem.org/Team:BostonU_HW/HP/Gold">Gold</a>
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            <a href="#" class="dropbtn">AWARDS</a>
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                  <a href="https://2016.igem.org/Team:BostonU_HW/Integrated_Practices">Integrated Practices</a>
 +
                  <a href="https://2016.igem.org/Team:BostonU_HW/Software">Software</a>
 +
            </div>
 +
        </li>
 +
        <li class="sliding-middle-out dropdown">
 +
            <a href="#" class="dropbtn">MEDAL CRITERIA </a>
 +
            <div class="dropdown-content">
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                  <a href="https://2016.igem.org/Team:BostonU_HW/Bronze">Bronze</a>
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                  <a href="https://2016.igem.org/Team:BostonU_HW/Silver">Silver</a>
 +
                  <a href="https://2016.igem.org/Team:BostonU_HW/Gold">Gold</a>
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  </div><!-- /.container-fluid -->
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</div>
  
  
  
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<div class="column full_size" >
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</body>
  
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<p>Here you can describe the results of your project and your future plans. </p>
 
  
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<h5>What should this page contain?</h5>
 
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<ul>
 
−
<li> Clearly and objectively describe the results of your work.</li>
 
−
<li> Future plans for the project </li>
 
−
<li> Considerations for replicating the experiments </li>
 
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</ul>
 
  
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 +
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 +
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 +
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 +
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<body>
 +
<!-- PAGE TITLE BANNER -->
 +
  <div id="greyWrapper">   
 +
    <div class="pageBanner">
 +
      <h3 id="pageTitle">RESULTS</h3>
 +
    </div>
 +
    <br><br><br><br>
 +
   
 +
   
 +
 +
 +
<div class="row" style="padding-top:50px; padding-bottom:50px;">
 +
  <div class="col-md-1"></div>
 +
  <div class="col-md-10" style="font-size: 3em; line-height: 130%;">Neptune paints a bright future for microfluidics</div>
 +
  <div class="col-md-1"></div>
 
</div>
 
</div>
  
−
<div class="column half_size" >
+
<div class="row" style="padding-top:100px; padding-bottom:100px;">
 +
  <div class="col-md-1"></div>
 +
  <div class="col-md-10" style="background-color: white; padding-top:50px; padding-bottom:50px;">
 +
    <div class="row">
 +
      <div class="col-md-1"></div>
 +
      <div class="col-md-10">
 +
        <div style="font-size: 2em; line-height: 150%; color:#355E62;">Benefits of Neptune to Synthetic Biologists</div>
 +
        <br><br><br>
 +
        <div>
 +
         
 +
          <video width="100%" controls>
 +
        <source src="https://static.igem.org/mediawiki/2016/f/f3/T--BostonU_HW--VIDEOBronzeIV_rcwolf.mp4" type="video/mp4">
 +
        Your browser does not support the video tag.
 +
      </video>
 +
      </div>
  
  
−
<h5> Project Achievements </h5>
+
        </div>
 +
      </div>
 +
      <div class="col-md-1"></div>
 +
    </div>
 +
  </div>
 +
  <div class="col-md-1"></div>
  
−
<p>You can also include a list of bullet points (and links) of the successes and failures you have had over your summer. It is a quick reference page for the judges to see what you achieved during your summer.</p>
 
  
−
<ul>
+
<br><br>
−
<li>A list of linked bullet points of the successful results during your project</li>
+
−
<li>A list of linked bullet points of the unsuccessful results during your project. This is about being scientifically honest. If you worked on an area for a long time with no success, tell us so we know where you put your effort.</li>
+
−
</ul>
+
  
 +
 +
<div class="row" style="padding-top:100px; padding-bottom:100px;">
 +
  <div class="col-md-1"></div>
 +
  <div class="col-md-10" style="background-color: white; padding-top:50px; padding-bottom:50px;">
 +
    <div class="row">
 +
      <div class="col-md-1"></div>
 +
      <div class="col-md-10">
 +
        <div style="font-size: 2em; line-height: 150%; color:#355E62;">Neptune Deliverables</div>
 +
        <br><br><br>
 +
        <div style="font-size: 1.5em; line-height: 140%;">
 +
          <ul>
 +
            <li>Liquid Flow Relations & User Constraints File</li>
 +
            <li>μShroom Mapper</li>
 +
            <li>Piston Rod Mechanical System for Valve and Dispenser Operation</li>
 +
            <li>MEC Board Integration for Modular Hardware Baseboard</li>
 +
            <li>Maped Mechanical Motion for Servo-Syringe Combinations</li>
 +
            <li>Scalable Electronics Designed to Support up to 200 servos</li>
 +
            <li>Constant Flow Rate Mapping for Servo-Syringe Combinations</li>
 +
            <li>Parametric 3D Printed Parts for Supporting Hardware Infrastructure</li>
 +
            <li>Evaluated Servo-Syringe Combinations</li>
 +
            <li>Arduino Mega Firmare to Control Servos for Valve and Dispenser Operation</li>
 +
            <li>User Interface to Specify Microfluidic Design</li>
 +
            <li>User Interface to Design Microfluidic Design</li>
 +
            <li>User Interface to Assist in the Build of Microfluidic Systems</li>
 +
            <li>User Interface to Guid a user through Assembly of Microfluidic Systems</li>
 +
            <li>User Interface to Control Microfluidic Systems by Communicating with Arduino Mega to Operate Valves and Dispensers</li>
 +
            <li>Packaged Software Tool for Installation</li>
 +
            <li>Verification of Neptune Tool Through Chip Design</li>
 +
          </ul> 
 +
      </div>
 +
      <br>
 +
      <div>
 +
        To read more detail on each of these deliverables and who is responsible for their contribution, please visit the Attributions Page.
 +
      </div>
 +
      <br><br>
 +
        </div>
 +
      </div>
 +
      <div class="col-md-1"></div>
 +
    </div>
 +
  </div>
 +
  <div class="col-md-1"></div>
 +
 +
 +
 +
 +
 +
 +
<br><br>
 +
 +
 +
 +
 +
 +
<div class="row" style="padding-top:50px; padding-bottom:50px; background-color: #D2D2D2">
 +
  <div class="col-md-1"></div>
 +
  <div class="col-md-10" style="font-size: 3em; line-height: 130%; text-align: right;">Considerations for Replication | Neptune is built to be modular, accessible, parametric, and expandable.</div>
 +
  <div class="col-md-1"></div>
 
</div>
 
</div>
  
 +
<div class="row" style="padding-top:100px; padding-bottom:100px;">
 +
  <div class="col-md-1"></div>
 +
  <div class="col-md-10" style="padding-top:50px; padding-bottom:50px; background-color:white;">
  
−
<div class="column half_size" >
 
  
−
<h5>Inspiration</h5>
+
    <div class="row">
−
<p>See how other teams presented their results.</p>
+
      <div class="col-md-3">
−
<ul>
+
      </div>
−
<li><a href="https://2014.igem.org/Team:TU_Darmstadt/Results/Pathway">2014 TU Darmstadt </a></li>
+
      <div class="col-md-9">
−
<li><a href="https://2014.igem.org/Team:Imperial/Results">2014 Imperial </a></li>
+
        <div style="font-size: 2em; line-height: 150%; color:#355E62;">OPEN SOURCE</div>
−
<li><a href="https://2014.igem.org/Team:Paris_Bettencourt/Results">2014 Paris Bettencourt </a></li>
+
      </div>
−
</ul>
+
    </div>
 +
    <div class="row" style="padding-top:20px; padding-bottom:20px;">
 +
      <div class="col-md-3">
 +
        <img src="https://static.igem.org/mediawiki/2016/1/1e/T--BostonU_HW--GitHubLogo_rcwolf.png" width="80%" style="padding-left:20px">
 +
      </div>
 +
      <div class="col-md-9">  
 +
        All of our materials are Open Source. This includes our software tool Neptune, our parametric 3-D Print (STL) files for the microfluidic and hardware infrastructure, and our firmware used to control the valves and dispensers of our system. If an individual wishes to use, modify, or reinvent our software, firmware, or hardware, all of the material to do so is readily available to them to download at their convenience from our public GitHub repository. Also, any of our supporting software tools (including Cura and OpenScad), are free. Users can download any of these resources using the links below.
 +
        <br><br>
 +
        <a href="https://github.com/CIDARLAB/Neptune" style="padding-right:20px"> <button type="button" class="btn btn-primary" id="down">DOWNLOAD NEPTUNE</button></a>
 +
        <a href="http://www.openscad.org/" style="padding-right:20px"> <button type="button" class="btn btn-primary" id="down">DOWNLOAD OPENSCAD</button></a>
 +
        <a href="https://ultimaker.com/en/products/cura-software" > <button type="button" class="btn btn-primary" id="down">DOWNLOAD CURA</button></a>
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 +
    <br>
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        <div style="font-size: 2em; line-height: 150%; color:#355E62;">INSTRUCTIONAL RESOURCES</div>
 +
      </div>
 +
    </div>
 +
    <div class="row" style="padding-top:20px; padding-bottom:20px;">
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      <div class="col-md-3">
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        <img src="https://static.igem.org/mediawiki/2016/f/f2/T--BostonU_HW--workersHat_rcwolf.png" width="90%" style="padding-left:20px">
 +
      </div>
 +
      <div class="col-md-9">
 +
        To ease the use of our tool, Neptune offers several features to the user. First, the user could simply email the developers, or visit our Github page where there would be instructions on how to get started, and some documentation. This would include what the user would need to download, and the steps to get Neptune running on the biologist's computer.
 +
<br><br>
 +
When the user first enters Neptune, they could also go through a guided tour using the 'Tour' button on the dashboard page. The guided tour would step through the entire application to show the user what they need to do to make their first microfluidic chip from top to bottom.
 +
<br><br>
 +
Otherwise, the user can visit our iGEM wiki page where they can view more documentation, tutorial videos, and so on. They could also reach out to the synthetic biology community to talk to other biologists and how they used Neptune for their research experiments. This interaction using Neptune would enable biologists around the world to share their ideas, get feedback, and progress the advancement of science.
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      <div class="col-md-9">
 +
        <div style="font-size: 2em; line-height: 150%; color:#355E62;">PARAMETRIC DESIGNS</div>
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    </div>
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 +
        <img src="https://static.igem.org/mediawiki/2016/3/37/T--BostonU_HW--parametricIcon_rcwolf.png" width="90%" style="padding-left:20px">
 +
      </div>
 +
      <div class="col-md-9">
 +
        All of our STL files used for 3-D printing hardware infrastructure are parametric. If the user decides to use a different servo than that which Neptune recommends, he or she may simply enter a few measurements into the  parameters listed at the top of the provided files and the designs will update automatically to reflect those changes.
 +
        <br><br>
 +
        Our software is designed to convert a mL amount to be dispensed into a PWM command to be sent to the arduino such that an even dispense rate is achieved for fluid movement through the microfluidic device. This conversion, however, is dependent on the specific servo/syringe combination the user has implemented. If the user decides to use a different servo/syringe setup than what is recommended by our system, he or she may still use our dispense conversion algorithm to control their system as it is also completely parametric.
 +
        <br><br>
 +
        <a href="https://github.com/CIDARLAB/iGEM2016-Hardware"> <button type="button" class="btn btn-primary">DOWNLOAD 3D PRINT FILES</button></a>
 +
      </div>
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    </div>
 +
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    <br>
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    <div class="row">
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      <div class="col-md-9">
 +
        <div style="font-size: 2em; line-height: 150%; color:#355E62;">LARGE FUNCTIONAL RANGE OF HARDWARE</div>
 +
      </div>
 +
    </div>
 +
    <div class="row" style="padding-top:20px; padding-bottom:20px;">
 +
      <div class="col-md-3">
 +
        <img src="https://static.igem.org/mediawiki/2016/9/90/T--BostonU_HW--syringeScale_rcwolf.png" width="90%" style="padding-left:20px">
 +
        <br>
 +
        <br>
 +
        <img src="https://static.igem.org/mediawiki/2016/4/42/T--BostonU_HW--MECboard_rcwolf.png" width="90%" style="padding-left:20px">
 +
        <br>
 +
        <br>
 +
        <img src="https://static.igem.org/mediawiki/2016/f/f2/T--BostonU_HW--workersHat_rcwolf.png" width="90%" style="padding-left:20px">
 +
      </div>
 +
      <div class="col-md-9">
 +
        Our Hardware system is highly adaptable for both small and large system requirements. Neptune is capable of running up to 200 servo/syringe combinations at once, fulfilling the need for the most demanding microfluidic system. This number is calculated by finding the bottleneck in data transfer from the computer to Arduino, and the transfer rate from Arduino to motor controller shield. Processing time in both the computer and Arduino are comparatively negligible.
 +
        <br><br>
 +
        Transfer to Arduino: 115,200 bits/second, 14,400 bytes/second
 +
        Transfer to motor controller: standard mode of I2C: 100,000 bits/second, 12,500 bytes/second
 +
        Bytes required for one command: 12
 +
        <br><br>
 +
        Therefore the maximum theoretical number of commands that can be sent at once is 12,500/12 = 1040. Including a safety margin of over 5x to ensure that all servo/syringe combinations can move 5x per second to ensure smooth motion all at once, Neptune’s set maximum is 200 servo/syringe combinations.
 +
        <br><br>
 +
        Neptune transforms the build area of a desktop CNC mill into that of an entire machine shop, and beyond. By milling square, modular components with pre-drilled holes for easy mounting Neptune can span a build area of one 4.2”x 4.2” square to hundreds of feet in any direction. This modularity, in addition to enabling huge build areas, allows for custom baseboard configurations to fix each project’s individual needs. The pre-drilled holes ensure proper component alignment and spacing, further adding to Neptune’s ease-of-use.
 +
 +
        <br><br>
 +
        <a href="https://github.com/CIDARLAB/iGEM2016-Hardware" style="padding-right:20px;"> <button type="button" class="btn btn-primary">DOWNLOAD FIRMWARE</button></a>
 +
        <a href="https://github.com/CIDARLAB/iGEM2016-Hardware"> <button type="button" class="btn btn-primary">DOWNLOAD 3D PRINT FILES</button></a>
 +
      </div>
 +
    </div>
 +
    <br>
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  <div class="col-md-10" style="font-size: 3em; line-height: 130%;">Future Plans for Neptune</div>
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        <div style="font-size: 2em; line-height: 150%; color:#355E62;">EXPERIMENT SCHEDULING & AUTOMATION THROUGH NEPTUNE</div>
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 +
        Neptune has the ability to guide a user through designing, building, and controlling a microfluidic system. Further development on this functionality will incorporate the automation of controlling an experiment in a microfluidic chip through Neptune. We plan to design a scheduling language which Neptune will use to schedule events such as opening or closing a valve or dispensing a certain amount of liquid at specific times. The user will be able to utilize this functionality in a graphical, intuitive way. This will enable a scientist to run a completely automated experiment through Neptune’s tool chain.
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        <div style="font-size: 2em; line-height: 150%; color:#355E62;">INTEGRATION OF SENSORS INTO SYSTEM</div>
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      <div class="col-md-10">
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        In order to allow a more precise control over a microfluidic system through Neptune, we plan to incorporate sensor data collection into the GUI. When running an experiment, automated monitoring of factors such as fluorescence, temperature, and pH can allow for a more intelligent experiment scheduling. For example, if cells in a cell trap need to reach a certain level of fluorescence before a nutrient is washed over them, our future plans for Neptune provide an interface where a biologist can monitor this fluorescence using sensors (such as those manufactured by Atlas Scientific), and schedule his or her program to make intelligent decisions to dispense nutrients based on the current level of fluorescence of those cells.
 +
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Latest revision as of 03:11, 20 October 2016


RESULTS





Neptune paints a bright future for microfluidics
Benefits of Neptune to Synthetic Biologists





Neptune Deliverables



  • Liquid Flow Relations & User Constraints File
  • μShroom Mapper
  • Piston Rod Mechanical System for Valve and Dispenser Operation
  • MEC Board Integration for Modular Hardware Baseboard
  • Maped Mechanical Motion for Servo-Syringe Combinations
  • Scalable Electronics Designed to Support up to 200 servos
  • Constant Flow Rate Mapping for Servo-Syringe Combinations
  • Parametric 3D Printed Parts for Supporting Hardware Infrastructure
  • Evaluated Servo-Syringe Combinations
  • Arduino Mega Firmare to Control Servos for Valve and Dispenser Operation
  • User Interface to Specify Microfluidic Design
  • User Interface to Design Microfluidic Design
  • User Interface to Assist in the Build of Microfluidic Systems
  • User Interface to Guid a user through Assembly of Microfluidic Systems
  • User Interface to Control Microfluidic Systems by Communicating with Arduino Mega to Operate Valves and Dispensers
  • Packaged Software Tool for Installation
  • Verification of Neptune Tool Through Chip Design

To read more detail on each of these deliverables and who is responsible for their contribution, please visit the Attributions Page.




Considerations for Replication | Neptune is built to be modular, accessible, parametric, and expandable.
OPEN SOURCE
All of our materials are Open Source. This includes our software tool Neptune, our parametric 3-D Print (STL) files for the microfluidic and hardware infrastructure, and our firmware used to control the valves and dispensers of our system. If an individual wishes to use, modify, or reinvent our software, firmware, or hardware, all of the material to do so is readily available to them to download at their convenience from our public GitHub repository. Also, any of our supporting software tools (including Cura and OpenScad), are free. Users can download any of these resources using the links below.


INSTRUCTIONAL RESOURCES
To ease the use of our tool, Neptune offers several features to the user. First, the user could simply email the developers, or visit our Github page where there would be instructions on how to get started, and some documentation. This would include what the user would need to download, and the steps to get Neptune running on the biologist's computer.

When the user first enters Neptune, they could also go through a guided tour using the 'Tour' button on the dashboard page. The guided tour would step through the entire application to show the user what they need to do to make their first microfluidic chip from top to bottom.

Otherwise, the user can visit our iGEM wiki page where they can view more documentation, tutorial videos, and so on. They could also reach out to the synthetic biology community to talk to other biologists and how they used Neptune for their research experiments. This interaction using Neptune would enable biologists around the world to share their ideas, get feedback, and progress the advancement of science.

PARAMETRIC DESIGNS
All of our STL files used for 3-D printing hardware infrastructure are parametric. If the user decides to use a different servo than that which Neptune recommends, he or she may simply enter a few measurements into the parameters listed at the top of the provided files and the designs will update automatically to reflect those changes.

Our software is designed to convert a mL amount to be dispensed into a PWM command to be sent to the arduino such that an even dispense rate is achieved for fluid movement through the microfluidic device. This conversion, however, is dependent on the specific servo/syringe combination the user has implemented. If the user decides to use a different servo/syringe setup than what is recommended by our system, he or she may still use our dispense conversion algorithm to control their system as it is also completely parametric.


LARGE FUNCTIONAL RANGE OF HARDWARE




Our Hardware system is highly adaptable for both small and large system requirements. Neptune is capable of running up to 200 servo/syringe combinations at once, fulfilling the need for the most demanding microfluidic system. This number is calculated by finding the bottleneck in data transfer from the computer to Arduino, and the transfer rate from Arduino to motor controller shield. Processing time in both the computer and Arduino are comparatively negligible.

Transfer to Arduino: 115,200 bits/second, 14,400 bytes/second Transfer to motor controller: standard mode of I2C: 100,000 bits/second, 12,500 bytes/second Bytes required for one command: 12

Therefore the maximum theoretical number of commands that can be sent at once is 12,500/12 = 1040. Including a safety margin of over 5x to ensure that all servo/syringe combinations can move 5x per second to ensure smooth motion all at once, Neptune’s set maximum is 200 servo/syringe combinations.

Neptune transforms the build area of a desktop CNC mill into that of an entire machine shop, and beyond. By milling square, modular components with pre-drilled holes for easy mounting Neptune can span a build area of one 4.2”x 4.2” square to hundreds of feet in any direction. This modularity, in addition to enabling huge build areas, allows for custom baseboard configurations to fix each project’s individual needs. The pre-drilled holes ensure proper component alignment and spacing, further adding to Neptune’s ease-of-use.






Future Plans for Neptune
EXPERIMENT SCHEDULING & AUTOMATION THROUGH NEPTUNE
Neptune has the ability to guide a user through designing, building, and controlling a microfluidic system. Further development on this functionality will incorporate the automation of controlling an experiment in a microfluidic chip through Neptune. We plan to design a scheduling language which Neptune will use to schedule events such as opening or closing a valve or dispensing a certain amount of liquid at specific times. The user will be able to utilize this functionality in a graphical, intuitive way. This will enable a scientist to run a completely automated experiment through Neptune’s tool chain.


INTEGRATION OF SENSORS INTO SYSTEM
In order to allow a more precise control over a microfluidic system through Neptune, we plan to incorporate sensor data collection into the GUI. When running an experiment, automated monitoring of factors such as fluorescence, temperature, and pH can allow for a more intelligent experiment scheduling. For example, if cells in a cell trap need to reach a certain level of fluorescence before a nutrient is washed over them, our future plans for Neptune provide an interface where a biologist can monitor this fluorescence using sensors (such as those manufactured by Atlas Scientific), and schedule his or her program to make intelligent decisions to dispense nutrients based on the current level of fluorescence of those cells.