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

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<p style="font-size: 2em; font-weight: bold" > Register for iGEM, have a great summer, and attend the Giant Jamboree. </p>
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<p style="font-size: 2em; font-weight: bold" > Validate that something you created (art & design, hardware, software, etc) performs its intended function. Provide thorough documentation of this validation on your team wiki. </p>
  
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<p> We're very excited to be part of the Jamboree, to see all the other amazing projects, to show everyone what we've accomplished through our hard work this summer. And we're excited to see you there too :) </p>
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<p>As described in the Bronze Medal section, we developed a fully integrated, end-to-end design suite for microfluidic devices. We also designed 3D printed hardware infrastructure for controlling these devices, and we designed a new and original hardware solution to controlling fluid dispension using servo motors. Putting the cherry on top, we also contributed to developing algorithms that help translate LFR specifications of microfluidic devices to lower level MINT descriptions. Ultimately, the intended function of our software and hardware is to enable researchers to design, fabricate and use microfluidics with a single, coherent workflow. Furthermore, this single workflow needs to interface with low cost tools, it needs to be simple and robust, and it should allow any researcher to make a microfluidic chip with ease. </p>
  
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<p style="font-size: 2em; font-weight: bold"> Meet all deliverables on the Requirements page (section 3), except those that specifically mention parts. </p>
+
<p> The best way to validate our workflow, our software and our hardware, would be to explore some of the microfluidic projects we did this summer. The following microfluidic designs were made within Neptune, using the LFR and MINT specifications to create the design schematics. Further, we obtained the 3D print schematics for the control infrastructure for these projects from Neptune. We designed the control infrastructure using the tutorials and specifications detailed by Neptune. Finally, we ran control tests to validate the function of our device through Neptune's control interface. </p>
 +
 
 +
<p> Here, we will briefly describe three microfluidic projects we worked on. We have pages for each of these projects, so follow the links for more detail! Our ability to execute these projects with Neptune and our hardware validates our workflow performs its intended function. </p>
 +
 
 +
<p style="font-size: 2em; font-weight: bold"> Convince the judges you have helped any registered iGEM team from high school, a different track, another university, or another institution in a significant way by, for example, mentoring a new team, characterizing a part, debugging a construct, modeling/simulating their system or helping validate a software/hardware solution to a synbio problem. </p>
  
  
 
<p>  
 
<p>  
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<p>Team Wiki: You're looking at her. </p>
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<p> MIT Collaboration </p>
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<p>Poster: Come by our table and take a look. </p>
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<p> NEU Collaboration </p>
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<p>Presentation: You'll love what you see. </p>
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<p> BU Collaboration </p>
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<p>Project Attributions: Please see out attributions page.</p>
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<p>Registry Part Pages: Hardware track. </p>
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<p>Sample Submission: hardware track.</p>
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−
<p>Safety Forms: Complete. </p>
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<p>Judging Forms: Complete. </p>
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</p>
 
</p>
  
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<p style="font-size: 2em; font-weight: bold"> Create a page on your team wiki with clear attribution of each aspect of your project. This page must clearly attribute work done by the students and distinguish it from work done by others, including host labs, advisors, instructors, sponsors, professional website designers, artists, and commercial services. </p>
+
<p style="font-size: 2em; font-weight: bold"> iGEM projects involve important questions beyond the lab bench, for example relating to (but not limited to) ethics, sustainability, social justice, safety, security, and intellectual property rights. Demonstrate how your team has identified, investigated, and addressed one or more of these issues in the context of your project. Your activity could center around education, public engagement, public policy issues, public perception, or other activities (see the human practices hub for more information and examples of previous teams' exemplary work). </p>
 +
 
 +
<p>Nona Partnership </p>
 +
 
 +
<p>Nona is a nonprofit organization established to help document, maintain, and increase community access to open source synthetic biology software tools. The motivation behind Nona stems from the observation that a large portion of synthetic biology software tools that are created, despite being incredibly useful for their purpose, often see only limited support, development, and often they never come to full fruition. Too often, a large proportion of software tools made in academia will only see a limited amount of updates and support before the original creators of the tool move onto different project; when this happens, the software tool loses all use, documentation ends, and old or new issues don’t get resolved. To many synthetic biology software tools do not receive enough support and community attention to reach fruition. </p>
 +
<p>Nona gives support to synthetic biology software by providing a platform to archive, document, host and distribute these tools. More so, Nona has a goal of culturing a community of researchers and developers around these tools: Nona aims to have a form where members of the synthetic biology community can discuss, ask and answer questions, and provide feedback about these software tools. And because the tools that Nona supports are all open source, there is a goal of fostering the growth of a developer community around these synthetic biology tools. Nona is a home for open source synthetic biology software tools, and we are proud to have partnered with Nona this summer as just a small part of our human practices ventures. </p>
 +
<p>What did we do? Well, to start off, Neptune is already under the Nona umbrella of software tools. This summer our team met with members of the Nona board to discuss the future of Neptune and Nona, as well other ways in which our team could contribute to the Nona community. We had a total of 3 main meetings, with a couple smaller correspondences in between. The following conclusions were reached regarding our collaboration: </p>
 +
 
 +
 
 +
<p>Building With Biology</p>
 +
 
 +
<p>We will continue to discuss our partnership with Nona under the gold medal requirements for integrated human practices. For now, we will look at a handful of other “beyond the bench” activities that we did. The first of these is the Building With Biology event at the Boston Museum of Science. This Building With Biology event is part of a NSF funded effort to stimulate synthetic biology public engagement and community outreach. Indeed, there is a big gap between the general public’s perception of synthetic biology, and the perception that researchers and engineers have toward synthetic biology; the Building with Biology event is one way we are trying to bridge that gap. During this daylong event, our iGEM team, as well as a number of other iGEM teams including our sister foundational research team and the MIT team, came to join the public in a day of conversation, education and outreach. </p>
 +
<p>Let us paint a picture of what this event was like, what we accomplished, and why this human practices activity is important. </p>
 +
<p>The first portion of this event was centered around having us the “scientific community” host little synthetic biology activities that are geared toward a range of audiences: The activities were simple such that they could be enjoyed by kids under the age of 10 (sometimes as young as 5,) but these activities had embedded in them big synthetic biology ideas, ideas that adults could ponder, and even people with a scientific background could enjoy. </p>
 +
 
 +
 +
<p>Summer Pathways </p>
 +
 
 +
<p>In much of the same spirit as in our participation in Building With Biology, our team collaborated with the BU foundational research team to host several activities for </p>
 +
 
 +
<p>Blog Collaboration</p>
  
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<p> Neptune is a design tool that implements the research done by many mentors and graduate student. Before us, other students developed single, abstract software tools toward microfluidic design. These tools saw limited to no use because they failed to integrate into a bigger system. We created the software for the Neptune user interface that wraps these different projects, and we created the hardware control infrastructure for the microfluidics that are generated from this workflow. We have also contributed to the algorithmic libraries of Neptune by developing a tool called Mushroom Mapper, which allows for a higher level of abstraction when specifying microfluidic chip designs. Here we attribute the different components behind Neptune, the ones created by other students and mentors. </p>
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<p>In one last collaboration with the BU foundational research team, together we published a reference blog to discuss the history and significance of patent practices in relation to synthetic biology. </p>
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<p>3DuF:</p>
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<p> 3DuF is a user friendly, open source application for creating microfluidic designs and design components that can then be fabricated with CAD tools. This application is embedded in Neptune as a visualization tool for the microfluidic chip design. This tool is currently in development by our mentor Josh Lippai. </p>
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        <p>MakerFluidics: </p>
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<p>MakerFluidics is a microfluidic fabrication protocol that leverages open, low cost, and easily accessible tools to fabricate microfluidics. In this toolchain, microfluidics are created using a CNC mill to create channels in a thermoplastic, biocompatible stock. MakerFluidics uses open source software, including 3DuF, and now Neptune. Neptune is developed to be compatible with MakerFluidics; in Neptune SVG design schematics are generated, ready to fabricate with a CNC mill. This protocol was developed by our mentor Ryan Silva. </p>
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<p>FluigiCore: </p>
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<p> Fluigi Core is a place and route tool that takes MINT files that the user inputs into Neptune, and it performs an optimization placing of channels, valves, and other components onto the microfluidic chip. In essence, Fluigi Core generates design schematics from the MINT standard microfluidic specification format you provide it. Neptune wraps Fluigi Core, it is the algorithmic library to our software. This program is currently in development by our mentor Radhakrishna Sanka. </p>
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<p>NetSynth:  </p>
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<p> NetSynth is a logic minimization library for Verilog. The original purpose of NetSynth was to take a Verilog description of a circuit, and convert this into a netlist of wires and gates that realize the design description. Our iGem team has joined the prior work of Prashant Vaidyanathan to refactor NetSynth into a tool that can also perform logic minimization on microfluidic designs. Prashant is responsible for originally repurposing NetSynth for microfluidic design, and our team has further contributed to this by integrating NetSynth outputs with the Mushroom Mapper tool we created. </p>
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<p>Open Source Venture </p>
  
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<p style="font-size: 2em; font-weight: bold"> Document at least one new substantial contribution to the iGEM community that showcases a project made with BioBricks. This contribution should be equivalent in difficulty to making and submitting a BioBrick part. </p>
 
  
 
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Revision as of 17:16, 16 October 2016


MEDAL CRITERIA: SILVER





Validate that something you created (art & design, hardware, software, etc) performs its intended function. Provide thorough documentation of this validation on your team wiki.

As described in the Bronze Medal section, we developed a fully integrated, end-to-end design suite for microfluidic devices. We also designed 3D printed hardware infrastructure for controlling these devices, and we designed a new and original hardware solution to controlling fluid dispension using servo motors. Putting the cherry on top, we also contributed to developing algorithms that help translate LFR specifications of microfluidic devices to lower level MINT descriptions. Ultimately, the intended function of our software and hardware is to enable researchers to design, fabricate and use microfluidics with a single, coherent workflow. Furthermore, this single workflow needs to interface with low cost tools, it needs to be simple and robust, and it should allow any researcher to make a microfluidic chip with ease.

The best way to validate our workflow, our software and our hardware, would be to explore some of the microfluidic projects we did this summer. The following microfluidic designs were made within Neptune, using the LFR and MINT specifications to create the design schematics. Further, we obtained the 3D print schematics for the control infrastructure for these projects from Neptune. We designed the control infrastructure using the tutorials and specifications detailed by Neptune. Finally, we ran control tests to validate the function of our device through Neptune's control interface.

Here, we will briefly describe three microfluidic projects we worked on. We have pages for each of these projects, so follow the links for more detail! Our ability to execute these projects with Neptune and our hardware validates our workflow performs its intended function.

Convince the judges you have helped any registered iGEM team from high school, a different track, another university, or another institution in a significant way by, for example, mentoring a new team, characterizing a part, debugging a construct, modeling/simulating their system or helping validate a software/hardware solution to a synbio problem.

MIT Collaboration

NEU Collaboration

BU Collaboration

iGEM projects involve important questions beyond the lab bench, for example relating to (but not limited to) ethics, sustainability, social justice, safety, security, and intellectual property rights. Demonstrate how your team has identified, investigated, and addressed one or more of these issues in the context of your project. Your activity could center around education, public engagement, public policy issues, public perception, or other activities (see the human practices hub for more information and examples of previous teams' exemplary work).

Nona Partnership

Nona is a nonprofit organization established to help document, maintain, and increase community access to open source synthetic biology software tools. The motivation behind Nona stems from the observation that a large portion of synthetic biology software tools that are created, despite being incredibly useful for their purpose, often see only limited support, development, and often they never come to full fruition. Too often, a large proportion of software tools made in academia will only see a limited amount of updates and support before the original creators of the tool move onto different project; when this happens, the software tool loses all use, documentation ends, and old or new issues don’t get resolved. To many synthetic biology software tools do not receive enough support and community attention to reach fruition.

Nona gives support to synthetic biology software by providing a platform to archive, document, host and distribute these tools. More so, Nona has a goal of culturing a community of researchers and developers around these tools: Nona aims to have a form where members of the synthetic biology community can discuss, ask and answer questions, and provide feedback about these software tools. And because the tools that Nona supports are all open source, there is a goal of fostering the growth of a developer community around these synthetic biology tools. Nona is a home for open source synthetic biology software tools, and we are proud to have partnered with Nona this summer as just a small part of our human practices ventures.

What did we do? Well, to start off, Neptune is already under the Nona umbrella of software tools. This summer our team met with members of the Nona board to discuss the future of Neptune and Nona, as well other ways in which our team could contribute to the Nona community. We had a total of 3 main meetings, with a couple smaller correspondences in between. The following conclusions were reached regarding our collaboration:

Building With Biology

We will continue to discuss our partnership with Nona under the gold medal requirements for integrated human practices. For now, we will look at a handful of other “beyond the bench” activities that we did. The first of these is the Building With Biology event at the Boston Museum of Science. This Building With Biology event is part of a NSF funded effort to stimulate synthetic biology public engagement and community outreach. Indeed, there is a big gap between the general public’s perception of synthetic biology, and the perception that researchers and engineers have toward synthetic biology; the Building with Biology event is one way we are trying to bridge that gap. During this daylong event, our iGEM team, as well as a number of other iGEM teams including our sister foundational research team and the MIT team, came to join the public in a day of conversation, education and outreach.

Let us paint a picture of what this event was like, what we accomplished, and why this human practices activity is important.

The first portion of this event was centered around having us the “scientific community” host little synthetic biology activities that are geared toward a range of audiences: The activities were simple such that they could be enjoyed by kids under the age of 10 (sometimes as young as 5,) but these activities had embedded in them big synthetic biology ideas, ideas that adults could ponder, and even people with a scientific background could enjoy.

Summer Pathways

In much of the same spirit as in our participation in Building With Biology, our team collaborated with the BU foundational research team to host several activities for

Blog Collaboration

In one last collaboration with the BU foundational research team, together we published a reference blog to discuss the history and significance of patent practices in relation to synthetic biology.

Open Source Venture