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

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When the team began designing the MARS Repository, we wanted to base it on the principles behind most complex synthetic biology protocols.
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The MARS Repository was created with the purpose of designing generalized chips relevant to synthetic biology.  
 
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We began by generalizing synthetic biology protocols into three key stages:
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Microfluidic devices are often highly specific, performing entire specialized experiments on a chip. This means that these chips are not useful or relevant to an average member of the synthetic biology community.
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<li>Isolation: Acquiring the desired genetic material</li>
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<li>Modification: Manipulated or processing genetic material</li>
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With this in mind, we set out to make the MARS repository. This repository would consist of generalized microfluidic chips that could be useful to any synthetic biologist.
<li>Quantification: Measuring the success of the previous two stages</li>
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These stages “fit” together to form the entirety of the protocols that are carried out everyday in synthetic biology labs.
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To determine what protocols synbiologist would find useful on a microfluidic devices, we reached out the the Biological Design Center located at Boston University. This community of synthetic biologists gave us insight as to what what procedures are performed every day in the average synbio lab. We were able to identify eight protocols integral to synthetic biology: Cell Lysis, DNA Digestion, Ligation, Transformation, PCR, Fluorescence Testing, Antibiotic Resistance Testing, and Cell Culturing. These eight protocols, as well as Cell Sorting, make up the nine chips currently located in the MARS repository.
 
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Each of the nine chips located in the MARS repository are located within one of three subcategories: 
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<img src="https://static.igem.org/mediawiki/2017/4/41/Isomodqua.png" >
 
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In the existing fields of microfluidics, each of these stages is taken care of on individual chips. However, when it comes time to replicate a full synbio procedure using these chips - it becomes difficult to “fit” them together realistically. This is due to the fact that most chips:
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These nine chips, each performing a basic individual protocol, can be combined together to perform more complex synthetic biology experiments.  
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                                Each chip is fully documented, providing all the necessary files for replication and usage. These files include:
 
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<li>Fabrication using different and complicated techniques such as soft lithography</li>
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<li>Design Files</li>
<li>Operated using varying hardware</li>
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<li>Manufacturing Specifications and Instructions</li>
<li>Lack thorough documentation required to run them</li>
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<li>Usage and Testing protocols</li>
<li>Do not have easily accessible design files </li>
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Furthermore, the majority of these chips are highly specialised to specific experimental protocols. As a result, they are not relevant in the context of day-to-day procedures in most synthetic biology labs.
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as well as other useful tools and resources to make them as accessible as possible.
 
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Revision as of 21:21, 29 October 2017

BostonU_HW

Repository

Explore the MARS Repository

The MARS Repository was created with the purpose of designing generalized chips relevant to synthetic biology.

Microfluidic devices are often highly specific, performing entire specialized experiments on a chip. This means that these chips are not useful or relevant to an average member of the synthetic biology community.

With this in mind, we set out to make the MARS repository. This repository would consist of generalized microfluidic chips that could be useful to any synthetic biologist.

To determine what protocols synbiologist would find useful on a microfluidic devices, we reached out the the Biological Design Center located at Boston University. This community of synthetic biologists gave us insight as to what what procedures are performed every day in the average synbio lab. We were able to identify eight protocols integral to synthetic biology: Cell Lysis, DNA Digestion, Ligation, Transformation, PCR, Fluorescence Testing, Antibiotic Resistance Testing, and Cell Culturing. These eight protocols, as well as Cell Sorting, make up the nine chips currently located in the MARS repository.

Each of the nine chips located in the MARS repository are located within one of three subcategories:



These nine chips, each performing a basic individual protocol, can be combined together to perform more complex synthetic biology experiments.

Each chip is fully documented, providing all the necessary files for replication and usage. These files include:
  1. Design Files
  2. Manufacturing Specifications and Instructions
  3. Usage and Testing protocols


as well as other useful tools and resources to make them as accessible as possible.

After consultation with researchers at BU’s Biological Design Center, we were able to identify nine essential synthetic biology protocols and generalize them into these three categories. After confirming that this chip selection was relevant with an iGEM team poll, we moved on to designing and iterating on chips. The resulting design files, fabrication instructions and usage protocols are housed here - easily accessible to synbiologists and structured in a standardised workflow.

Isolation

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Integer volutpat, mi feugiat blandit feugiat, ante nisl dictum lacus, in egestas ligula nulla eu ex. Quisque vel justo congue, volutpat neque at, placerat nulla. Nam malesuada tellus sed justo pretium, eu vulputate mauris elementum. Donec elementum gravida ipsum id rhoncus.

Modification

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Quantification

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Integer volutpat, mi feugiat blandit feugiat, ante nisl dictum lacus, in egestas ligula nulla eu ex. Quisque vel justo congue, volutpat neque at, placerat nulla. Nam malesuada tellus sed justo pretium, eu vulputate mauris elementum. Donec elementum gravida ipsum id rhoncus.

Isolation

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Cellular Lysis

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DNA Digestion

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Cell Sorting

Modification

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Transformation

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PCR

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Ligation

Quantification

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Antibiotic Resistance

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Fluorescence

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Cell Culturing