Team:BostonU/DataSheet

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<li><a href="#">Considerations</a>  
<li><a href="#">Considerations</a>  
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<li><a href="https://2012.igem.org/Team:BostonU/Advancement">Synthetic Biology Advancement</a></li>
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<li><a href="https://2012.igem.org/Team:BostonU/NEGEM">New England iGEM Regional Meeting</a></li>
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<li><a href="https://2012.igem.org/Team:BostonU/NEGEM">New England iGEM Regional Meeting</a></li>
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<li><a href="https://2012.igem.org/Team:BostonU/Human Practices">Human Practices</a></li>  
<li><a href="https://2012.igem.org/Team:BostonU/Human Practices">Human Practices</a></li>  
<li><a href="https://2012.igem.org/Team:BostonU/Safety">Safety</a></li>
<li><a href="https://2012.igem.org/Team:BostonU/Safety">Safety</a></li>
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JUMP TO...<br>
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<a href="#bu-wellesley_wiki_content">Top</a><br>
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<a href="#DSIntro">Introduction</a><br>
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<a href="#DataApp">Our Approach</a><br>
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<a href="#Proto">Our Prototype</a><br>
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<a href="#fb">Prototype Feedback</a><br>
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<h9>An Introduction to Data Sheets</h9>
<h9>An Introduction to Data Sheets</h9>
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In many fields of engineering, such as electrical engineering, data sheets are a mechanism to document part data such that the behavior of a part is captured and can be shared with other groups. Ideally, the information on these sheets should be robust enough to allow any group to use the part in a different context effectively, given the information captured on these data sheets.
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<img src="https://static.igem.org/mediawiki/2012/9/98/Exdatasheet.png" width = "375px">
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<img src="https://static.igem.org/mediawiki/2012/3/31/Arkin_datasheet.png" width = "375px">
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Canton et al. 2008 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Arkin 2008
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Several groups have started developing the ideas that should be on such a data sheet for DNA parts. Canton et. al included information such as performance, reliability and compatibility. Arkin suggested that general device data, cell-cell communication measurements, DNA-binding protein domain measurements and therapeutic measurements could be documented and shared as well. A sharing standard is sought, but there is still no standard mechanism for sharing part information amongst synthetic biologists.
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<h9>Our Approach</h9>
<h9>Our Approach</h9>
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Our approach to sharing characterization data through a data sheet is to break information into four major sections: <i> General Datasheet Information</i>, <i>Growth/Measurement Conditions</i>, <i>Part Information</i> and <i>Data Analysis</i>.
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<b>General Datasheet Information:</b> Here a brief abstract of the findings of the characterization, author, and date information are included in addition to other relevant comments and conclusions. Also included here would be links or references to related parts and datasheets.
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<b>Growth/Measurement Conditions:</b> In this section, all experimental growth conditions and measurement settings are documented. The experimental conditions include controls used and is similar to an abbreviated methods section in a journal article. This includes who built the parts and what assembly method/protocol are used. It also includes when during the process things are tested and how. Some popular measurement techniques are based on fluorescence of a molecular fluorophore such as microscopy, flow data, or plate reading. Other measurements such as gel imaging and DNA sequencing are taken and these measurements are listed here.
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<b>Part Information:</b> Here we include all part and device information. If the device consists of multiple parts, all parts are listed and if parts have special features, these are also be defined. Additionally, the assembly method and any scars created by the assembly and the vector backbone are defined in this section. This section has enough information to trace back to a full sequence while including abstract functions of these sequences.
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<b>Data Analysis:</b> This section includes a variety of analyses based on the data collected. All analysis in this section derive from the experimental settings described in the Growth/Measurement Conditions section. Depending upon the device, the appropriate analyses might differ, but we start a basic set of analyses such as gel images, sequencing data and flow cytometry bar graphs or curves. For more complicated circuits such as signaling circuits, other analyses might be more appropriate to define its function.
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Currently our datasheets are intended only for human consumption, but we are developing them to be producible and consumable with the Clotho Platform.
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<h9>Our Prototype</h9>
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Below is a prototype of our proposed data sheet. This shows our proposed layout and information for one of our BioBrick constructs, <a href="http://partsregistry.org/Part:BBa_K783067">BBa_K783067</a>. We are working towards creating this data sheet from information stored in our Clotho database. The bottom image shows the start of our coding towards generating the data sheet. We're working closely with our mentor, Evan, to create the scripts needed to call information out of Clotho to automatically produce a data sheet.
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<br>While our current plan is to generate a PDF file for our parts, we ultimately plan to have an html output from this process so future iGEM teams who use Clotho will be able to easily generate the data sheets required for the Registry pages for their submitted Parts. If teams utilize Clotho throughout the summer, this will save those teams a lot of time at the end of the summer when they are submitting their new DNA parts for the competition.
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<img src="https://static.igem.org/mediawiki/2012/5/51/Budatasheet.png" width = "600px">
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<img src="https://static.igem.org/mediawiki/2012/6/67/Budatacode.png" width = "800px">
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<h9>Feedback on the Prototype</h9>
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Inspired from the feed back we received from the Jamboree, we decided to create a forum where the iGEM community can give us feedback to our prototype data sheet design. After you have looked at the prototype, please take a few minutes to go to the <a href="http://ung.igem.org/forum/Topic_List?n=iGEM%3EiGEM%202012">Forum Page</a> and click on comment under the topic of "Help Us to Help iGEM". We really appreciate any type of feedback we receive. Hope to hear from you all!
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<h8>References</h8>
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[1] B. Canton et al. “Refinement and standardization...” Nature Biotech 26(7). 2008.
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[2] A. Arkin "Setting the standard in synthetic biology" Nature Biotech 26(7). 2008.
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Latest revision as of 21:13, 26 October 2012

BostonU iGEM Team: Welcome


Data Sheet




An Introduction to Data Sheets

    In many fields of engineering, such as electrical engineering, data sheets are a mechanism to document part data such that the behavior of a part is captured and can be shared with other groups. Ideally, the information on these sheets should be robust enough to allow any group to use the part in a different context effectively, given the information captured on these data sheets.


    Canton et al. 2008                                                                 Arkin 2008

    Several groups have started developing the ideas that should be on such a data sheet for DNA parts. Canton et. al included information such as performance, reliability and compatibility. Arkin suggested that general device data, cell-cell communication measurements, DNA-binding protein domain measurements and therapeutic measurements could be documented and shared as well. A sharing standard is sought, but there is still no standard mechanism for sharing part information amongst synthetic biologists.

Our Approach

    Our approach to sharing characterization data through a data sheet is to break information into four major sections: General Datasheet Information, Growth/Measurement Conditions, Part Information and Data Analysis.

    General Datasheet Information: Here a brief abstract of the findings of the characterization, author, and date information are included in addition to other relevant comments and conclusions. Also included here would be links or references to related parts and datasheets.
    Growth/Measurement Conditions: In this section, all experimental growth conditions and measurement settings are documented. The experimental conditions include controls used and is similar to an abbreviated methods section in a journal article. This includes who built the parts and what assembly method/protocol are used. It also includes when during the process things are tested and how. Some popular measurement techniques are based on fluorescence of a molecular fluorophore such as microscopy, flow data, or plate reading. Other measurements such as gel imaging and DNA sequencing are taken and these measurements are listed here.
    Part Information: Here we include all part and device information. If the device consists of multiple parts, all parts are listed and if parts have special features, these are also be defined. Additionally, the assembly method and any scars created by the assembly and the vector backbone are defined in this section. This section has enough information to trace back to a full sequence while including abstract functions of these sequences.
    Data Analysis: This section includes a variety of analyses based on the data collected. All analysis in this section derive from the experimental settings described in the Growth/Measurement Conditions section. Depending upon the device, the appropriate analyses might differ, but we start a basic set of analyses such as gel images, sequencing data and flow cytometry bar graphs or curves. For more complicated circuits such as signaling circuits, other analyses might be more appropriate to define its function.

    Currently our datasheets are intended only for human consumption, but we are developing them to be producible and consumable with the Clotho Platform.

Our Prototype

    Below is a prototype of our proposed data sheet. This shows our proposed layout and information for one of our BioBrick constructs, BBa_K783067. We are working towards creating this data sheet from information stored in our Clotho database. The bottom image shows the start of our coding towards generating the data sheet. We're working closely with our mentor, Evan, to create the scripts needed to call information out of Clotho to automatically produce a data sheet.

    While our current plan is to generate a PDF file for our parts, we ultimately plan to have an html output from this process so future iGEM teams who use Clotho will be able to easily generate the data sheets required for the Registry pages for their submitted Parts. If teams utilize Clotho throughout the summer, this will save those teams a lot of time at the end of the summer when they are submitting their new DNA parts for the competition.








Feedback on the Prototype

    Inspired from the feed back we received from the Jamboree, we decided to create a forum where the iGEM community can give us feedback to our prototype data sheet design. After you have looked at the prototype, please take a few minutes to go to the Forum Page and click on comment under the topic of "Help Us to Help iGEM". We really appreciate any type of feedback we receive. Hope to hear from you all!

    References
    [1] B. Canton et al. “Refinement and standardization...” Nature Biotech 26(7). 2008.
    [2] A. Arkin "Setting the standard in synthetic biology" Nature Biotech 26(7). 2008.



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