Team:BostonU/Acknowledgements

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<th colspan="2" scope="col"><h2>CIDAR Lab</h2></th>
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     <th scope="col"><header3>Professor Douglas Densmore</header3><br>Primary Investigator, CIDAR Lab<br><br>We would like to thank Professor Densmore for his lab space and his support throughout the summer.</th>
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     <td scope="col"><h3>Professor Douglas Densmore</h3><strong>Primary Investigator, CIDAR Lab at Boston University</strong><br>We would like to thank Professor Densmore for use of his lab space and his support throughout the summer.</td>
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         <th scope="col">As synthetic biology continues to expand, researchers are producing a greater variety of novel and innovative genetic circuits. This research revolves around a standard design-build-test cycle that defines the timeline of a project from its conception. The design and assembly of constructs depends on a thorough understanding of their individual components, making thorough part characterization data essential. The fact that there is currently little standardization in DBT workflows and poorly documented standard parts libraries represents an increasingly significant stymying factor to the growth of the field, especially as more laboratories continue to share resources and data. We seek to strengthen the traditional design-build-test cycle fundamental to synthetic biology with a formalized workflow defined by bio-design automation software tools and built upon a thoroughly characterized library of parts.</th>
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<td scope="col"><h3>Dr. Ernst Oberortner</h3><strong>Postdoctoral Researcher, CIDAR Lab at Boston University</strong><br>We would also like to thank Dr. Ernst Oberortner for his help with <a href="http://eugenecad.org/" target="_blank">Eugene</a> and the <a href="https://2014.igem.org/Team:BostonU/Encoder">priority encoder</a> design.</td>
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<h2>Motivation and Background</h2>
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We will complete a library of basic parts currently composed of existing ribosomal binding sites and terminators from the <a href="http://cidarlab.org/" target="_blank">CIDAR Lab</a> by adding a series of <a href="https://2014.igem.org/Team:BostonU/TandemPromoters">tandem promoters</a>, <a href="https://2014.igem.org/Team:BostonU/FusionProteins">fusion proteins</a>, and <a href="https://2014.igem.org/Team:BostonU/Backbones">vector backbones</a>. These parts will will then be cloned using the <a href="https://2014.igem.org/Team:BostonU/MoClo">MoClo</a> assembly method in multiplexing reactions to create a library of transcriptional units. Data will be gathered for these TUs using flow cytometry in conjunction with the <a href="https://synbiotools.bbn.com/" target="_blank">TASBE Tools</a> developed at <a href="http://www.bbn.com/" target="_blank">BBN Technologies</a> to characterize all the parts in our library. The TASBE Tools allow for calibrated measurement of gene expression in absolute units of fluorescence, and will allow for effectively designing multi-TU genetic circuits. We hypothesize that guiding the design and construction of complex circuits with our characterization data and workflow will streamline the traditional design-build-test cycle and aid in a more efficient process for the assembly of novel devices.
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As a measurement team, we will also use our flow cytometer and the TASBE Tools to enhance the documentation of existing Registry parts. We will contribute our entire basic parts and TU libraries to the Registry to enable other synthetic biology groups to rely on well-characterized parts and methods for their research.
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<td scope="col"><h3>Orit Shaer</h3><strong>Primary Investigator, HCI Lab at Wellesley College</strong><br>We would like to thank Professor Orit Shaer for teaching us more about Bio-design Automation and for allowing us to collaborate with her lab to learn more about integrating computational tools with experimental lab work. We would also like to thank the Human Computer Interaction (HCI) lab at Wellesley for allowing us to use the Google Glass in our lab.
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<td scope="col"><h3>Ariela Esmurria</h3><br>We would like to thank high school student Ariela Esmurria for helping us with the Interlab study.</td>
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<td scope="col"><h3>Diego Cuerda Gil</h3><br>We would like to thank Diego Cuerda Gil for his help in finishing cloning origins of replication.</td>
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<td colspan="2" scope="col"><br><h2>Corporate Collaborations</h2></td>
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        <td scope="col"><h3>Dr. Jacob Beal</h3><br><strong>Research Scientist, BBN Technologies</strong><br>We would like to thank Dr. Jacob Beal from BBN Technologies for teaching us how to use the BBN Synthetic Biology <a href="https://synbiotools.bbn.com/">TASBE Tools</a> and helping us troubleshoot the software if an error happened.</td></tr>
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<td colspan="2" scope="col"><br><h2>Contributions</h2></td>
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        <td scope="col" colspan="2">The wetlab work was completed by Yash Agarwal (fusion proteins), Alan Pacheco (new vector backbones), and Katie Lewis (tandem promoters). Our advisor, Traci Haddock, and our mentor, Evan Appleton, trained us in the lab and provided us troubleshooting advice throughout the project. All team members and advisors contributed to the wiki. Alan designed the wiki framework. Ariela Esmurria, a high school student volunteer, did the wetlab work for the Interlab Study.
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The genetic device graphics were all generated from <a href = "http://www.pigeoncad.org/"> Pigeon</a>.
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<p>Bhatia, S. & Densmore, D. Pigeon: a design visualizer for synthetic biology. ACS Synth. Biol. 2, 348–350 (2013). </p>
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        <td scope="col" colspan="2">We'd like to thank all of our sponsors for their generous support. Without the support from the following Boston University departments and corporate sponsors, we would not have been able to compete in iGEM. We would specifically like to thank: <ol type="I"><li>Financial sponsors: Boston University, UROP, and Center of Synthetic Biology (CoSBi) <li>Supplies sponsors: Tecan, BD, Epoch, BioLabs <li>BDAC for sponsoring our NEGEM lunches </ol>
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<br><br><center><strong><h3>Thank you very much! Without your generous support, this project would not have been possible!</h3></strong><center></td>
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Latest revision as of 02:31, 18 October 2014



Acknowledgements

CIDAR Lab

Professor Douglas Densmore

Primary Investigator, CIDAR Lab at Boston University
We would like to thank Professor Densmore for use of his lab space and his support throughout the summer.

Dr. Ernst Oberortner

Postdoctoral Researcher, CIDAR Lab at Boston University
We would also like to thank Dr. Ernst Oberortner for his help with Eugene and the priority encoder design.

Academic

Orit Shaer

Primary Investigator, HCI Lab at Wellesley College
We would like to thank Professor Orit Shaer for teaching us more about Bio-design Automation and for allowing us to collaborate with her lab to learn more about integrating computational tools with experimental lab work. We would also like to thank the Human Computer Interaction (HCI) lab at Wellesley for allowing us to use the Google Glass in our lab.

Ariela Esmurria


We would like to thank high school student Ariela Esmurria for helping us with the Interlab study.

Diego Cuerda Gil


We would like to thank Diego Cuerda Gil for his help in finishing cloning origins of replication.


Corporate Collaborations

Dr. Jacob Beal


Research Scientist, BBN Technologies
We would like to thank Dr. Jacob Beal from BBN Technologies for teaching us how to use the BBN Synthetic Biology TASBE Tools and helping us troubleshoot the software if an error happened.


Contributions
The wetlab work was completed by Yash Agarwal (fusion proteins), Alan Pacheco (new vector backbones), and Katie Lewis (tandem promoters). Our advisor, Traci Haddock, and our mentor, Evan Appleton, trained us in the lab and provided us troubleshooting advice throughout the project. All team members and advisors contributed to the wiki. Alan designed the wiki framework. Ariela Esmurria, a high school student volunteer, did the wetlab work for the Interlab Study.

The genetic device graphics were all generated from Pigeon.

Bhatia, S. & Densmore, D. Pigeon: a design visualizer for synthetic biology. ACS Synth. Biol. 2, 348–350 (2013).



Sponsors
We'd like to thank all of our sponsors for their generous support. Without the support from the following Boston University departments and corporate sponsors, we would not have been able to compete in iGEM. We would specifically like to thank:
  1. Financial sponsors: Boston University, UROP, and Center of Synthetic Biology (CoSBi)
  2. Supplies sponsors: Tecan, BD, Epoch, BioLabs
  3. BDAC for sponsoring our NEGEM lunches


Thank you very much! Without your generous support, this project would not have been possible!







Our Sponsors

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