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$179 pledged of $850 goal
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By Ben Kellman
$179 pledged of $850 goal
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About

Preface

We have already built the competition ready version of SBiDer! You can view our tool, extensive documentation and tutorials on our iGEM team wiki at:  http://2014.igem.org/Team:UCSD_Software

This kickstarter page is here to get us the last few dollars we need to resolve a registration issue that arose due to a last minute rule change from iGEM HQ.  The goal is set for $850 USD to make sure we meet our goal given the short notice (the money disappears if you don't).  We would be glad for the $850 but we can make use of up to $3,000.  Any excess funds, if we are so lucky, will be forwarded to next year's UCSD iGEM team.  That team will continue this work.

The competition starts October 30th so we need this fundraising to move fast.

Goal

The UCSD iGEM team built a web tool that allows users to visualize the network of synthetic genetic circuits that can interact with one another. We have also done some basic modeling about how these synthetic circuits will interact. By building this tool, we ease the difficulty of designing complex genetic circuits. Instead of focusing on the optimization of a user’s circuit design as previous tools have done, we instead focused on the representation of existing knowledge and how to leverage that knowledge to facilitate: 1. the reuse of existing components in a user’s design, 2. access to data for modeling, and 3. access to the literature for educational purposes. 

Aims/Deliverables

  • Network database of genetic devices  -  We have connected known genetic devices together via device input and outputs to create a network of devices that could potentially be linked together. We define a genetic device as a DNA construct transformed into cells that can cause expression of some protein in response to stimuli (or input). While prior work in this field has involved the creation a library of “modules” and components that can be used in a genetic circuit design, these libraries are either not accessible publicly or difficult to use. We started this project by mining an existing but under-descriptive database. We built upon this foundation by incorporating data from the literature - this data includes not only the device design, but also literature references and characterization data. We also provide a framework by which our database can be updated through our web tool client.
  • Web interface for novel genetic device discovery  -  This interface will allow researchers to query our database network with logic operators to elicit subnetworks that constitute a composite genetic device that takes a particular  set of inputs that lead to a specific or set of outputs; the use of logical operators such as “AND”, “OR”, and “NOR” is derived from the electrical engineering culture that has motivated the field. The novelty of our project stems from the fact that our tool not only allows for part discovery and novel genetic device discovery, but it will also be a tool to help facilitate researchers in access data buried in the scientific literature. Younger researchers may benefit from this alternative method for accessing the literature especially if they are unfamiliar with the current mode of searching the literature for particular authors.
  • Validation of Network and Modeling  -  A challenge here was determining whether or not the genetic devices returned by our web application were novel and biologically viable.  Novelty was achieved using network analytic techniques describing the increased connectivity and complexity of the database relative to the input circuitry.  Validity of our initial network was determined using biochemical knowledge and existing validations from the literature. With the aggregated characterization data we also modeled the steady state behavior of these circuits; the dynamic behavior of the circuit is important in determining its overall behavior.

Educational Implications

The UCSD iGEM team is composed of students with a diverse academic background. Most students will have either a more biological/experimental background while others will have a more computational background. Some of the challenges we faced in this project included teaching these students basic and more complicated programming concepts. Also construction and validation of the network will involve considerable understanding of biochemical mechanisms. We are also inviting many younger students to take part in our lessons who will have no significant academic training. By inviting younger students, we hope to expose students to interdisciplinary research early on in their academic career. Several of the current iGEM students have begun discussing extending our tool for next year’s competition.

Risks and challenges

Our primary challenge after success at the iGEM competition will be disseminating our tool. This will be achieved through standard channels such as publication.

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Support

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    Pledge $5 or more About $5

    A high five. (via email for those outside of San Diego county)

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    A sincere thank you note. + a highfive

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    A sincere thank you note signed by the whole team. + a highfive

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    A signed picture of the SBiDer team.

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    One of our UCSD iGEM competition t-shirts.

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    Your company's logo on our presentation at the iGEM competition.
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Funding period

- (11 days)