Team:UCSD Software/Safety

From 2014.igem.org

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                    <li><div class="btn btn-lg" id="safety">Safety</div></li>
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                  <h1>SBiDer</h1>
 
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                  <p>Our site</p>
 
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                  <h1>Another example headline.</h1>
 
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                  <p>Cras justo odio, dapibus ac facilisis in, egestas eget quam.</p>
 
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                  <p><a class="btn btn-lg btn-primary" href="#" role="button">Learn more</a></p>
 
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                  <h1>One more for good measure.</h1>
 
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                  <p>Nullam id dolor id nibh ultricies vehicula ut id elit.</p>
 
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<h1>SBiDer: Synthetic Biocircuit Developer</h1>
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</style>
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<h3>Abstract</h3>
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        <nav class="navbar nav-justified" role="navigation" id='nav'>
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                <div class="btn-group  btn-group btn-group-justified">
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                    <div class="btn btn-lg " id="home">Home</div>
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                    <div class="btn btn-lg " id="team">Team</div>
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                    <div class="btn btn-lg " id="project">Project</div>
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                    <div class="btn btn-lg " id="doc">Documentation</div>
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                    <div class="btn btn-lg" id="notebook">Notebook</div>
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                    <div class="btn btn-lg" id="safety">Safety</div>
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                    <div class="btn btn-lg" id="attributions">Sponsors</div>
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                    <div class="btn btn-lg" id="achieve">Achievements</div>
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                    <div class="btn btn-lg" id="logo"><a href = "https://igem.org/Main_Page"><img src = "http://i.imgur.com/mGHw11P.png?1"></a></div>
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<h1>Safety</h1>
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<h3>Safety Training</h3>
<p>
<p>
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Genetic circuits are often difficult to engineer, requiring months to design, build, and test each individual genetic device involved in the circuit. SBiDer, a web tool developed by the UCSD Software iGEM team, will leverage existing devices to construct a database with consideration for the function of each device interpreted as boolean logic. The data can be queried by the user through SBiDer's visual interface to explore circuit designs. The displayed circuit's literature reference, characterization data, and images of included devices can be viewed through the built-in table. Basic validation of the circuit performance is also provided within in the interface. SBiDer's web of information can be expanded through user-generated additions to the database to improve the efficiency of the application and the accuracy of the models.
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Safety is an important aspect of the iGEM project requirements; we understand that and take safety training seriously. As a software team, we do no work in any wet lab capacity, but just as safety training teaches best practices and behaviours in lab, we have used our safety training to employ best practices and behaviours in developing software. We have covered topics including but not limited to: using GitHub, commenting/documenting code, and how to abstract/re-factor code. </p>
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<p> As a team, we were really interested in Wet Lab testing (and validation) of our work. Unfortunately, given that this is our first year at iGEM and hence we received limited funding and resources, we had to prioritize certain other tasks over wet lab work. We'll still likely be involved in UCSD's iGEM team next year, and will push for additional funding and resources to make wet lab testing possible. </p>
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<h1>Project Description</h1>
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We did not use formal lab safety materials as we did not work in any lab at all.  
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<h3>Problem Statement</h3>
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Synthetic genetic circuits created by synthetic biologists have yielded exciting applications such as biofuels production and cancer killing bacteria. These circuits are often difficult to engineer, requiring months to design, build, and test each individual genetic device involved in the circuit. Although there are many genetic devices that have been built, re-using these devices often requires a time-consuming review of the literature. The UCSD Software iGEM team will address this challenge by creating a web-tool that leverages existing genetic devices to create complex genetic circuits. We will accomplish this by:
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<li>building a comprehensive database that captures the behavior, composition, and interactions of existing genetic devices in the literature</li>
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<h3>Who is responsible for biological safety at our institution?</h3>
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<li>constructing and visualizing the network of all synthetic genetic circuits that can interact with one another</li>
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<li>devising algorithms to search this network for the set of genetic devices that can be used to construct a complex genetic circuit.</li>
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<li>Perform some basic validation via kinetic modelling.</li>
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<h3>Aim 1 - Building a Database</h3>
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We will mine the scientific literature for existing genetic devices and then construct a database that captures device characteristics such as:
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Department of Environment, Health & Safety at UCSD. The project has not been discussed with the department as we anticipate no safety hazards. You can find the biosafety guidelines of our institution <a href = "http://blink.ucsd.edu/safety/research-lab/biosafety/">here.</a>
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<li>composition of devices</li>
 
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We will design our database by rigorously constructing an entity relationship diagram and then normalizing these relationships to construct tables for a relational database.
 
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<h3>Aim 2 - Constructing Network of Interacting Devices</h3>
 
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We will connect known genetic devices together via device input and outputs to create a network of devices that can interact. 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). We will  develop a web interface to facilitate access to the complex network that we have constructed. Our Web interface makes extensive use of Cytoscape, an open source bioinformatics software package for metabolic network visualization and simulation.  In addition, the interface will generate SBOL Visual Images, a standard language that is easily understood by synthetic biologists all over the world.  Users can also update our database with additional devices through this interface.  Using the Cynetshare framework, users can share their circuit designs</p>
 
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<h3>Aim 3 - Searching the Network</h3>
 
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This interface will allow researchers to query our database network for a circuit design expressed as logical operators such as “AND”, “OR”, and “NOR”, and retrieve the subnetwork of genetic devices that satisfies the circuit design. To Perform our search  we modified several traditional graph search algorithms to traverse this graph, including but not limited to Prim’s algorithm (minimum spanning tree), Dijkstra’s algorithm and a breadth-first search. Results are visualized graphically in our web interface
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Also, you may find the regulations that govern biosafety in general in research laboratories in the United States <a href = "http://sis.nlm.nih.gov/enviro/labsafety.html">here.</a>
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<h3>Risks of our projects in the future</h3>
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This project has been constructed exclusively in silico. Therefore, we anticipate no risk or safety issues for our team from any wetlab experiments. However, as we are only developing software and not interacting at all with any biological components, we cannot foresee any new safety risks in combining pathogens in any new and novel way. Working and constructing new and novel biological circuits are at the risk of the experimenter. We cannot accept responsibility for any kind of hazards or risk arising from the results returned from our work. The safety of our fellow scientists is one of our utmost priorities, hence, any lab that wishes to use SBiDer for their own research purposes must, at all times, keep the biosafety regulations of their own institution and country in mind.
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<p><a href = "https://igem.org/Safety/Safety_Form?team_id=1353">Click here</a> to view our completed safety form.</p>
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<li><a href="https://2014.igem.org/Team:UCSD_Software">Home</a> </li>
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<li><a href="https://2014.igem.org/Team:UCSD_Software/Safety">Safety</a> </li>
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Latest revision as of 02:46, 18 October 2014


Safety

Safety Training

Safety is an important aspect of the iGEM project requirements; we understand that and take safety training seriously. As a software team, we do no work in any wet lab capacity, but just as safety training teaches best practices and behaviours in lab, we have used our safety training to employ best practices and behaviours in developing software. We have covered topics including but not limited to: using GitHub, commenting/documenting code, and how to abstract/re-factor code.

As a team, we were really interested in Wet Lab testing (and validation) of our work. Unfortunately, given that this is our first year at iGEM and hence we received limited funding and resources, we had to prioritize certain other tasks over wet lab work. We'll still likely be involved in UCSD's iGEM team next year, and will push for additional funding and resources to make wet lab testing possible.

We did not use formal lab safety materials as we did not work in any lab at all.

Who is responsible for biological safety at our institution?

Department of Environment, Health & Safety at UCSD. The project has not been discussed with the department as we anticipate no safety hazards. You can find the biosafety guidelines of our institution here.

Also, you may find the regulations that govern biosafety in general in research laboratories in the United States here.

Risks of our projects in the future

This project has been constructed exclusively in silico. Therefore, we anticipate no risk or safety issues for our team from any wetlab experiments. However, as we are only developing software and not interacting at all with any biological components, we cannot foresee any new safety risks in combining pathogens in any new and novel way. Working and constructing new and novel biological circuits are at the risk of the experimenter. We cannot accept responsibility for any kind of hazards or risk arising from the results returned from our work. The safety of our fellow scientists is one of our utmost priorities, hence, any lab that wishes to use SBiDer for their own research purposes must, at all times, keep the biosafety regulations of their own institution and country in mind.

Click here to view our completed safety form.

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