Project Description

From 2007.igem.org

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  Our project for iGEM 2007 involves modeling the dynamics of the spread of an epidemic within a population.  The
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== Overview ==
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model will be multiscale, specifically covering the molecular biology of the phage-host interaction, the spread of
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With the end of the summer on the horizon, now is the time to publish a short description of your team's project on the iGEM 2007 wiki (see the [https://2007.igem.orgcalendar.cgi advanced schedule]).  These descriptions, along with your finished team website, establish the identity of iGEM online and provide inspiration to future iGEM teams. Your project description will broadcast your accomplishments to the rest of the Synthetic Biology community and the world at large.
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the phage within an isolated subpopulation, and the spread of the phage between artificially connected
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subpopulations.  Integrating these levels of modeling to produce varying high-level population epidemic behavior by
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changing, for example, promoter strengths for the production of relevant proteins is one of the key aspects of our
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project.  Building an understanding of high-level dynamics from the very lowest level of organization will
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demonstrate our ability to more accurately predict the epidemiological outcome.
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  For our host and phage we will use E. Coli and lambda phage respectively.  We select this host-phage pair because
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The project description should be one or two paragraphs in length and contain the level of detail you would find in the abstract of a peer-reviewed article, without necessarily the formality. Remember that you can update your description as your project develops, but plan on writing a complete version now. We will use your project description to create an iGEM 2007 world map and in other promotional material.  Besides, after seeing all the other descriptions you may realize that a team you thought of as your competitor could actually be your collaborator!
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they are both so well understood and documented and therefore we can more easily model their interaction,  
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particularly at the molecular level. Lambda phage is also interesting because it can either immediately replicate
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itself and kill the host cell or it can insert its DNA and lie dormant.  This adds a degree of flexibility to our
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model that allows us to check the model robustness for slightly different phage. As part of the project we have
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designed a reporter plasmid to generate florescent proteins to indicate which pathway the virus has taken.  This
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plasmid, along with the use of a phage modified to be florescent, will allow us to determine how the population acts
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and verify our models.
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  At the highest level of our modeling we will use air traffic data with 96-well plates and a liquid handling
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While some teams have elected to host their team website on their own servers or on [http://openwetware.org/wiki/IGEM OpenWetWare], the official project description must be published on the iGEM 2007 wiki.
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system to indicate how a virus might spread via air traffic.  Since a person can now get around the world before a
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virus manifests symptoms, this information is relevant to epidemiological studies.  Using this model we can examine
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== How to add your project description ==
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how shutting down certain airports or groups of airports might help to limit or prevent the spread of a virus
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To avoid namespace collisions (which occur when different pages are created with the same name), all of your team's pages should be named by convention by prefixing your team name and a slash to the desired page's name.  This creates a [http://en.wikipedia.org/wiki/Wikipedia:Subpages Subpage].  The [[Example|Example Team]] demonstrates this: the [[Example/Project Description | Project Description]] page for the Example team, (the team is named ''Example'') is located at:
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through air travel.
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<nowiki>[[Example/Project Description]]</nowiki>.
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While the Example team's main page is located at:
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<nowiki>[[Example]]</nowiki>
 +
 
 +
For more information on how subpages work, please consult the [http://en.wikipedia.org/wiki/Wikipedia:Subpages mediawiki subpage documentation].
 +
 
 +
== Project Descriptions Guidelines and Examples ==
 +
This year, your project description
 +
* should briefly tell the story of the members and motivations of your team,
 +
* should describe the goal of your team's project, with enough background information to demonstrate to one of your peers why your project is interesting, and
 +
* should provide a summary of your team's progress toward that goal.
 +
 
 +
What follows are three project descriptions published in the middle of the summer last year by iGEM 2006 teams.  Use them as a reference for writing your own, but consider expanding upon their form  - no guidance was given last year.  Please do tell a little about the story of your team.  And remember, if you follow the links, you can see how all of these descriptions evolved and changed as time marched towards the Jamboree and the teams refined their projects.
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 +
 
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; [http://www.macteria.co.uk/6.html An Arsenic Biosensor] - University of Edinburgh iGEM 2006 team
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: The aim is to develop a bacterial biosensor that responds to a range of arsenic concentrations and produces a change in pH that can be calibrated in relation to arsenic concentration.  The novelty of this approach will help many under-developed countries, in particular Bangladesh, to detect arsenic contamination in water.  The proposed device will be more economical, portable and easier to use in comparison with other detectors.  After considerable research and further brainstorming, we have designed three possible mechanisms to attain our goal.  Given the stipulated time for the competition we intend to achieve mechanism 2 which is a 4 device system with three detectable outputs based on whether there is no arsenic, 5 ppb of arsenic or 20 ppb of arsenic present. So far device 1 for the system is almost in the stages of completion.  Two biobrick parts ArsR and lacZ have already been added to the registry.  Characterization of the parts required for device 2 to be finished very soon. A realistic model of the whole system is being developed to help us make reasonable predictions about different parts of the system
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; [http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser Molecular Prey-Predator Oscillator] - Imperial College iGEM 2006 team
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: Oscillators are a fundamental building block in many fields of engineering and are a widespread phenomenon in biology. Building a biological oscillator is thus a critical step forward in the field of Synthetic Biology. The major goal of Imperial College’s 2006 entry into the iGEM competition was to create a stable biological oscillator, improving on past designs such as Elowitz’s repressilator. The team investigated into natural biological oscillators and sought to mimic Lotka-Volterra predator-prey interactions with a molecular system. The model was adapted to molecular interactions between prey (n-acyl homoserine lactone (AHL)) and predator (AiiA (AHL-lactonase) + LuxR). The design strategy of the project was an engineering based cycle of specification, design, modeling, testing, and implementation. Parts were constructed and individually tested before the final construct was assembled. Our ongoing parts testing shows correlation to our mathematical models, suggesting that the design could be successful.
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; [http://openwetware.org/index.php?title=IGEM:MIT/2006/Blurb&oldid=45354 Engineering Pleasant-Smelling Bacteria] - MIT iGEM 2006 team
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: This summer, MIT's iGEM 2006 team is developing bacteria that smell pleasant. We have inserted several genes into bacterial genomes to make the cells produce wintergreen, jasmine, floral, and fruit scents. Scents can act as natural biological tags and have many extended applications. By attaching the scent tag to a case-sensitive promoter, we can engineer a cellular system to report on environmental conditions. Also, since E. coli naturally produce a fecal smelling compound, we feel that engineering our system will be useful to scientists worldwide as it will make lab work with E. coli bacteria a little less painful. Other bacteria are responsible for producing human odor problems in the mouth, armpits, and feet. By implementing our system in these foul smelling bacteria, we could potentially develop bacterial deoderant. In addition, we could implement our system in yeast, thereby producing new flavors and scents in bread and beer.

Latest revision as of 19:58, 31 July 2007

Overview

With the end of the summer on the horizon, now is the time to publish a short description of your team's project on the iGEM 2007 wiki (see the advanced schedule). These descriptions, along with your finished team website, establish the identity of iGEM online and provide inspiration to future iGEM teams. Your project description will broadcast your accomplishments to the rest of the Synthetic Biology community and the world at large.

The project description should be one or two paragraphs in length and contain the level of detail you would find in the abstract of a peer-reviewed article, without necessarily the formality. Remember that you can update your description as your project develops, but plan on writing a complete version now. We will use your project description to create an iGEM 2007 world map and in other promotional material. Besides, after seeing all the other descriptions you may realize that a team you thought of as your competitor could actually be your collaborator!

While some teams have elected to host their team website on their own servers or on OpenWetWare, the official project description must be published on the iGEM 2007 wiki.

How to add your project description

To avoid namespace collisions (which occur when different pages are created with the same name), all of your team's pages should be named by convention by prefixing your team name and a slash to the desired page's name. This creates a Subpage. The Example Team demonstrates this: the Project Description page for the Example team, (the team is named Example) is located at: 

[[Example/Project Description]].

While the Example team's main page is located at: 

[[Example]]

For more information on how subpages work, please consult the mediawiki subpage documentation.

Project Descriptions Guidelines and Examples

This year, your project description

  • should briefly tell the story of the members and motivations of your team,
  • should describe the goal of your team's project, with enough background information to demonstrate to one of your peers why your project is interesting, and
  • should provide a summary of your team's progress toward that goal.

What follows are three project descriptions published in the middle of the summer last year by iGEM 2006 teams. Use them as a reference for writing your own, but consider expanding upon their form - no guidance was given last year. Please do tell a little about the story of your team. And remember, if you follow the links, you can see how all of these descriptions evolved and changed as time marched towards the Jamboree and the teams refined their projects.


An Arsenic Biosensor - University of Edinburgh iGEM 2006 team
The aim is to develop a bacterial biosensor that responds to a range of arsenic concentrations and produces a change in pH that can be calibrated in relation to arsenic concentration. The novelty of this approach will help many under-developed countries, in particular Bangladesh, to detect arsenic contamination in water. The proposed device will be more economical, portable and easier to use in comparison with other detectors. After considerable research and further brainstorming, we have designed three possible mechanisms to attain our goal. Given the stipulated time for the competition we intend to achieve mechanism 2 which is a 4 device system with three detectable outputs based on whether there is no arsenic, 5 ppb of arsenic or 20 ppb of arsenic present. So far device 1 for the system is almost in the stages of completion. Two biobrick parts ArsR and lacZ have already been added to the registry. Characterization of the parts required for device 2 to be finished very soon. A realistic model of the whole system is being developed to help us make reasonable predictions about different parts of the system
Molecular Prey-Predator Oscillator - Imperial College iGEM 2006 team
Oscillators are a fundamental building block in many fields of engineering and are a widespread phenomenon in biology. Building a biological oscillator is thus a critical step forward in the field of Synthetic Biology. The major goal of Imperial College’s 2006 entry into the iGEM competition was to create a stable biological oscillator, improving on past designs such as Elowitz’s repressilator. The team investigated into natural biological oscillators and sought to mimic Lotka-Volterra predator-prey interactions with a molecular system. The model was adapted to molecular interactions between prey (n-acyl homoserine lactone (AHL)) and predator (AiiA (AHL-lactonase) + LuxR). The design strategy of the project was an engineering based cycle of specification, design, modeling, testing, and implementation. Parts were constructed and individually tested before the final construct was assembled. Our ongoing parts testing shows correlation to our mathematical models, suggesting that the design could be successful.
Engineering Pleasant-Smelling Bacteria - MIT iGEM 2006 team
This summer, MIT's iGEM 2006 team is developing bacteria that smell pleasant. We have inserted several genes into bacterial genomes to make the cells produce wintergreen, jasmine, floral, and fruit scents. Scents can act as natural biological tags and have many extended applications. By attaching the scent tag to a case-sensitive promoter, we can engineer a cellular system to report on environmental conditions. Also, since E. coli naturally produce a fecal smelling compound, we feel that engineering our system will be useful to scientists worldwide as it will make lab work with E. coli bacteria a little less painful. Other bacteria are responsible for producing human odor problems in the mouth, armpits, and feet. By implementing our system in these foul smelling bacteria, we could potentially develop bacterial deoderant. In addition, we could implement our system in yeast, thereby producing new flavors and scents in bread and beer.
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