Team:Queens Canada/flight

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<img src="http://2012.igem.org/wiki/images/c/cf/Trollface.jpg" align="right" height="200"></img>
<h1>Flight of the Flagellin</h1>
<h1>Flight of the Flagellin</h1>
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<b>Flight of the Flagellin takes protein structures and give them a hilarious, fun, new perspective.</b><br>
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<b>Flight of the Flagellin takes protein structures and give them a hilarious, fun, new perspective.</b>
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<p>As a part of our 2012 iGEM project, we plan on using dance to explain concepts associated with synthetic biology, as well as our own research.
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</p>
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<br>
<br>
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<p>We will make dance into our own unique tool for teaching others scientific concepts, as an alternative to use powerpoint presentations.
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<p>What is this page really? Well, we recently discovered how easy it is to import 3D protein structures into an open-source flight simulator called FlightGear. It seems pretty ridiculous, but this could be a great way of teaching protein or molecular structure to people both young and old. It's also really surreal to be bringing some of the smallest units of life, and exploring them, in the setting of some of the largest man-made vehicles.</p>
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</p>
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<p>Flying is just fun. Lots of people play flight simulators just to fly around some generated landscape. Now in this case, you're flying our somebody's hard earned scientific data instead. With the amount of work that went into getting this data, it's hard to say whether we're taking full advantage of it and using it to its full potential, or just completely bastardizing it.</p>
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<br>
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<p>Something like this could also lead into new games, like EteRNA or Fold-it, in which the player is assigned the puzzle of solving a protein or RNA structure. The higher your score, the better you did, and your solution can actually contribute to scientific data. More specifically, we can swap out that plane model for, say, a ligand. Then, using this same idea, we can power docking experiments, in which players have to try and land a ligand in the active site of an enzyme, for example. This kind of computer modelling is common practice in drug design.</p>
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<p>In our presentation at the 2012 iGEM conference, we plan on incorporating dance into our presentation as a means of conveying our ideas, and demonstrating our work in a unique method. After the iGEM competition, our group hopes to continue sharing our ideas, and creating new routines to help teach people about other scientific concepts from any field of research.
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<hr>
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</p>
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<h1>The Game</h1>
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<img src="http://2012.igem.org/wiki/images/f/f6/Fgfs-screen-006.png" height="200" align="right"></img>
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<p>Download and Installation: </p>
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<p>First download and install the game from <a href="http://www.flightgear.org/">http://www.flightgear.org/</a>
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<p>Next, download and install the Flight of the Flagellin Maps! We wish we could make this a little bit easier but, we're inexperienced! Follow these step by step instructions:</p>
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<ul>
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<li>Download and extract the map files: <a href="http://ubuntuone.com/0tDBQNcyBm43iPw3SW7St8">proteinflight.zip</a>
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<li>Install the map files:
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<ol>
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<li>Edit Objects/w080n40/w072n42/1777947.stg with any simple text editor.
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<li>Scroll to the bottom of the file.
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<li>Replace YOURPATHHERE with the file path to your downloads folder, or wherever you choose to store the protein models.
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<li>Copy the Objects and Terrain folder to your Flightgear Scenery folder, ex: c:\Program Files\FlightGear\data\Scenery.
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</ol>
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<li>Run flightgear and pick to take off from the Boston Airport! (ID:KBOS)
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</ul>
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<img src="http://2012.igem.org/wiki/images/f/fd/Helicopter.png" height="200" align="right"></img>
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<p>Below are a series of challenges that we have made in our level:</p>
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<h1>Interested?</h1>
 
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There are many different ways to be involved with our group. We are
 
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seeking people to dance, as well as people interested helping with
 
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funding, filming, music or other media. More importantly, we are also
 
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looking for people who are interested in contributing advice, their own art, or any thoughts on what we'll be working on.
 
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Please write us at <a href="mailto:synthetiq@qgemteam.com">synthetiq@qgemteam.com</a>.
 
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We are looking forward to hearing from you!
 
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<h3>Challenge #1: Flight of the Flagellin</h3>
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</body>
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<p>
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</html>
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In your glider, fly down through the helical constant domain of the flagellin monomer, landing safely in the Boston airport. (Right in time for the world finals :) ). Bonus: The larger the aircraft you can fly through, the better.</p>
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<!-- Body Language:
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<p>Starting Coordinates:<br>
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Why not just use a diagram, or 3D animation?
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Latitude:    42.472766<br>
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This is definitely a question we need to consider when making our routine. And the answer to that question is body language. The way we interpret another human or animal's movements is very different from what can be represented with a diagram or animation. In a way, it adds a 4th dimension: expression.
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Longitude:    -71.028729<br>
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Altitude ASL: 27059.96<br>
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Heading:     166.5<br>
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</p>
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For example, imagine you're waiting at a bus stop and an old friend that happens to be walking by notices and cheerily walks over the say hi. Your natural response is excitement and happiness to be seeing your friend. You immediately respond with a smile. On the other hand, imagine you're at a bus stop and a stranger is walking by, angrily. Your natural response is defensive. You interpret the emotion and sense a potential danger.
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<h3>Challenge #2: Red Fluorescent Protein</h3>
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<p>
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Land a helicopter on the chromophore of RFP. To make it easier, we've put a nice flat landing pad there for you.</p>
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<img src="http://2012.igem.org/wiki/images/3/3f/Beta.png" height="200" align="right"></img>
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This applies when we dance as well. Rather than showing you pictures and saying, "This is what a flagella looks like.", we use our body language to communicate the image of flagella. This forces you into interpreting the motion of flagella rotation and how we express ourselves as dance.
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<h3>Challenge #3: Land on beta sheet</h3>
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--!>
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<p>
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Land any plane on the beta sheet. The larger the plane, the better. Need more of a challenge? Make the betasheet smaller.</p>
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<h3>Import your own proteins!</h3>
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<p>Here we'll talk a bit about how we actually did it. Basically,</p>
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<ol>
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<li><a href="http://epmv.scripps.edu/">Get the ePMY version of Blender</a> or another 3D design software.
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<li>Import PDB files, increase the size, rotate and manipulate as needed. Save as .AC format <a href="http://wiki.flightgear.org/Blender">See this link for the plugin.</a>
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<li>Insert your objects into your favourite city using <a href="http://wiki.flightgear.org/Howto:Place_3D_objects_with_the_UFO">this guide.</a>
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<li>Fly, fly away!
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</ol>

Latest revision as of 01:50, 27 October 2012

Control


Flight of the Flagellin

Flight of the Flagellin takes protein structures and give them a hilarious, fun, new perspective.

What is this page really? Well, we recently discovered how easy it is to import 3D protein structures into an open-source flight simulator called FlightGear. It seems pretty ridiculous, but this could be a great way of teaching protein or molecular structure to people both young and old. It's also really surreal to be bringing some of the smallest units of life, and exploring them, in the setting of some of the largest man-made vehicles.

Flying is just fun. Lots of people play flight simulators just to fly around some generated landscape. Now in this case, you're flying our somebody's hard earned scientific data instead. With the amount of work that went into getting this data, it's hard to say whether we're taking full advantage of it and using it to its full potential, or just completely bastardizing it.

Something like this could also lead into new games, like EteRNA or Fold-it, in which the player is assigned the puzzle of solving a protein or RNA structure. The higher your score, the better you did, and your solution can actually contribute to scientific data. More specifically, we can swap out that plane model for, say, a ligand. Then, using this same idea, we can power docking experiments, in which players have to try and land a ligand in the active site of an enzyme, for example. This kind of computer modelling is common practice in drug design.


The Game

Download and Installation:

First download and install the game from http://www.flightgear.org/

Next, download and install the Flight of the Flagellin Maps! We wish we could make this a little bit easier but, we're inexperienced! Follow these step by step instructions:

  • Download and extract the map files: proteinflight.zip
  • Install the map files:
    1. Edit Objects/w080n40/w072n42/1777947.stg with any simple text editor.
    2. Scroll to the bottom of the file.
    3. Replace YOURPATHHERE with the file path to your downloads folder, or wherever you choose to store the protein models.
    4. Copy the Objects and Terrain folder to your Flightgear Scenery folder, ex: c:\Program Files\FlightGear\data\Scenery.
  • Run flightgear and pick to take off from the Boston Airport! (ID:KBOS)

Below are a series of challenges that we have made in our level:

Challenge #1: Flight of the Flagellin

In your glider, fly down through the helical constant domain of the flagellin monomer, landing safely in the Boston airport. (Right in time for the world finals :) ). Bonus: The larger the aircraft you can fly through, the better.

Starting Coordinates:
Latitude: 42.472766
Longitude: -71.028729
Altitude ASL: 27059.96
Heading: 166.5

Challenge #2: Red Fluorescent Protein

Land a helicopter on the chromophore of RFP. To make it easier, we've put a nice flat landing pad there for you.

Challenge #3: Land on beta sheet

Land any plane on the beta sheet. The larger the plane, the better. Need more of a challenge? Make the betasheet smaller.

Import your own proteins!

Here we'll talk a bit about how we actually did it. Basically,

  1. Get the ePMY version of Blender or another 3D design software.
  2. Import PDB files, increase the size, rotate and manipulate as needed. Save as .AC format See this link for the plugin.
  3. Insert your objects into your favourite city using this guide.
  4. Fly, fly away!