Team:Davidson-MissouriW/Tools

From 2010.igem.org

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         <div id="mission_box"> <h2> iGEM Davidson – Missouri Western 2010: Tools </h2>
         <div id="mission_box"> <h2> iGEM Davidson – Missouri Western 2010: Tools </h2>
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             <h3>The team has designed several tools in conjunction with our iGem project.</h3>
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             <h3>The team has designed several tools to guide and support our iGEM project.</h3>
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        <div id="Veripart">
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            <a href="http://72.22.219.205/sequence">
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                <h3>VeriPart</h3>
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            </a><a NAME="veripart">
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            <table cellpadding=0 cellspacing=0>
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                        <td width=30>
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                        <td width=580>
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                            <p>Verifying BioBrick parts can be difficult and tedious by hand.  To solve this problem, we have developed a tool to identify BioBrick parts within a given DNA sequence.  When a sequence is entered, the program checks the last archived version of the BioBrick Parts Registry and returns the best matched part.  If your desired part is not found, you can attempt to align the sequence you entered with the part you desire.  When a device is found in your sequence, you can click to view the sequences of individual parts.  An alignment of the sequence with the part is presented to the user allowing for easier sequence analysis.</p>
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                        <td align=center width=600>
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                <a href="http://72.22.219.205/sequence"><img src="http://2010.igem.org/wiki/images/3/32/Davidson-MissouriWveripart.png" alt="Veri" width=400/></a>
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        <br><br>
         <div id="Oligator">
         <div id="Oligator">
             <a href="http://gcat.davidson.edu/igem10/index.html">
             <a href="http://gcat.davidson.edu/igem10/index.html">
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         <div id="Optimoose">
         <div id="Optimoose">
             <a href="http://gcat.davidson.edu/igem10/opt/opt_index.html">
             <a href="http://gcat.davidson.edu/igem10/opt/opt_index.html">
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                 <h3>The Optimoose</h3>
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                 <h3>Optimus</h3>
             </a><a NAME="optimoose">
             </a><a NAME="optimoose">
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                             <p>The Optimoose is a tool designed to allow the user to evaluate the expression level of a gene sequence in <i>E. coli</i> using either RCBS-PC or the CAI formula.  Additionally, the user has the option to optimize or deoptimize the sequence by using one of those two formulas. If the optimized or deoptimized option is selected, the user will be given a new sequence whose codons have been changed to reflect the best, or worst, codons as determined by the selected formula. Assuming the entered sequence is in frame, the amino acid sequence is preserved.
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                             <p>Optimus is a tool designed to allow the user to evaluate the expression level of a gene sequence in <i>E. coli</i> using either RCBS-PC or the CAI formula.  Additionally, the user has the option to optimize or deoptimize the sequence by using one of those two formulas. If the optimized or deoptimized option is selected, the user will be given a new sequence whose codons have been changed to reflect the best, or worst, codons as determined by the selected formula. Assuming the entered sequence is in frame, the amino acid sequence is preserved.
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The Optimoose was designed to allow us to assign a given "weight" to the items, based on their protein production, to fill up the knapsack.</p>
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Optimus serves as a mechanism by which we can engineer optimized and deoptimized sequences which represent a given "weight" to the items in a knapsack based on their protein production.</p>
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                         <td align=center width=600>
                         <td align=center width=600>
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                             <a href="http://gcat.davidson.edu/igem10/opt/opt_index.html"><img src="http://2010.igem.org/wiki/images/f/ff/Davidson-MissouriWoptimoose.png" alt="Tools" width=280/></a>
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                             <a href="http://gcat.davidson.edu/igem10/opt/opt_index.html"><img src="http://2010.igem.org/wiki/images/2/25/Davidson-MissouriWoptimus.png" alt="Tools" width=280/></a>
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             <a NAME="Simulator">
             <a NAME="Simulator">
             <a href="http://2010.igem.org/wiki/images/4/4a/ConstructSim.zip">
             <a href="http://2010.igem.org/wiki/images/4/4a/ConstructSim.zip">
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                 <h3>Construct Simulation</h3>
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                 <h3>SimuLox</h3>
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                         <td align=center width=600>
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                             <a href="http://2010.igem.org/wiki/images/4/4a/ConstructSim.zip"><img src="http://2010.igem.org/wiki/images/f/fe/Davidson-MissouriWsteph.png" alt="sim" width=355/></a>
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                             <a href="http://2010.igem.org/wiki/images/4/4a/ConstructSim.zip"><img src="http://2010.igem.org/wiki/images/8/87/Davidson-MissouriWconsim.png" alt="sim" width=355/></a>
                         </td>
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         </div>
         </div>
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        <div id="Veripart">
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         <center><a href="#main_wrapper">Top</a></center>
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            <a href="http://72.22.219.205/sequence">
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                <h3>VeriPart</h3>
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            </a><a NAME="veripart">
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                        </td>
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                        <td width=580>
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                            <p>Verifying BioBrick parts can be difficult and tedious by hand.  To solve this problem, we have developed a tool to identify BioBrick parts and devices in a given DNA sequence.  When a sequence is entered, the program checks the last archived version of the BioBrick Parts Registry.  If your desired part is not found, you can attempt to align the sequence you entered with the part you desire.  Since this search uses a real-time version of the registry, it can potentially find additional parts.  When a device is found in your sequence, you can click to view the sequences of individual parts.</p>
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                        </td>
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                        <td align=center width=600>
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                <a href="http://72.22.219.205/sequence"><img src="http://2010.igem.org/wiki/images/3/32/Davidson-MissouriWveripart.png" alt="Veri" width=400/></a>
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            </table>
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        </div>
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        <div id="game">
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            <a href="http://72.22.219.205/knapsack">
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                <h3>Knapsack Game</h3>
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            </a><A NAME="Knapsack">
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                            <p>We designed a game to simulate the knapsack problem.  This game is an educational tool that could have a broad impact in educational settings, from middle school to undergraduate courses that discuss NP-complete problems.  The game has two modes: tutorial and challenge, each of which asks the player to fill a knapsack of a certain capacity with given weighted items.  The tutorial gives tips about the type of problem and only uses six weighted items.  The challenge offers no help and asks the player to choose from nine weighted items. </p>
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                        </td>
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                        <td align=center width=600>
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                            <a href="http://72.22.219.205/knapsack"><img src="http://2010.igem.org/wiki/images/d/da/Davidson-MissouriWknapsack.png" alt="" width=300/></a>
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         <center><a href="#menu">Top</a></center>
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Latest revision as of 22:19, 22 October 2010

iGEM Davidson – Missouri Western 2010: Tools

The team has designed several tools to guide and support our iGEM project.













SimuLox

In order to better understand our fluorescent protein - TetA constructs, we designed a simulation of the cre-lox system. This simulation allows the user to test our pre-determined constructs as well as custom constructs from any number of promoters, lox sites, fluorescent proteins, essential genes, and/or terminators. The program will then show either a single, animated simulation that will allow the user to see how the lox sites interact, or it will run many simulations and then generate a histogram that shows the distribution of what fluorescent proteins were expressed. In addition, if the user chooses to include weights for the "items" and a capacity for the knapsack the program will tell you whether or not your construct has exceeded the capacity. In order to run the program, download the jar file. To see the actual percentages behind the histogram, the program needs to be run through a command line tool, but other than that simply double clicking the jar file to run it should be sufficient.

sim


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