DNAmazingResult: Difference between revisions

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=Overview=
=Overview=
[[Image:Resultsum.png|500px|right]]
[[Image:Resultsum.png|500px|right]]
Basically, during the summer we have successfully developed the following features for the first version of DNAmazing:




<font size="20" face="arial" color="red">"One-click" feature to get the results(Automatic generation of folding path, crossover positions, and staple sequence)</font>
<br>
<br>
Basically, during the summer we have successfully developed the following features for the first version of DNAmazing:




[[Thermal stability calculation of sticky ends]]


<html>
<a href="http://openwetware.org/wiki/Oneclickfeature"><font size="3" color="red">1."One-click" feature to get the results (Automatic generation of folding path, crossover positions, and staple sequence) </a></font></html>


Bonus: Basic user-friendly interface




=="One-click" feature to get the results==
The DNAmazing program successfully
*Perform the automatic generation of possible scaffold folding paths from users' input and crossover positions for 2D DNA Origami structures
*Generate possible sticky end sequences
*Generate staple sequences with sticky ends which are necessary to conduct wet lab experiments for 2D DNA Origami structures.
With the "one-click" feature, the processing of DNA Origami design can be accelerated as users no longer have to do the raster filling (the folding path) manually which is definitely tedious for large and complex structure.
===Automatic generation of possible folding paths and crossover positions===
===Generation of possible sticky end sequences===
===Generation of staple sequences===


<html>
<a href="http://openwetware.org/wiki/Thermal_stability_calculation_of_sticky_ends"><font size="3" color="blue">2.Thermal stability calculation of sticky ends</a></font>
</html>


==Bonus: Basic user-friendly interface==
===The User Interface (GUI)===
GUI or graphic user interface is constructed to create a friendly environment for users to design their DNA origami. Our GUI is generated using Window form application in Visual studio 2010. Our software has three main tools to support the DNA Origami design with sticky end, to design, and to analyze the thermaldynamic properties of sticky ends.


====Generate DNAO====
For the first component, staples’ sequences used for the correct folding of DNA Origami with sticky ends are generated. User are required to define the size and shape of the structures they want to design by first input the frame size, and then choose the null squares (the location which will not be occupied by the scaffold). This would help the program to understand the DNA Origami design.
<center>
[[Image:1.png]]
</center>
After obtaining the parameters required, the program will generate different possible scaffold ways and ask users to choose one of their interest.
<center>                                     
[[Image:GUI_3.png]]
</center>
Users can also choose to add sticky end by enter the number of sticky end they need and specify the sequence and location of sticky ends in the scaffold.
<center>                 
[[Image:GUI_4.png]]
</center>
Final staple sequences are generated and appear in the result window.
<center>
[[Image:GUI_5.png]]
</center>


====Generate sticky end sequence====
To support generation of sticky end, as well as, to ensure that the sticky end will not affect the scaffold folding, an additional component is provided. User can choose to manually input a DNA sequence, and the program can help to check for the most stabilizing binding position in the scaffold. The binding energy is also calculated for users’ reference.
<center>
[[Image:newStick.png‎|700px]]
</center>
User can also ask the program to generate the sticky end sequence with the defined length. DNA sequences with binding energy higher than a limit defined are given. The below image illustrates the output of sticky ends' sequence generation.
<center>
[[Image:GUI_7.png‎|700px]]
</center>


====Thermaldynamic analysis====
<html>
The other component of the software is also to support the sticky end analysis in which thermal dynamic values of the sequence are calculated. Users need to enter the sequence they want to analyze, together with the condition in which they would test the DNA (total DNA strand concentration, Na+ concentration, and melting temperatures). Thermaldynamics value including deltaG, deltaS, deltaH, and Tm are provided in the results pages.
<a href="http://openwetware.org/wiki/Bonus:_Basic_user-friendly_interface"><font size="3" color="purple">3. Bonus: Basic user-friendly interface</a></font>
<center>
</html>
[[Image:GUI_8newer.png‎|700px]]
<br>
</center>
<br>
<br>
=Discussion=
Although DNAmazing has performed well some basic functions of CAD programs, due to the a different approach that we have taken (lithography-like inputting, automatic generation of folding path, automatic generation of staples sequences with sticky ends), there certainly have been some issues related to the initial results and the efficiency of the program.  


</div>
Regarding the processing time of the program,we observed that some large structures ( larger than 20x20 squares) may take long time for the program to handle the Hamiltonian algorithm, yet the results for smaller structures are very nice. In fact, medium smiling faces (12x12 squares) take only 5 to 10 seconds to get the final results; whereas  tradition CAD programs may take us at least 10 minutes to get the first step done: drawing of scaffold strands. This can be improved by employing parallel computing technique to accelerate the speed of the DNAmazing.
The scaffolding ways produced by DNAmazing tend to be symmetric as a filtering process was developed to optimize and select the best possible results from Hamiltonian circuit. This feature has not been observed in other programs because users design the scaffold folding pathways themselves. However, we observed some strange results for some exceptional structures with very complicated holes. We believe that the only way to  "mature" the algorithm is to carry out more tests.

Latest revision as of 22:40, 2 November 2011

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<div class="extra"> <div id="page_1"> <div class="main" style="padding-top:10px; padding-bottom:10px"> <!--header --> <header> <a href="index.html" id="logo">DNAmazing asfsaf. Smart. Effective</a> <nav> <ul id="menu"> <li class="nav1"><a href="http://openwetware.org/wiki/User:NUS_Dnamazing">Home</a></li> <li class="nav2"><a href="http://openwetware.org/wiki/DNAmazingMission">Mission</a></li> <li class="nav3"><a href="http://openwetware.org/wiki/DNAmazingProcess">Process</a></li> <li class="nav4"><a href="http://openwetware.org/wiki/DNAmazingResult">Results</a></li> <li class="nav5"><a href="http://openwetware.org/wiki/DNAmazingResources">Resources</a></li> </ul> </nav> </header> <!--header end-->


</div> </div>

</div> </html>

Overview




Basically, during the summer we have successfully developed the following features for the first version of DNAmazing:


<html> <a href="http://openwetware.org/wiki/Oneclickfeature"><font size="3" color="red">1."One-click" feature to get the results (Automatic generation of folding path, crossover positions, and staple sequence) </a></font></html>



<html> <a href="http://openwetware.org/wiki/Thermal_stability_calculation_of_sticky_ends"><font size="3" color="blue">2.Thermal stability calculation of sticky ends</a></font> </html>



<html> <a href="http://openwetware.org/wiki/Bonus:_Basic_user-friendly_interface"><font size="3" color="purple">3. Bonus: Basic user-friendly interface</a></font> </html>


Discussion

Although DNAmazing has performed well some basic functions of CAD programs, due to the a different approach that we have taken (lithography-like inputting, automatic generation of folding path, automatic generation of staples sequences with sticky ends), there certainly have been some issues related to the initial results and the efficiency of the program.

Regarding the processing time of the program,we observed that some large structures ( larger than 20x20 squares) may take long time for the program to handle the Hamiltonian algorithm, yet the results for smaller structures are very nice. In fact, medium smiling faces (12x12 squares) take only 5 to 10 seconds to get the final results; whereas tradition CAD programs may take us at least 10 minutes to get the first step done: drawing of scaffold strands. This can be improved by employing parallel computing technique to accelerate the speed of the DNAmazing. The scaffolding ways produced by DNAmazing tend to be symmetric as a filtering process was developed to optimize and select the best possible results from Hamiltonian circuit. This feature has not been observed in other programs because users design the scaffold folding pathways themselves. However, we observed some strange results for some exceptional structures with very complicated holes. We believe that the only way to "mature" the algorithm is to carry out more tests.

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