User:NUS Dnamazing: Difference between revisions

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<div class="main" style="padding-top:10px; padding-bottom:10px">
<div class="main" style="padding-top:10px; padding-bottom:10px">
=Everything you need to know about DNAmazing in 5 minutes=
=     Everything you need to know about DNAmazing in 5 minutes=
 
==1. What is DNAmazing?==
==1. What is DNAmazing?==
DNAmazing is a software dedicated for the design of DNA Origami structures. Like other CAD program in DNA Origami, such as caDNAnano, Nanoengineer, to name a few, DNAmazing helps designers determine the sequence of DNA strands.  
DNAmazing is a software dedicated for the design of DNA Origami structures. Like other CAD (computer-aided design) program in DNA Origami, such as caDNAnano and Nanoengineer, to name a few, DNAmazing helps designers determine the sequence of DNA strands. However, DNAmazing program is markedly different from other available software by its ability to automatically generate the folding path of the scaffold strand, its "one-click" feature, and calculation of the thermal stability of sticky ends.
 
==2. Why another CAD program while there are several good ones?==
==2. Why another CAD program while there are several good ones?==
Besides the basic functions of a CAD program in DNA Origami, DNAmazing was build on the vision of visualizing the applications of DNA Origami in the future: DNA motors operate on a complicated traffic system made by DNA Origami, complex nanoelectric circuits build from DNA Origami molds, and the organization of metal nanoparticles on DNA Origami platforms. These future  DNA Origami designs are usually too complex to get the footprint done manually (the generation of the folding path, the determination of crossover positions, and the merging of staples sequences. Furthermore, these systems must find a way to interact with external devices, particles and environment. The best way may be the fabrication of stick ends which act as connection sites. Hence, CAD programs DNAmazing is expected to fulfill these gaps.
Despite having the basic functions of a CAD program in DNA Origami, DNAmazing was built on the vision of applications of DNA Origami in the future: DNA motors operating on a complicated traffic system made by DNA Origami method, complex nanoelectric circuits built from DNA Origami molds, and the organization of metal nanoparticles on DNA Origami platforms. However, these future  DNA Origami designs are usually too complex to accomplish manually (the generation of the folding path, the determination of crossover positions, and the merging of staple sequences). Furthermore, these systems must be able to interact with external devices, particles and environment. To fulfill these requirements, the best way is the fabrication of sticky ends which act as connection sites between the DNA Origami and external objects. Currently, to the best of our knowledge, these features are not focused in CAD programs for DNA origami, though we believe they are crucial in the future development of DNA Origami.
 
==3. Why are we interested in creating DNAmazing?==
==3. Why are we interested in creating DNAmazing?==
Firstly, we conceive that a good DNA Origami structure must start from the good design, in other words a good CAD program. Furthermore, our group had an idea of creating a complex traffic system on which DNA "motorcycles" operated. As mentioned above, this idea requires both the complexity of the system and the design of sticky ends as steps for DNA motorcycles. Hence, we decided to develop a CAD program from scratch as Rothermund did when he invented the technique of DNA Origami.
Firstly, we conceive that a good DNA Origami structure must start from the good design, in other words a good CAD program. Furthermore, in the beginning our group had an idea of creating a complex traffic system on which DNA "motorcycles" operated. As mentioned above, this idea requires both the complexity of the system and the design of sticky ends as steps for DNA motorcycles. Hence, we decided to develop a CAD program from scratch for this purpose as Rothermund did in 3 months before he invented the technique of DNA Origami. This is really a challenge as we have a different approach to design the CAD program compared to existing ones, and none of our team members has been trained in computer science.
[[DNAmazingMission]]


==4. What are the goals and our achievements in this project?==
==4. What are the goals and our achievements in this project?==
'''Goals:'''
'''Goals:'''
DNAmazing was expected to
DNAmazing is expected to
----
----
   
   
# Automatically generate folding path
# Automatically generate various folding pathways
# Automatically determine crossover position
# Automatically determine crossover position
# Automatically generate DNA staple sequence
# Automatically generate DNA staple sequences
# Design of sticky ends
# Design of sticky ends
# Basic chemical toolkits to determine the chemical properties of stick ends
# Estimate the thermal stability of sticky ends via the calculation of free energy, enthalpy, entropy, and melting point.


<br>
<br>
<br>
 
'''Achievements:'''
'''Achievements:'''
DNAmazing is able to
DNAmazing is able to
----
----


# Automatically generate the folding of small and medium DNA Origami structures with arbitrary holes and shapes. Larger structures may take longer time to compute the possible folding paths.
# Automatically generate the folding of small and medium DNA Origami structures with arbitrary holes and shapes.
# Select the most suitable folding paths for DNA Origami
# Select the most suitable folding paths for DNA Origami
# Automatically determine crossover position
# Automatically determine crossover positions
# Automatically generate DNA staple sequence
# Automatically generate DNA staple sequences
# Design of sticky ends
# Design of sticky ends
# Basic chemical toolkits to determine the chemical properties of stick ends
# Determine the thermal stability of stick ends
# Bonus: Provide basic user-friendly interface.
# Bonus: Provide basic user-friendly interface.
More details about our results can be found here [[DNAmazingResult]]


==5. What are DNAmazing features?==
==5. What are DNAmazing features and how are they compared to other developed CAD programs?==
*Lithography-like Inputting
*Lithography-like Inputting
*"One-click" to results (Automatic generation of folding path, crossover positions, and staple sequence)
*"One-click" to results (Automatic generation of folding path, crossover positions, and staple sequence)
*Sticky ends generation
*Sticky ends generation
*Computational Toolkits
*Thermodynamics calculation
*User-friendly interface
*User-friendly interface
*No programming required
*No programming required
*Free and Open Source
*Free and Open Source
If you are interested in how we develop the program, visit [[DNAmazingProcess]]


==6. How can I run the DNAmazing?==
==6. How can I run the DNAmazing?==
==7. What are future developments?==
It is easy to run and experience the program. [Download it here http://www.mediafire.com/?bqynvxhbgpcs7yo].
 
==7. What are the current limitations and future developments?==
Problems:
*The first version of DNAmazing may have long processing time to handle complicated or large structures.
*There may be some exceptional structures which may not handled properly
*The program is only used for 2D Origami
*Due to the limitation of time, the results of DNAmazing which have been compared to other CAD programs have not been tested in wet lab experiments.
Future developments:
*Parallel computing or improvement on the algorithm may be considered to reduce the processing time
*As the principles and layout has been developed for 2D, DNAmazing can be extended into the regime of 3D Origami with curved structures
*More rigid computational tools can be included to analyze the chemical properties of sticky ends.
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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>

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Everything you need to know about DNAmazing in 5 minutes

1. What is DNAmazing?

DNAmazing is a software dedicated for the design of DNA Origami structures. Like other CAD (computer-aided design) program in DNA Origami, such as caDNAnano and Nanoengineer, to name a few, DNAmazing helps designers determine the sequence of DNA strands. However, DNAmazing program is markedly different from other available software by its ability to automatically generate the folding path of the scaffold strand, its "one-click" feature, and calculation of the thermal stability of sticky ends.

2. Why another CAD program while there are several good ones?

Despite having the basic functions of a CAD program in DNA Origami, DNAmazing was built on the vision of applications of DNA Origami in the future: DNA motors operating on a complicated traffic system made by DNA Origami method, complex nanoelectric circuits built from DNA Origami molds, and the organization of metal nanoparticles on DNA Origami platforms. However, these future DNA Origami designs are usually too complex to accomplish manually (the generation of the folding path, the determination of crossover positions, and the merging of staple sequences). Furthermore, these systems must be able to interact with external devices, particles and environment. To fulfill these requirements, the best way is the fabrication of sticky ends which act as connection sites between the DNA Origami and external objects. Currently, to the best of our knowledge, these features are not focused in CAD programs for DNA origami, though we believe they are crucial in the future development of DNA Origami.

3. Why are we interested in creating DNAmazing?

Firstly, we conceive that a good DNA Origami structure must start from the good design, in other words a good CAD program. Furthermore, in the beginning our group had an idea of creating a complex traffic system on which DNA "motorcycles" operated. As mentioned above, this idea requires both the complexity of the system and the design of sticky ends as steps for DNA motorcycles. Hence, we decided to develop a CAD program from scratch for this purpose as Rothermund did in 3 months before he invented the technique of DNA Origami. This is really a challenge as we have a different approach to design the CAD program compared to existing ones, and none of our team members has been trained in computer science. DNAmazingMission

4. What are the goals and our achievements in this project?

Goals: DNAmazing is expected to

  1. Automatically generate various folding pathways
  2. Automatically determine crossover position
  3. Automatically generate DNA staple sequences
  4. Design of sticky ends
  5. Estimate the thermal stability of sticky ends via the calculation of free energy, enthalpy, entropy, and melting point.


Achievements: DNAmazing is able to

  1. Automatically generate the folding of small and medium DNA Origami structures with arbitrary holes and shapes.
  2. Select the most suitable folding paths for DNA Origami
  3. Automatically determine crossover positions
  4. Automatically generate DNA staple sequences
  5. Design of sticky ends
  6. Determine the thermal stability of stick ends
  7. Bonus: Provide basic user-friendly interface.

More details about our results can be found here DNAmazingResult

5. What are DNAmazing features and how are they compared to other developed CAD programs?

  • Lithography-like Inputting
  • "One-click" to results (Automatic generation of folding path, crossover positions, and staple sequence)
  • Sticky ends generation
  • Thermodynamics calculation
  • User-friendly interface
  • No programming required
  • Free and Open Source

If you are interested in how we develop the program, visit DNAmazingProcess

6. How can I run the DNAmazing?

It is easy to run and experience the program. [Download it here http://www.mediafire.com/?bqynvxhbgpcs7yo].

7. What are the current limitations and future developments?

Problems:

  • The first version of DNAmazing may have long processing time to handle complicated or large structures.
  • There may be some exceptional structures which may not handled properly
  • The program is only used for 2D Origami
  • Due to the limitation of time, the results of DNAmazing which have been compared to other CAD programs have not been tested in wet lab experiments.

Future developments:

  • Parallel computing or improvement on the algorithm may be considered to reduce the processing time
  • As the principles and layout has been developed for 2D, DNAmazing can be extended into the regime of 3D Origami with curved structures
  • More rigid computational tools can be included to analyze the chemical properties of sticky ends.
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