Team:CBNU-Korea/Project/BD/Method

From 2012.igem.org

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href="https://2012.igem.org/Team:CBNU-Korea/Team">TEAM</a></li>
href="https://2012.igem.org/Team:CBNU-Korea/Team">TEAM</a></li>
<li class="PROJECT"><a href="#">PROJECT</a></li>
<li class="PROJECT"><a href="#">PROJECT</a></li>
-
<li class="NOTEBOOK"><a href="#">NOTEBOOK</a></li>
+
<li class="NOTEBOOK"><a
 +
href="https://2012.igem.org/Team:CBNU-Korea/Notebook">NOTEBOOK</a></li>
</ul>
</ul>
<ul>
<ul>
-
<li class="SAFETY"><a href="#">SAFETY</a></li>
+
<li class="SAFETY"><a
-
<li class="JUDGING"><a href="#">JUDGING</a></li>
+
href="https://2012.igem.org/Team:CBNU-Korea/Safety">SAFETY</a></li>
-
<li class="iGEM"><a href="#">iGEM</a></li>
+
<li class="JUDGING"><a
 +
href="https://2012.igem.org/Team:CBNU-Korea/JG/judging">JUDGING</a></li>
 +
<li class="iGEM"><a href="https://2012.igem.org/"
 +
target="_blank">iGEM</a></li>
</ul>
</ul>
</div>
</div>
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</div>
</div>
<div id="CB_sub_menu">
<div id="CB_sub_menu">
-
<ul>
+
<div id="CB_sub_mobile_menu">+ MENU</div>
 +
<ul class="CB_ul">
<li class="OVERVIEW"><a
<li class="OVERVIEW"><a
href="https://2012.igem.org/Team:CBNU-Korea/Project">01 +
href="https://2012.igem.org/Team:CBNU-Korea/Project">01 +
Overview</a></li>
Overview</a></li>
-
<li class="BD"><a href="#">02 + Brick Designer</a></li>
+
<li class="BD"><a
-
<li id="li_sub" class="BD_Overview">- Overview</li>
+
href="https://2012.igem.org/Team:CBNU-Korea/Project/BD/Overview">02
-
<li id="li_sub" class="BD_Method">- Method</li>
+
+ Brick Designer</a></li>
 +
<li id="li_sub" class="BD_Overview"><a
 +
href="https://2012.igem.org/Team:CBNU-Korea/Project/BD/Overview">-
 +
Overview</a></li>
 +
<li id="li_sub" class="BD_Method"><a href="#">- Method</a></li>
<li class="MGD"><a
<li class="MGD"><a
href="https://2012.igem.org/Team:CBNU-Korea/Project/GD/Overview">03
href="https://2012.igem.org/Team:CBNU-Korea/Project/GD/Overview">03
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</div>
</div>
<div id="CB_sub_main">
<div id="CB_sub_main">
-
<div id="CB_sub_img"></div>
+
<div id="CB_sub_img">
 +
<img
 +
src="https://static.igem.org/mediawiki/2012/6/6e/CBK_overlay_001.png">
 +
</div>
<div id="CB_sub_cont">
<div id="CB_sub_cont">
-
<h1>1. Overview</h1>
+
<h1>1. BioBrick Database</h1>
-
<p>- The importance of the transfer, saving and management of
+
<p>- The program will be installed and run in the local
-
bio-information is now closely related to the computers. Nowadays
+
computer. When the program is distributed to the user. If the
-
bio-informatics are used in many fields from simple biological
+
whole information about BioBrick is included in the install
-
models to complicated algorithm forecast and more. And in
+
program, this will not only increase the size of the install file,
-
synthetic biology, since designing a biological circuit by using
+
but also the user won’t need all of these informations. So we made
-
the computer became available, it has opened a new era. In the
+
our program allow the users to choose the BioBrick information
-
past, synthetic biology used to find subjects like a genetic part
+
that they want, and download it selectively.</p>
-
that is about a specific purpose and the connection between the
+
<p>- To bring the already registered BioBrick data, our program
-
fastest designing process only by experiments. But now in the
+
parse and save the simple informations(ID, Name, Description,
-
future of synthetic biology, experiment and the computational
+
Type) that is registered in
-
designing program must be in a mutual relationship. The purpose of
+
http://partsregistry.org/fasta/parts/All_Parts.</p>
-
our project is to increase the efficiency of the experiment by
+
<img src="https://static.igem.org/mediawiki/2012/9/95/CBK_A_001.png">
-
using the designing process of BioBrick prior to the experiment,
+
<p>- All this saved information, will be shown in the download
-
and improve the efficiency of the connection between the next
+
screen for the user. By choosing the BioBrick that the user wants,
-
experiment conducted by the program user.</p>
+
and pressing the download button, the Bricks information (Suparts,
 +
Sequence, Status, Rating etc.) will be saved in the local database
 +
after parsed by XML Part Information (http://partsregistry.org/
 +
xml/part.+BioBrick Name).</p>
 +
<img src="https://static.igem.org/mediawiki/2012/7/75/CBK_A_002.png">
 +
<img src="https://static.igem.org/mediawiki/2012/4/41/CBK_A_003.png">
 +
<p>- DB Tables</p>
 +
<img src="https://static.igem.org/mediawiki/2012/5/54/CBK_A_004.png" width="450px">
 +
<img src="https://static.igem.org/mediawiki/2012/2/2a/CBK_A_005.png" width="450px">
 +
<div id="scrolltotop"></div>
 +
 
 +
<h1>2. The user's BioBrick</h1>
 +
<p>- If the user wants to use a BioBrick with their own style,
 +
not the BioBrick that is already registered in the program, they
 +
can personally add a new BioBrick and design it.</p>
<div id="scrolltotop"></div>
<div id="scrolltotop"></div>
-
<h1>2. Feature</h1>
+
<h1>3. Management of Sequence</h1>
-
<h2>2-1. BioBrick Data Download</h2>
+
<h2>3-1. Suffix, Prefix, Scar</h2>
-
<p>- The registered BioBrick information needed for designing
+
<p>- The program automatically process the restriction enzyme
-
in this program, can be easily downloaded without being typed in.</p>
+
between the Bricks when the user designs the BioBrick. By pressing
-
<h2>2-2. Design</h2>
+
the ‘Scar’ icon and including the BioBrick in there, the program
-
<p>- The user can arrange the BioBrick in any sequence they
+
will analyze the sequences of the Bricks and automatically choose
-
want. And if they want, the user can put a proper Prefix, Suffix
+
where to make the adequate Scar form.</p>
-
restriction enzyme site between the Bricks by the software.</p>
+
<h2>3-2. Cloning</h2>
-
<p>- By selecting the Plasmid Backbone and the restriction
+
<p>- When the user selects the Plasmid Backbone, the program
-
enzyme in sequence, the cloning will be done automatically.</p>
+
will check the sequence and find the restriction enzyme site. If
-
<h2>2-3. Screen Shot</h2>
+
the Plasmid Backbone does not include in the restriction site of
-
<p>- The BioBrick that the user designed from the program is
+
Prefix, Suffix, then the user has to choose another plasmid
-
saved in image files to be readily used in Wiki or documents.</p>
+
backbone.</p>
-
<h2>2-4. Various Storage Formats</h2>
+
<p>- When the user choose one restriction site from each of
-
<p>- The project in designing in progress can be saved or
+
Prefix, Suffix and press the ‘OK’ button. it will process the
-
imported. Also, by saving the informations as a SBOL, GenBank,
+
designed BioBrick and the Plasmid Backbone sequence and show it on
-
Fasta form, the user can use the information that they design in
+
the screen.</p>
-
other programs as well.</p>
+
<div id="scrolltotop"></div>
<div id="scrolltotop"></div>
-
<h1>3. The process of the program designing</h1>
+
<h1>4. Screen Shot function</h1>
-
<h2>3-1. Problem Recognition</h2>
+
<p>- The teams participating the iGEM with experiments should
-
<p>- In many common laboratories today, there is a limit that
+
register first in BioBrick. In this process, the informations
-
the user themselves has to put in the BioBrick Data, and draw it
+
about BioBricks in Wiki Pages and documents can be used through
-
as an image after they finish the design. So we decided to develop
+
graphic work.We hope that our program will lighten the load used
-
the designing a program that, based on BioBrick DataBase, directly
+
in those kind of progress, so the users can be more focused on the
-
provide designing process with convenient additional functions as
+
experiment. This program is made to design and save the images at
-
well.</p>
+
the same time.</p>
-
<h2>3-2. Requirement Checking</h2>
+
-
<p>- We checked on other programs that many people are using
+
-
nowadays, and analyzed the steps that are needed in designing.</p>
+
-
<p>- For the connection within other programs that can be used
+
-
after the experiment, we checked on the needs of the saving
+
-
methods on GenBank, SBOL, Fasta.</p>
+
-
<h2>3-2. Design</h2>
+
-
<p>- Visual Studio 2010, 2012 (C#)</p>
+
-
<p>- Windows 7</p>
+
-
<p>- OleDB (MS OFFICE)</p>
+
-
<p>- * When running the program, Microsoft Runtime is required.</p>
+
-
<h2>3-2. Discussion and Feedback</h2>
+
-
<p>- Our team members repeated testing the program, finding the
+
-
errors and fixing the problems.</p>
+
<div id="scrolltotop"></div>
<div id="scrolltotop"></div>
-
<h1>4. Future Work</h1>
+
<h1>5. BioBrick Data Export</h1>
-
<p>Our program is now version 1.0.0, and will be updated and
+
<p>- Our program can save the BioBrick that the user designed
-
offer better information and performance about the designing
+
in various forms. The user can use the data right away without any
-
process in next versions. First, simplification of the
+
additional work.</p>
-
registration process of the iGEM Part will be offered. The
+
<h2>5-1. SBOL</h2>
-
registration of BioBrick is now available only in online. But by
+
<p>- SBOL(Synthetic Biology Open Language) is the exchange
-
co-working with iGEM, we will develop a better functioning
+
standard for the genetic tools, the device modules, and the
-
program, and make it possible to design and register the Brick at
+
explanation of the system data. We use libSBOLc(SBOL C library) to
-
the same time. Secondly, we are planning to add a communication
+
save the designed information as a SBOL form, so that itcan be
-
function between the users. This function will help the users to
+
easily transferred to the user.</p>
-
share opinions, and discuss designing information about a specific
+
<h2>5-2. Genbank</h2>
-
Brick. This discussion will help the users improve their
+
<p>- This program is designed to save the information as
-
experiment or project. Third, the expression rate will be produced
+
Genbank form, and we referred the form from
-
in a numerical value. The expression rate value is a score that
+
http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.</p>
-
will show the users how the expression of the BioBrick designed by
+
<h2>5-3. Fasta</h2>
-
cloning is working in the experiment. To make it as a score,
+
<p>
-
theoretical background and algorithm based on a lot of data are
+
- The Fasta file was made to be saved as seen in below.<br>
-
required. The last is the import of the files with various saving
+
<br> > Part_Name Type "Description"<br> Sequence
-
forms. Nowadays we can only save the designed BioBrick data after
+
</p>
-
exporting it. But the next version of the program will be improved
+
-
to read the data modified and saved in other process, and reading,
+
-
processing and saving it will be available as well.</p>
+
<div id="scrolltotop"></div>
<div id="scrolltotop"></div>
</div>
</div>

Latest revision as of 01:01, 27 September 2012

Brick Designer

- Method

1. BioBrick Database

- The program will be installed and run in the local computer. When the program is distributed to the user. If the whole information about BioBrick is included in the install program, this will not only increase the size of the install file, but also the user won’t need all of these informations. So we made our program allow the users to choose the BioBrick information that they want, and download it selectively.

- To bring the already registered BioBrick data, our program parse and save the simple informations(ID, Name, Description, Type) that is registered in http://partsregistry.org/fasta/parts/All_Parts.

- All this saved information, will be shown in the download screen for the user. By choosing the BioBrick that the user wants, and pressing the download button, the Bricks information (Suparts, Sequence, Status, Rating etc.) will be saved in the local database after parsed by XML Part Information (http://partsregistry.org/ xml/part.+BioBrick Name).

- DB Tables

2. The user's BioBrick

- If the user wants to use a BioBrick with their own style, not the BioBrick that is already registered in the program, they can personally add a new BioBrick and design it.

3. Management of Sequence

3-1. Suffix, Prefix, Scar

- The program automatically process the restriction enzyme between the Bricks when the user designs the BioBrick. By pressing the ‘Scar’ icon and including the BioBrick in there, the program will analyze the sequences of the Bricks and automatically choose where to make the adequate Scar form.

3-2. Cloning

- When the user selects the Plasmid Backbone, the program will check the sequence and find the restriction enzyme site. If the Plasmid Backbone does not include in the restriction site of Prefix, Suffix, then the user has to choose another plasmid backbone.

- When the user choose one restriction site from each of Prefix, Suffix and press the ‘OK’ button. it will process the designed BioBrick and the Plasmid Backbone sequence and show it on the screen.

4. Screen Shot function

- The teams participating the iGEM with experiments should register first in BioBrick. In this process, the informations about BioBricks in Wiki Pages and documents can be used through graphic work.We hope that our program will lighten the load used in those kind of progress, so the users can be more focused on the experiment. This program is made to design and save the images at the same time.

5. BioBrick Data Export

- Our program can save the BioBrick that the user designed in various forms. The user can use the data right away without any additional work.

5-1. SBOL

- SBOL(Synthetic Biology Open Language) is the exchange standard for the genetic tools, the device modules, and the explanation of the system data. We use libSBOLc(SBOL C library) to save the designed information as a SBOL form, so that itcan be easily transferred to the user.

5-2. Genbank

- This program is designed to save the information as Genbank form, and we referred the form from http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.

5-3. Fasta

- The Fasta file was made to be saved as seen in below.

> Part_Name Type "Description"
Sequence

Retrieved from "http://2012.igem.org/Team:CBNU-Korea/Project/BD/Method"