Team:CBNU-Korea/Project/GD/Overview

From 2012.igem.org

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<h1>1. Overview</h1>
<h1>1. Overview</h1>
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<p>- The importance of the transfer, saving and management of
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<h2>1-1. Predicting Essential Genes</h2>
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bio-information is now closely related to the computers. Nowadays
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<p>
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bio-informatics are used in many fields from simple biological
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<strong>Need of the Analysis of Essential Genes</strong>
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models to complicated algorithm forecast and more. And in
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</p>
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synthetic biology, since designing a biological circuit by using
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<p>It is thought that today, Synthetic Biology has reached a
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the computer became available, it has opened a new era. In the
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plateau. Since the success of the experiment that re-synthesizes
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past, synthetic biology used to find subjects like a genetic part
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the genome and insert it into the cell, it seems that Synthetic
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that is about a specific purpose and the connection between the
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Biology is not developing. But if somebody can design a genome and
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fastest designing process only by experiments. But now in the
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synthesize it, synthetic biology can take off again. Then what do
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future of synthetic biology, experiment and the computational
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we need to design a genome? First, we need information about
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designing program must be in a mutual relationship. The purpose of
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essential genes. An essential gene is a gene that is critical for
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our project is to increase the efficiency of the experiment by
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survival. If you have the information about the essential gene,
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using the designing process of BioBrick prior to the experiment,
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you are in a superior state in making human artificial cell in a
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and improve the efficiency of the connection between the next
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true sense. Because it means that you already have the ability to
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experiment conducted by the program user.</p>
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make the brick. All you have to do is make a brick with our
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<div id="scrolltotop"></div>
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program developed for you according to the sequence of the
 +
essential genes, and conduct experiments.</p>
 +
<p>
 +
<strong>The Present of the Analysis of Essential Genes</strong>
 +
</p>
 +
<p>Essential genes are being analyzed in many places, such as
 +
in DEG or PATRIC.</p>
 +
<p>
 +
<strong>The Problem of the Analysis of Essential Genes</strong>
 +
</p>
 +
<p>Essential genes known today are mostly discovered with in
 +
vitro experiments. As seen in the chart above, the result of the
 +
experiment can vary according to conditions and methods. We bring
 +
forth a problem about this. We believe that to give meaning to a
 +
result, it has to be accurate. Also the analysis method of
 +
essential genes used today takes a lot of time and labor. To
 +
address this we use a bio-informatics way and find essential
 +
genes.</p>
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<h1>2. Feature</h1>
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<h2>1-2. Analysis of Essential Genes</h2>
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<h2>2-1. BioBrick Data Download</h2>
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<p>
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<p>- The registered BioBrick information needed for designing
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<strong>Definition of Essential Genes</strong>
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in this program, can be easily downloaded without being typed in.</p>
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</p>
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<h2>2-2. Design</h2>
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<p>As we are using the computer to find essential genes, we
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<p>- The user can arrange the BioBrick in any sequence they
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can't use the existing method to analogize essential genes with
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want. And if they want, the user can put a proper Prefix, Suffix
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experiments. We assume that if essential genes are critical to
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restriction enzyme site between the Bricks by the software.</p>
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living, every organism must have it. So we approached the problem
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<p>- By selecting the Plasmid Backbone and the restriction
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with the assumption that an essential gene is a gene that every
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enzyme in sequence, the cloning will be done automatically.</p>
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living thing will has.</p>
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<h2>2-3. Screen Shot</h2>
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<p>
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<p>- The BioBrick that the user designed from the program is
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<strong>Significance of the Analysis of Essential Genes</strong>
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saved in image files to be readily used in Wiki or documents.</p>
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</p>
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<h2>2-4. Various Storage Formats</h2>
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<p>We are proud of our analysis methods. You will see that our
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<p>- The project in designing in progress can be saved or
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analysis result is not that different from that proved with
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imported. Also, by saving the informations as a SBOL, GenBank,
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experiments. Our analysis results do more than finding essential
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Fasta form, the user can use the information that they design in
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genes. With this, you can understand the metabolic process and
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other programs as well.</p>
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furthermore have a good chance to synthesize an artificial cell.</p>
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<div id="scrolltotop"></div>
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<h1>3. The process of the program designing</h1>
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<h2>1-3. Developing of the Minimal Genome Designer</h2>
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<h2>3-1. Problem Recognition</h2>
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<p>
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<p>- In many common laboratories today, there is a limit that
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<strong>The Purpose of Minimal Genome Designer</strong>
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the user themselves has to put in the BioBrick Data, and draw it
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</p>
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as an image after they finish the design. So we decided to develop
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<p>The purpose of our program is fundamentally to understand
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the designing a program that, based on BioBrick DataBase, directly
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the structure and the principle of the genome. However, we will
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provide designing process with convenient additional functions as
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not stop at understanding the information about genome, but hope
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well.</p>
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that you can go on to build your own genome by using the brick in
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<h2>3-2. Requirement Checking</h2>
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your experiment.</p>
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<p>- We checked on other programs that many people are using
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<p>
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nowadays, and analyzed the steps that are needed in designing.</p>
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<strong>Advantages of Minimal Genome Designer</strong>
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<p>- For the connection within other programs that can be used
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</p>
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after the experiment, we checked on the needs of the saving
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<p>Minimal Genome Designer will make you easily understand the
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methods on GenBank, SBOL, Fasta.</p>
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genome, by showing you the structure. Providing various
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<h2>3-2. Design</h2>
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information about the gene and the genome, our program will
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<p>- Visual Studio 2010, 2012 (C#)</p>
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shorten your time to design the experiment. This also means that
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<p>- Windows 7</p>
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you can save money as well. We have tried and verified so that
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<p>- OleDB (MS OFFICE)</p>
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Minimal Genome Designer can procure reliability. The results made
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<p>- * When running the program, Microsoft Runtime is required.</p>
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by Minimal Genome Designer can be used as a new background
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<h2>3-2. Discussion and Feedback</h2>
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information for your experiment.</p>
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<p>- Our team members repeated testing the program, finding the
+
-
errors and fixing the problems.</p>
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<div id="scrolltotop"></div>
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<h1>4. Future Work</h1>
 
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<p>Our program is now version 1.0.0, and will be updated and
 
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offer better information and performance about the designing
 
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process in next versions. First, simplification of the
 
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registration process of the iGEM Part will be offered. The
 
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registration of BioBrick is now available only in online. But by
 
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co-working with iGEM, we will develop a better functioning
 
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program, and make it possible to design and register the Brick at
 
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the same time. Secondly, we are planning to add a communication
 
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function between the users. This function will help the users to
 
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share opinions, and discuss designing information about a specific
 
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Brick. This discussion will help the users improve their
 
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experiment or project. Third, the expression rate will be produced
 
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in a numerical value. The expression rate value is a score that
 
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will show the users how the expression of the BioBrick designed by
 
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cloning is working in the experiment. To make it as a score,
 
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theoretical background and algorithm based on a lot of data are
 
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required. The last is the import of the files with various saving
 
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forms. Nowadays we can only save the designed BioBrick data after
 
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exporting it. But the next version of the program will be improved
 
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to read the data modified and saved in other process, and reading,
 
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processing and saving it will be available as well.</p>
 
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<div id="scrolltotop"></div>
 
</div>
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Revision as of 07:58, 26 September 2012

Minimal Genome Designer

- Overview

1. Overview

1-1. Predicting Essential Genes

Need of the Analysis of Essential Genes

It is thought that today, Synthetic Biology has reached a plateau. Since the success of the experiment that re-synthesizes the genome and insert it into the cell, it seems that Synthetic Biology is not developing. But if somebody can design a genome and synthesize it, synthetic biology can take off again. Then what do we need to design a genome? First, we need information about essential genes. An essential gene is a gene that is critical for survival. If you have the information about the essential gene, you are in a superior state in making human artificial cell in a true sense. Because it means that you already have the ability to make the brick. All you have to do is make a brick with our program developed for you according to the sequence of the essential genes, and conduct experiments.

The Present of the Analysis of Essential Genes

Essential genes are being analyzed in many places, such as in DEG or PATRIC.

The Problem of the Analysis of Essential Genes

Essential genes known today are mostly discovered with in vitro experiments. As seen in the chart above, the result of the experiment can vary according to conditions and methods. We bring forth a problem about this. We believe that to give meaning to a result, it has to be accurate. Also the analysis method of essential genes used today takes a lot of time and labor. To address this we use a bio-informatics way and find essential genes.

1-2. Analysis of Essential Genes

Definition of Essential Genes

As we are using the computer to find essential genes, we can't use the existing method to analogize essential genes with experiments. We assume that if essential genes are critical to living, every organism must have it. So we approached the problem with the assumption that an essential gene is a gene that every living thing will has.

Significance of the Analysis of Essential Genes

We are proud of our analysis methods. You will see that our analysis result is not that different from that proved with experiments. Our analysis results do more than finding essential genes. With this, you can understand the metabolic process and furthermore have a good chance to synthesize an artificial cell.

1-3. Developing of the Minimal Genome Designer

The Purpose of Minimal Genome Designer

The purpose of our program is fundamentally to understand the structure and the principle of the genome. However, we will not stop at understanding the information about genome, but hope that you can go on to build your own genome by using the brick in your experiment.

Advantages of Minimal Genome Designer

Minimal Genome Designer will make you easily understand the genome, by showing you the structure. Providing various information about the gene and the genome, our program will shorten your time to design the experiment. This also means that you can save money as well. We have tried and verified so that Minimal Genome Designer can procure reliability. The results made by Minimal Genome Designer can be used as a new background information for your experiment.

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