Team:CBNU-Korea/Project/GD/Overview

From 2012.igem.org

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<li class="HOME"><a
<li class="HOME"><a
href="https://2012.igem.org/Team:CBNU-Korea">HOME</a></li>
href="https://2012.igem.org/Team:CBNU-Korea">HOME</a></li>
-
<li class="TEAM"><a href="#">TEAM</a></li>
+
<li class="TEAM"><a
 +
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 +
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+ Brick Designer</a></li>
+ Brick Designer</a></li>
<li class="MGD"><a href="#">03 + Minimal Genome Designer</a></li>
<li class="MGD"><a href="#">03 + Minimal Genome Designer</a></li>
-
<li id="li_sub" class="MGD_Overview">- Overview</li>
+
<li id="li_sub" class="MGD_Overview"><a href="#">-
-
<li id="li_sub" class="MGD_Method">- Method</li>
+
Overview</a></li>
-
<li id="li_sub" class="MGD_Analysis">- Analysis</li>
+
<li id="li_sub" class="MGD_Method"><a
 +
href="https://2012.igem.org/Team:CBNU-Korea/Project/GD/Method">-
 +
Method</a></li>
 +
<li id="li_sub" class="MGD_Analysis"><a
 +
href="https://2012.igem.org/Team:CBNU-Korea/Project/GD/Analysis">-
 +
Analysis</a></li>
<li class="DOWNLOAD"><a
<li class="DOWNLOAD"><a
href="https://2012.igem.org/Team:CBNU-Korea/Project/Download">04
href="https://2012.igem.org/Team:CBNU-Korea/Project/Download">04
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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. Overview</h1>
-
<p>- The importance of the transfer, saving and management of
+
<h2>1-1. Predicting Essential Genes</h2>
-
bio-information is now closely related to the computers. Nowadays
+
<p>
-
bio-informatics are used in many fields from simple biological
+
<strong>1) Need of the Analysis of Essential Genes</strong>
-
models to complicated algorithm forecast and more. And in
+
</p>
-
synthetic biology, since designing a biological circuit by using
+
<p>It is thought that today, Synthetic Biology has reached a
-
the computer became available, it has opened a new era. In the
+
plateau. Since the success of the experiment that re-synthesizes
-
past, synthetic biology used to find subjects like a genetic part
+
the genome and insert it into the cell, it seems that Synthetic
-
that is about a specific purpose and the connection between the
+
Biology is not developing. But if somebody can design a genome and
-
fastest designing process only by experiments. But now in the
+
synthesize it, synthetic biology can take off again. Then what do
-
future of synthetic biology, experiment and the computational
+
we need to design a genome? First, we need information about
-
designing program must be in a mutual relationship. The purpose of
+
essential genes. An essential gene is a gene that is critical for
-
our project is to increase the efficiency of the experiment by
+
survival. If you have the information about the essential gene,
-
using the designing process of BioBrick prior to the experiment,
+
you are in a superior state in making human artificial cell in a
-
and improve the efficiency of the connection between the next
+
true sense. Because it means that you already have the ability to
-
experiment conducted by the program user.</p>
+
make the brick. All you have to do is make a brick with our
-
<div id="scrolltotop"></div>
+
program developed for you according to the sequence of the
 +
essential genes, and conduct experiments.</p>
 +
<p>
 +
<strong>2) 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>
 +
<img src="https://static.igem.org/mediawiki/2012/1/11/CBK_B_001.png">
 +
<p>
 +
<strong>3) 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>
-
<h1>2. Feature</h1>
+
<h2>1-2. Analysis of Essential Genes</h2>
-
<h2>2-1. BioBrick Data Download</h2>
+
<p>
-
<p>- The registered BioBrick information needed for designing
+
<strong>1) Definition of Essential Genes</strong>
-
in this program, can be easily downloaded without being typed in.</p>
+
</p>
-
<h2>2-2. Design</h2>
+
<p>As we are using the computer to find essential genes, we
-
<p>- The user can arrange the BioBrick in any sequence they
+
can't use the existing method to analogize essential genes with
-
want. And if they want, the user can put a proper Prefix, Suffix
+
experiments. We assume that if essential genes are critical to
-
restriction enzyme site between the Bricks by the software.</p>
+
living, every organism must have it. So we approached the problem
-
<p>- By selecting the Plasmid Backbone and the restriction
+
with the assumption that an essential gene is a gene that every
-
enzyme in sequence, the cloning will be done automatically.</p>
+
living thing will has.</p>
-
<h2>2-3. Screen Shot</h2>
+
<p>
-
<p>- The BioBrick that the user designed from the program is
+
<strong>2) Significance of the Analysis of Essential
-
saved in image files to be readily used in Wiki or documents.</p>
+
Genes</strong>
-
<h2>2-4. Various Storage Formats</h2>
+
</p>
-
<p>- The project in designing in progress can be saved or
+
<p>We are proud of our analysis methods. You will see that our
-
imported. Also, by saving the informations as a SBOL, GenBank,
+
analysis result is not that different from that proved with
-
Fasta form, the user can use the information that they design in
+
experiments. Our analysis results do more than finding essential
-
other programs as well.</p>
+
genes. With this, you can understand the metabolic process and
 +
furthermore have a good chance to synthesize an artificial cell.</p>
 +
 
 +
<h2>1-3. Developing of the Minimal Genome Designer</h2>
 +
<p>
 +
<strong>1) The Purpose of Minimal Genome Designer</strong>
 +
</p>
 +
<p>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.</p>
 +
<p>
 +
<strong>2) Advantages of Minimal Genome Designer</strong>
 +
</p>
 +
<p>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.</p>
<div id="scrolltotop"></div>
<div id="scrolltotop"></div>
-
<h1>3. The process of the program designing</h1>
+
<h1>2. Function</h1>
-
<h2>3-1. Problem Recognition</h2>
+
 
-
<p>- In many common laboratories today, there is a limit that
+
<h2>2-1. Viewer</h2>
-
the user themselves has to put in the BioBrick Data, and draw it
+
 
-
as an image after they finish the design. So we decided to develop
+
<p>1) The program is installed and run in a local computer. The
-
the designing a program that, based on BioBrick DataBase, directly
+
local database isn't included in the program, and to see the
-
provide designing process with convenient additional functions as
+
database you should have access to the server that we constructed.
-
well.</p>
+
</p>
-
<h2>3-2. Requirement Checking</h2>
+
<p>2) The program consists of the circular viewer on the upper
-
<p>- We checked on other programs that many people are using
+
left, and the linear viewer below, and a Genome list on the right.</p>
-
nowadays, and analyzed the steps that are needed in designing.</p>
+
<p>3) First, select a gene in the Genome List on the right. You
-
<p>- For the connection within other programs that can be used
+
may select it on the Tree View, or by searching the gene that you
-
after the experiment, we checked on the needs of the saving
+
want. After selection, the information of the gene will be shown
-
methods on GenBank, SBOL, Fasta.</p>
+
in graphic. You can see more information about the relevant gene
-
<h2>3-2. Design</h2>
+
and the genome on the Genome Information in the middle.</p>
-
<p>- Visual Studio 2010, 2012 (C#)</p>
+
<p>4) If you move the reading glass image of the circular
-
<p>- Windows 7</p>
+
viewer, you can see the relevant location in linear graphic. By
-
<p>- OleDB (MS OFFICE)</p>
+
using the linear scroll bar, you can change the linear location.
-
<p>- * When running the program, Microsoft Runtime is required.</p>
+
If you click the relevant square image in the linear viewer, you
-
<h2>3-2. Discussion and Feedback</h2>
+
can see more information about the gene(Like sequences, length,
-
<p>- Our team members repeated testing the program, finding the
+
location, Synb_id, function, product and more).</p>
-
errors and fixing the problems.</p>
+
<p>5) With the check box on the lower right-hand corner of the
 +
circular viewer, you can check the gene of your choice.</p>
 +
<p>6) By checking the By COG check box, you can see each of the
 +
COG functions of each gene. Choose the COG function in the scroll
 +
box that appears after you check, then you can see the genes
 +
including that function.</p>
 +
<p>7) If you check the DEG Only check box, you can see the
 +
informations that DEG has found in vitro in visual.</p>
 +
<p>8) If you check the EG Only check box, you can see the
 +
information on essential genes that we gain through analysis in
 +
visual.</p>
 +
<p>9) Select 'History' in the Genome List menu, then you can
 +
see all the genes that have seen all along easily.</p>
 +
 
 +
<h2>2-2. Unique Genome Designer</h2>
 +
 
 +
<p>1) Shows the information of essential genes that can exist
 +
in each section.(Function, Product, COG number etc.)</p>
 +
<p>2) Shows the frequency of the essential genes in each
 +
section that are analyzed using 82 different species.</p>
 +
<p>3) Shows the frequency of the COG of each section that is
 +
analyzed using 82 different species.</p>
 +
<p>4) By choosing each section of 20 in the screen, the
 +
essential genes that can be inserted in the relevant area will be
 +
listed.</p>
 +
<p>5) The user can put the wanted essential gene In each
 +
section and see the processing situation. When the whole 478
 +
essential genes are put in all sections, the design is completed.
 +
</p>
 +
<p>7) The user can save and import the designing situation as a
 +
XML form at their convenience.</p>
 +
<p>8) When the user complete the design, the designed minimal
 +
genome can be saved as a XML form and it could be viewed at
 +
Viewer.</p>
<div id="scrolltotop"></div>
<div id="scrolltotop"></div>
-
<h1>4. Future Work</h1>
+
<h1>3. Future Work</h1>
-
<p>Our program is now version 1.0.0, and will be updated and
+
<p>
-
offer better information and performance about the designing
+
Our ultimate objective is to make a program that can build a complete minimum genome. Well do we know the information that we need to realize our goal. First, we analogize essential genes that every species is supposed to have. And we are aware of the fact that to achieve this goal, our analysis method needs higher reliability. Therefore, we are going to use the same method on a different genus (For example, like Mycoplasma, Salmonella, that the essential gene is already identified experimentally), and secure the reliability of our analysis method. Secondly, we will expand the analysis of specific gene. We consider that there are genes located on each species and levels which represent the function of the location. We have estimated the specific genes of species level and analyzed them in this year. And if we keep up our study then we can analyze the genes that have been shown the characteristic of specific species, and then we will presume specific gene of upper levels such as species, genus, family, order, and etc in a same way. Futhermore, we are going to finally figure out the genes that represent feature of the location. We are expecting that if we use the analyze result of specific gene, our program will have more wealthy and precise results. Thirdly, we presume accurate arrangement of essential gene that we analyzed.  Because we mostly concentrated on the analysis of strand pattern, it isn’t enough to provide accurate arrangement. However we know that we need the information of the order of genes to make complete design software. Thus we are going to analyze this and improve the completeness of our Designer.<br>
-
process in next versions. First, simplification of the
+
We believe that if this analysis becomes perfect, our analysis method will secure reliability and give you the accurate outcome. Also hoping that you will use our program more actively, we are planning to provide information you will need(For example, restriction enzyme sites, Gene map, the culture conditions of different species). We hope our program Minimal Genome Designer will provide the fundamental information for your experiment in the near future.
-
registration process of the iGEM Part will be offered. The
+
</p>
-
registration of BioBrick is now available only in online. But by
+
-
co-working with iGEM, we will develop a better functioning
+
-
program, and make it possible to design and register the Brick at
+
-
the same time. Secondly, we are planning to add a communication
+
-
function between the users. This function will help the users to
+
-
share opinions, and discuss designing information about a specific
+
-
Brick. This discussion will help the users improve their
+
-
experiment or project. Third, the expression rate will be produced
+
-
in a numerical value. The expression rate value is a score that
+
-
will show the users how the expression of the BioBrick designed by
+
-
cloning is working in the experiment. To make it as a score,
+
-
theoretical background and algorithm based on a lot of data are
+
-
required. The last is the import of the files with various saving
+
-
forms. Nowadays we can only save the designed BioBrick data after
+
-
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 01:43, 27 October 2012

Minimal Genome Designer

- Overview

1. Overview

1-1. Predicting Essential Genes

1) 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.

2) The Present of the Analysis of Essential Genes

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

3) 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

1) 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.

2) 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

1) 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.

2) 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.

2. Function

2-1. Viewer

1) The program is installed and run in a local computer. The local database isn't included in the program, and to see the database you should have access to the server that we constructed.

2) The program consists of the circular viewer on the upper left, and the linear viewer below, and a Genome list on the right.

3) First, select a gene in the Genome List on the right. You may select it on the Tree View, or by searching the gene that you want. After selection, the information of the gene will be shown in graphic. You can see more information about the relevant gene and the genome on the Genome Information in the middle.

4) If you move the reading glass image of the circular viewer, you can see the relevant location in linear graphic. By using the linear scroll bar, you can change the linear location. If you click the relevant square image in the linear viewer, you can see more information about the gene(Like sequences, length, location, Synb_id, function, product and more).

5) With the check box on the lower right-hand corner of the circular viewer, you can check the gene of your choice.

6) By checking the By COG check box, you can see each of the COG functions of each gene. Choose the COG function in the scroll box that appears after you check, then you can see the genes including that function.

7) If you check the DEG Only check box, you can see the informations that DEG has found in vitro in visual.

8) If you check the EG Only check box, you can see the information on essential genes that we gain through analysis in visual.

9) Select 'History' in the Genome List menu, then you can see all the genes that have seen all along easily.

2-2. Unique Genome Designer

1) Shows the information of essential genes that can exist in each section.(Function, Product, COG number etc.)

2) Shows the frequency of the essential genes in each section that are analyzed using 82 different species.

3) Shows the frequency of the COG of each section that is analyzed using 82 different species.

4) By choosing each section of 20 in the screen, the essential genes that can be inserted in the relevant area will be listed.

5) The user can put the wanted essential gene In each section and see the processing situation. When the whole 478 essential genes are put in all sections, the design is completed.

7) The user can save and import the designing situation as a XML form at their convenience.

8) When the user complete the design, the designed minimal genome can be saved as a XML form and it could be viewed at Viewer.

3. Future Work

Our ultimate objective is to make a program that can build a complete minimum genome. Well do we know the information that we need to realize our goal. First, we analogize essential genes that every species is supposed to have. And we are aware of the fact that to achieve this goal, our analysis method needs higher reliability. Therefore, we are going to use the same method on a different genus (For example, like Mycoplasma, Salmonella, that the essential gene is already identified experimentally), and secure the reliability of our analysis method. Secondly, we will expand the analysis of specific gene. We consider that there are genes located on each species and levels which represent the function of the location. We have estimated the specific genes of species level and analyzed them in this year. And if we keep up our study then we can analyze the genes that have been shown the characteristic of specific species, and then we will presume specific gene of upper levels such as species, genus, family, order, and etc in a same way. Futhermore, we are going to finally figure out the genes that represent feature of the location. We are expecting that if we use the analyze result of specific gene, our program will have more wealthy and precise results. Thirdly, we presume accurate arrangement of essential gene that we analyzed. Because we mostly concentrated on the analysis of strand pattern, it isn’t enough to provide accurate arrangement. However we know that we need the information of the order of genes to make complete design software. Thus we are going to analyze this and improve the completeness of our Designer.
We believe that if this analysis becomes perfect, our analysis method will secure reliability and give you the accurate outcome. Also hoping that you will use our program more actively, we are planning to provide information you will need(For example, restriction enzyme sites, Gene map, the culture conditions of different species). We hope our program Minimal Genome Designer will provide the fundamental information for your experiment in the near future.

Retrieved from "http://2012.igem.org/Team:CBNU-Korea/Project/GD/Overview"