Team:SUSTC-Shenzhen-B/july

From 2012.igem.org

(Difference between revisions)
 
(10 intermediate revisions not shown)
Line 395: Line 395:
                         <ul id="topnav" class="sf-menu">
                         <ul id="topnav" class="sf-menu">
                             <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B">Home</a></li>
                             <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B">Home</a></li>
-
                             <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/july">Software</a>
+
                             <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/project.overview">Project Overview</a></li>
 +
                            <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/introduction">Software</a>
                             <ul>
                             <ul>
-
                                     <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/july">Overview</a></li>
+
                                     <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/introduction">Overview</a></li>
                                     <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/algorithm">Algorithm</a></li>
                                     <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/algorithm">Algorithm</a></li>
-
                                     <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/achievements">Achievements</a></li>
+
                                     <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/achievements">Results</a></li>
                                     <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/Download">Download</a></li>
                                     <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/Download">Download</a></li>
                                     <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/comment">Comment</a></li>
                                     <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/comment">Comment</a></li>
Line 434: Line 435:
                                   <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/august">August</a></li>
                                   <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/august">August</a></li>
                                   <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/September">September</a></li>
                                   <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/September">September</a></li>
-
                                   <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/October">October</a></li>
+
                                    
                               </ul>
                               </ul>
                             </li>
                             </li>
Line 443: Line 444:
                                   <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/high.school.visits">High School Visits</a></li>
                                   <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/high.school.visits">High School Visits</a></li>
                                   <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/SynBio.intro">SynBio Intro</a></li>
                                   <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/SynBio.intro">SynBio Intro</a></li>
-
                                   <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/October">October</a></li>
+
                                    
                               </ul>
                               </ul>
                             </li>
                             </li>
                         </ul><!-- topnav -->
                         </ul><!-- topnav -->
                     </nav><!-- nav -->
                     </nav><!-- nav -->
-
                   
+
                    
-
                    <ul id="sn">
+
-
                     <li><a href="http://twitter.com" title="Twitter"><span class="icon-img" style="background:url(/wiki/images/1/1a/Sustc-b1-social-twitter.png)"></span></a></li>
+
-
                        <li><a href="http://plus.google.com" title="Google+"><span class="icon-img" style="background:url(/wiki/images/7/70/Sustc-b1-social-google.png)"></span></a></li>
+
-
                        <li><a href="http://facebook.com" title="Facebook"><span class="icon-img" style="background:url(/wiki/images/a/a7/Sustc-b1-social-facebook.png)"></span></a></li>
+
-
                        <li><a href="http://pinterest.com" title="pinterest"><span class="icon-img" style="background:url(/wiki/images/b/bb/Sustc-b1-social-pinterest.png)"></span></a></li>
+
-
                    </ul>
+
                     <div class="clear"></div>
                     <div class="clear"></div>
                 </section>
                 </section>
Line 470: Line 465:
              
              
<article>
<article>
-
                <h2>July</h2>
+
                            <h1><p>July</p></h1>
-
                 <h3><span class="STYLE10">Abstract</span></h3>
+
                 <h3 class="STYLE10">Abstract</h3>
                 <p>This is the first week that we started our team work. We hold a meeting to allocate everyone’s work. We are divided into 3 groups. The first group is focused on reading paper to learn what is terminator. The second group is responsible for software. The third group should build a web page for our software. None of us is specialist for computer language or biology, so our work is hard.</p>
                 <p>This is the first week that we started our team work. We hold a meeting to allocate everyone’s work. We are divided into 3 groups. The first group is focused on reading paper to learn what is terminator. The second group is responsible for software. The third group should build a web page for our software. None of us is specialist for computer language or biology, so our work is hard.</p>
<br>
<br>
-
                 <h3><span class="STYLE10">Week 1</span></h3>
+
                 <h3 class="STYLE10">Week 1</h3>
-
                 <h3><span class="STYLE10">7.15.2012-7.21.2012</span></h3>
+
                 <h3 class="STYLE10">7.15.2012-7.21.2012</h3>
-
<p>7.15.2012</p>
+
<p class="STYLE11">7.15.2012</p>
<p>Paper Group:</p>
<p>Paper Group:</p>
<p>1. We read some paper, focused on studying two of them.</p>
<p>1. We read some paper, focused on studying two of them.</p>
Line 486: Line 481:
<p>2. We borrowed a couple of books about C# and web design from the library.</p>
<p>2. We borrowed a couple of books about C# and web design from the library.</p>
<br>
<br>
-
<p>7.16.2012</p>
+
<p class="STYLE11">7.16.2012</p>
<p>Paper Group:</p>
<p>Paper Group:</p>
<p>1. We created a table of terminator efficiency including fields of name, description, sequence, stem, loop, tail and efficiency.</p>
<p>1. We created a table of terminator efficiency including fields of name, description, sequence, stem, loop, tail and efficiency.</p>
Line 497: Line 492:
<p>2. We spent the whole night in solving a simple but strange problem. Fortunately we conquered it.</p>
<p>2. We spent the whole night in solving a simple but strange problem. Fortunately we conquered it.</p>
<br>
<br>
-
<p>7.17.2012</p>
+
<p class="STYLE11">7.17.2012</p>
<p>Paper Group:</p>
<p>Paper Group:</p>
<p>1. We found some information on terminator and some specific terminators, learned the progress of writing our RNA fold program.</p>
<p>1. We found some information on terminator and some specific terminators, learned the progress of writing our RNA fold program.</p>
Line 506: Line 501:
<p>1. We learned how to use dreamweaver to design a simple web page.</p>
<p>1. We learned how to use dreamweaver to design a simple web page.</p>
<p>2. We learned how to build a database.</p>
<p>2. We learned how to build a database.</p>
-
<br>
+
<span class="STYLE11"><br>
-
<p>7.18.2012</p>
+
</span>
 +
<p class="STYLE11">7.18.2012</p>
<p>Paper Group:</p>
<p>Paper Group:</p>
<p>1. We visited some terminator structure and mechanism websites.</p>
<p>1. We visited some terminator structure and mechanism websites.</p>
Line 519: Line 515:
<p>3. We were still trying to design a user-friendly web page.</p>
<p>3. We were still trying to design a user-friendly web page.</p>
<br>
<br>
-
<p>7.19.2012</p>
+
<p class="STYLE11">7.19.2012</p>
<p>Paper Group:</p>
<p>Paper Group:</p>
<p>1. We read some paper on terminator efficiency and found lots of models about the mechanism of terminator.</p>
<p>1. We read some paper on terminator efficiency and found lots of models about the mechanism of terminator.</p>
Line 531: Line 527:
<p>2. We built up the basic structure of our web page.</p>
<p>2. We built up the basic structure of our web page.</p>
<br>
<br>
-
<p>7.20.2012</p>
+
<p class="STYLE11">7.20.2012</p>
<p>Paper Group:</p>
<p>Paper Group:</p>
<p>1. We read some paper on two RNA polymerase termination models, which has a higher view of terminator mechanism; and paper on termination mechanism models.</p>
<p>1. We read some paper on two RNA polymerase termination models, which has a higher view of terminator mechanism; and paper on termination mechanism models.</p>
Line 542: Line 538:
<p>2. We continued improving our web page.</p>
<p>2. We continued improving our web page.</p>
<br>
<br>
-
<p>7.21.2012</p>
+
<p class="STYLE11">7.21.2012</p>
<p>Paper Group:</p>
<p>Paper Group:</p>
<p>1. We did a second view of all paper and “why we do a research of terminator efficiency”.</p>
<p>1. We did a second view of all paper and “why we do a research of terminator efficiency”.</p>
Line 552: Line 548:
<p>1. We finished the UI of our windows application program.</p>
<p>1. We finished the UI of our windows application program.</p>
<p>2. We continued improving our web page.</p>
<p>2. We continued improving our web page.</p>
-
 
+
                  
-
            <div class="cleaner h40"></div>
+
                 <div class="clear"></div>
-
            </div>   
+
-
            <div class="col col13 no_margin_right">
+
-
                 <h2>Week Diary</h2>
+
-
                 <ul class="tmo_ul_list">
+
-
                    <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/july">week 1</a></li>
+
-
                    <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/week 2">week 2</a></li>
+
-
                    <li><a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/week 3">week 3</a></li>
+
-
                </ul>
+
-
</font>   
+
-
 
+
-
<div class="clear"></div>
+
         <div class="separator line"></div>
         <div class="separator line"></div>
                  
                  
Line 570: Line 555:
                     <div class="one_fourth">
                     <div class="one_fourth">
                         <span class="dropcap4">1</span>
                         <span class="dropcap4">1</span>
-
                         <h4>Design Ideas</h4>
+
                         <h4>week 1</h4>
                         <p>Pellentesque enim lacus, viverra eu egestas vel, imperdiet non felis. Aliquam erat volutpat. Nullam facilisis aliquet eleifend.</p>
                         <p>Pellentesque enim lacus, viverra eu egestas vel, imperdiet non felis. Aliquam erat volutpat. Nullam facilisis aliquet eleifend.</p>
 +
                        <a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/july">Read More</a>
                     </div>
                     </div>
                     <div class="one_fourth">
                     <div class="one_fourth">
                       <span class="dropcap4">2</span>
                       <span class="dropcap4">2</span>
-
                         <h4>Problem Areas</h4>
+
                         <h4>week 2</h4>
                         <p>Pellentesque enim lacus, viverra eu egestas vel, imperdiet non felis. Aliquam erat volutpat. Nullam facilisis aliquet eleifend.</p>
                         <p>Pellentesque enim lacus, viverra eu egestas vel, imperdiet non felis. Aliquam erat volutpat. Nullam facilisis aliquet eleifend.</p>
 +
                        <a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/week 2">Read More</a>
                     </div>
                     </div>
                     <div class="one_fourth">
                     <div class="one_fourth">
                       <span class="dropcap4">3</span>
                       <span class="dropcap4">3</span>
-
                         <h4>Green Garden</h4>
+
                         <h4>week 3</h4>
                         <p>Pellentesque enim lacus, viverra eu egestas vel, imperdiet non felis. Aliquam erat volutpat. Nullam facilisis aliquet eleifend.</p>
                         <p>Pellentesque enim lacus, viverra eu egestas vel, imperdiet non felis. Aliquam erat volutpat. Nullam facilisis aliquet eleifend.</p>
 +
                        <a href="https://2012.igem.org/Team:SUSTC-Shenzhen-B/week 3">Read More</a>
                     </div>
                     </div>
-
                    <div class="one_fourth lastcols">
+
                                </article>
-
                      <span class="dropcap4">4</span>
+
                <div class="clear"></div>
-
                        <h4>Planting Areas</h4>
+
            </section>
-
                        <p>Pellentesque enim lacus, viverra eu egestas vel, imperdiet non felis. Aliquam erat volutpat. Nullam facilisis aliquet eleifend.</p>
+
            </div>
-
                    </div>
+
        </div>
-
            </article>
+
        <!-- END MAIN CONTENT -->
-
 
-
 
-
 
-
 
-
                <div class="cleaner h40"></div>
 
-
 
-
                      <div class="cleaner"></div>
 
-
                    </form>
 
-
                    <div class="cleaner"></div>
 
-
                </div>
 
-
            </div>
 
-
<br>
 
                 </article>
                 </article>

Latest revision as of 21:26, 26 October 2012

Title

July

Abstract

This is the first week that we started our team work. We hold a meeting to allocate everyone’s work. We are divided into 3 groups. The first group is focused on reading paper to learn what is terminator. The second group is responsible for software. The third group should build a web page for our software. None of us is specialist for computer language or biology, so our work is hard.


Week 1

7.15.2012-7.21.2012

7.15.2012

Paper Group:

1. We read some paper, focused on studying two of them.

2. We tried to find paper on terminator efficiency, but we didn’t make much progress.

Software Group:

We wrote a small program with C++. It can return LH and nt when input stem loop and T tail sequence. If delta G is known, it will give d score automatically.

Web Group:

1. We prepared the first draft wiki and decided to improve it later when we have more experience on web design.

2. We borrowed a couple of books about C# and web design from the library.


7.16.2012

Paper Group:

1. We created a table of terminator efficiency including fields of name, description, sequence, stem, loop, tail and efficiency.

2. We searched web of knowledge and google scholar for transcription terminator paper.

3. We emailed authors of those paper to clear out confution and ask questions about T.E.

Software Group:

We learned some basic knowledge of C#, wrote a program to calculate d score and nt. But users have to type in the free energy. Web group:

1. We learned how to build a simple web page.

2. We spent the whole night in solving a simple but strange problem. Fortunately we conquered it.


7.17.2012

Paper Group:

1. We found some information on terminator and some specific terminators, learned the progress of writing our RNA fold program.

2. We searched more terminator efficiency data, read some materials about how to write a paper, what to be prepared and concerned.

Software Group:

We continued our C# programming study, improved our program to calculate d score and nt.

Web Group:

1. We learned how to use dreamweaver to design a simple web page.

2. We learned how to build a database.


7.18.2012

Paper Group:

1. We visited some terminator structure and mechanism websites.

2. We read a paper about terminator; contacted several researchers to get information. We tried to imitate existing algorithm to determine terminator’s secondary structure. The first version of the program has been developed and we are going to test it.

3. We added more records to the TE database.

Software Group:

We improved the input validation program and made the class-”d_score_calculator” more usable. We read the manual of mfold and calculated the free energy of 1-loop by ourselves. But the free energy of 2-loop is still a problem.

Web Group:

1. We designed our team logo; learned how to build a server for our website.

2. We obtained and installed all the softwares we are going to use.

3. We were still trying to design a user-friendly web page.


7.19.2012

Paper Group:

1. We read some paper on terminator efficiency and found lots of models about the mechanism of terminator.

2. We learned some knowledge about double terminator which we didn’t know before. He also built a database about terminator efficiency which is a big contribution to our group.

Software Group:

1. We converted Liu Xing’s C++ program into C#, added the input validation function. Then we created an interface for the hairpin score calculation.

2. We calculated the free energy of 2-loop containing a bulge loop and a hairpin loop.

Web Group:

1. We learned how to use WPF to build a windows program and updated our server.

2. We built up the basic structure of our web page.


7.20.2012

Paper Group:

1. We read some paper on two RNA polymerase termination models, which has a higher view of terminator mechanism; and paper on termination mechanism models.

2. We updated and optimized TE database.

3. We improved the stem loop determination algorithm and modularized program.

Software Group:

We programmed the algorithm to make sure the structure of the terminator is clear.

Web Group:

1. We continued building a windows program.

2. We continued improving our web page.


7.21.2012

Paper Group:

1. We did a second view of all paper and “why we do a research of terminator efficiency”.

2. We updated our database again.

Software Group:

1. We continued optimizing our algorithm.

2. We read some paper and material. We can create the algorithm based on one pair of “closing base pair”.

Web Group:

1. We finished the UI of our windows application program.

2. We continued improving our web page.

1

week 1

Pellentesque enim lacus, viverra eu egestas vel, imperdiet non felis. Aliquam erat volutpat. Nullam facilisis aliquet eleifend.

Read More
2

week 2

Pellentesque enim lacus, viverra eu egestas vel, imperdiet non felis. Aliquam erat volutpat. Nullam facilisis aliquet eleifend.

Read More
3

week 3

Pellentesque enim lacus, viverra eu egestas vel, imperdiet non felis. Aliquam erat volutpat. Nullam facilisis aliquet eleifend.

Read More
South University of Science and Technology of China