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| <div class="hp_s2t2">                  Presentation about lectures of synthetic biology                           Member ZhangYijuan introduces synthetic biology</div> | | <div class="hp_s2t2">                  Presentation about lectures of synthetic biology                           Member ZhangYijuan introduces synthetic biology</div> |
| <div class="hp_s2p1"><img src="https://static.igem.org/mediawiki/2013/5/5f/Xmusoftware_outreach_pho10.jpg"><img src="https://static.igem.org/mediawiki/2013/d/d9/Xmusoftware_outreach_pho11.jpg"></div> | | <div class="hp_s2p1"><img src="https://static.igem.org/mediawiki/2013/5/5f/Xmusoftware_outreach_pho10.jpg"><img src="https://static.igem.org/mediawiki/2013/d/d9/Xmusoftware_outreach_pho11.jpg"></div> |
- | <div class="hp_s2t2">                         Enthusiastic interaction among seniors                                              Xiamen University's iGEM team members and seniors </div> | + | <div class="hp_s2t2">                         Enthusiastic interaction among seniors  |
- | </br></br></br>
| + | |
- | <!--游园会-->
| + | |
- | <a name="_gardenparty" id="_gardenparty"></a>
| + | |
- | <div class="hp_s2h1">Themed Garden Party of Synthetic Biology</div>
| + | |
- | <div class="hp_s2t1">      In order to publicize synthetic biology and iGEM, we held a themed garden party of synthetic biology in Guihua Mountain Building in our campus on July 17th 2013, after the cathedra. The party started at 2:00 pm and lasted for 3.5 hours, oriented to the high schools form summer camp of Fujian Province.</div>
| + | |
- | <div class="hp_s2t1">      Themed show of synthetic biology came first. We introduced systematically basic content of synthetic biology and its security issues to our high school audience, as well as ABCs of iGEM. Synthetic biology knowledge, safety and security principles, rules and regulations for operation were our chief presentation with the help of multimedia.</div>
| + | |
- | <div class="hp_s2t1">      Then games took their turn. We had lantern riddles, handing some synthetic biology riddles witch leads to proper nouns so as to help remembering, on lanterns. We had DNA difference spotting, putting two DNAs of tiny differences together as a challenge for insight and memory. Noticeably and proudly we create a new game in the foundation of Fold-it, a protein folding game. Scores will be marked on the basis of qualities of protein models.(link: http://verycd.gdajie.com/topics/2817908/) Last but not least, we alter and redesigned Sanguosha into a new card game: Synthetic-biology-sha. It was a combination of theories of experiment operation and bacteria, as a joyful way for our campers to learn more about synthetic biology.</div>
| + | |
- | <div class="hp_s2t1">      Except for that, our specially designed poster series were a great attraction which received high opinions from all folks.</div>
| + | |
- | <div class="hp_s2p1"><img src="https://static.igem.org/mediawiki/2013/0/05/Xmusoftware_outreach_pho13.jpg"><img src="https://static.igem.org/mediawiki/2013/5/53/Xmusoftware_outreach_pho14.jpg"></div>
| + | |
- | <div class="hp_s2t2">          Seniors from summer camp take part in the game of lantern riddles                                        Game of protein folding</div>
| + | |
- | <div class="hp_s2p1"><img src="https://static.igem.org/mediawiki/2013/2/28/Xmusoftware_outreach_pho15.jpg"><img src="https://static.igem.org/mediawiki/2013/8/8f/Xmusoftware_outreach_pho16.jpg"></div>
| + | |
- | <div class="hp_s2t2">         Students are playing game of protein folding with intense enthusiasm                    Game scene in finding differences among DNA</div>
| + | |
- | <div class="hp_s2p1"><img src="https://static.igem.org/mediawiki/2013/6/6c/Xmusoftware_outreach_pho17.jpg"><img src="https://static.igem.org/mediawiki/2013/9/93/Xmusoftware_outreach_pho18.jpg"></div>
| + | |
- | <div class="hp_s2t2">                    Members of iGEM introduce Synthetic-biology-sha                                      Members of Xiamen University's iGEM team</div>
| + | |
- | </br></br></br>
| + | |
- | <!--隧道涂鸦-->
| + | |
- | <a name="_doodles" id="_doodles"></a>
| + | |
- | <div class="hp_s2h1">Doodles of Synthetic Biology</div>
| + | |
- | <div class="hp_s2t1">       Furong Tunnel, one of the Xiamen University's main tourist attractions, visited by more than 1,000 people per day statistically, witnessed the doodles of iGEMers form Xiamen University. The doodle mainly includes the combination between experiment and assembly language, stressing the core of iGEM software team: assembly language for the software, experiment for the verification.</div>
| + | |
- | <div class="hp_s2p1"><img src="https://static.igem.org/mediawiki/2013/8/8b/Xmusoftware_outreach_pho19.jpg"></div>
| + | |
- | <div class="hp_s2t2">                                    iGEM paintings in Fu-Rong tunnel</div>
| + | |
- | <div class="hp_s2t1">      Our Human Practice was an acceleration for popularization of synthetic biology, iGEM and entries of Xiamen University for XMU_Software this year, an education of its safety and security for further step; a platform for academic exchange with other domestic iGEM teams. It was indeed a success as, if no more than, expected.</div>
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- | </br></br></br></br></br></br></br></br></br></br>
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- | </div>
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- | </div>
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- | <img src="https://static.igem.org/mediawiki/2013/f/f9/Xmusoftware_background.png" width="1348px">
| + | |
- | <div class="notebook_title">NOTEBOOK</div>
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- | </div>
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- |
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- | <div class="navi_text">
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- | <a id="notebook_navi1" class="navi3" href="#_tool" onmouseover="navi1();" onmouseout="navi11();">TOOLS</a>
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- | <a id="notebook_navi2" class="navi4" href="#_journal" onmouseover="navi2();" onmouseout="navi21();">JOURNAL</a>
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- | <a id="notebook_navi3" class="navi5" href="javascript:void(0)" onmouseover="navi3();" onmouseout="navi31();">Back To Top</a>
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- | </div>
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- |
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- | <!--tools-->
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- | <div id="notebook_s2"><a name="_tool" id="_tool"></a>
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- | <img src="https://static.igem.org/mediawiki/2013/8/8d/Xmusoftware_block.png" width="1348px" class="sep_photo">
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- | <div class="sep_title">TOOLS</div>
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- | <div class="sep_number">01</div>
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- | </div>
| + | |
- | <!--3个工具-->
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- | <div id="notebook_s2m2">
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- | <!--工具图像--->
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- | <div id="notebook_s2m2n1">
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- | <div id="notebook_s2m2p1"><img src="https://static.igem.org/mediawiki/2013/f/f7/Xmusoftware_notebook_tool1.png" class="notebook_s2m2p1" onmouseover="notebook_s2m2c1();" onmouseout="notebook_s2m2c2();"></div>
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- | <div id="notebook_s2m2p2"><img src="https://static.igem.org/mediawiki/2013/b/b5/Xmusoftware_notebook_tool2.png" class="notebook_s2m2p1" onmouseover="notebook_s2m2c3();" onmouseout="notebook_s2m2c4();"></div>
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- | <div id="notebook_s2m2p3"><img src="https://static.igem.org/mediawiki/2013/e/e1/Xmusoftware_notebook_tool3.png" class="notebook_s2m2p1" onmouseover="notebook_s2m2c5();" onmouseout="notebook_s2m2c6();"></div>
| + | |
- | </div>
| + | |
- | <!--工具名称-->
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- | <div id="notebook_s2m2n2">
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- | <div id="notebook_s2m2t1" class="notebook_s2t3">XMind</div>
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- | <div id="notebook_s2m2t2" class="notebook_s2t3">PowerPoint</div>
| + | |
- | <div id="notebook_s2m2t3" class="notebook_s2t3">Robert's Rules of Order</div>
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- | </div>
| + | |
- | <!--3个绿色连接线-->
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- | <div id="notebook_s2m2n3">
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- | <div id="notebook_s2m2b1" class="notebook_s2m2b1"></div>
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- | <div id="notebook_s2m2b2" class="notebook_s2m2b1"></div>
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- | <div id="notebook_s2m2b3" class="notebook_s2m2b1"></div>
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- | </div>
| + | |
- | <!--文本-->
| + | |
- | <div id="notebook_s2m2n4">
| + | |
- | <div id="notebook_s2m2a1" class="notebook_s2t4">XMind</div>
| + | |
- | <div id="notebook_s2m2a2" class="notebook_s2t5">The software was used for record our brainstorm and make new ideas. It is free! And it has so many models for new users to build up their own models.</div></br>
| + | |
- | <div id="notebook_s2m2a3" class="notebook_s2t4">PowerPoint</div>
| + | |
- | <div id="notebook_s2m2a4" class="notebook_s2t5">That Powerpoint is used for reporting our progress and giving presentations. Thus we practice it and study how to tell a funny story.</div></br>
| + | |
- | <div id="notebook_s2m2a5" class="notebook_s2t4">Robert's Rules of Order</div>
| + | |
- | <div id="notebook_s2m2a6" class="notebook_s2t5">This book guided us on how to make a meeting effective. And it really worth the hornor.</div>
| + | |
- | </div>
| + | |
- | <!--工具标题-->
| + | |
- | <div id="notebook_s2m2n5">TOOLS</div>
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- | </div>
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- | </div>
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- |
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- | <div id="notebook_s3"><a name="_journal" id="_journal"></a>
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- | <!--分界栏-->
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- | <img src="https://static.igem.org/mediawiki/2013/8/8d/Xmusoftware_block.png" width="1348px" class="sep_photo">
| + | |
- | <div class="sep_title">JOURNAL</div>
| + | |
- | <div class="sep_number">02</div>
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- | </div>
| + | |
- | <!--日记-->
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- | <div id="notebook_s3m2">
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- | <!--镂空圆,上-->
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- | <div class="notebook_s3p0"></div>
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- | <div class="notebook_s3p00"></div>
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- | </div>
| + | |
- |
| + | |
- | <!--三月日记标题栏-->
| + | |
- | <div id="notebook_s3m2n1" onClick="march();">
| + | |
- | <img src="https://static.igem.org/mediawiki/2013/5/5f/Xmusoftware_notebook_date.png">
| + | |
- | <div class="notebook_s3t1">MARCH</div>
| + | |
- | <div class="notebook_s3t2">2013.3</div>
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- | </div>
| + | |
- | <!--三月日记滑动栏-->
| + | |
- | <div id="notebook_s3m2n2">
| + | |
- | <div class="notebook_s3t3">
| + | |
- | <!--日记1 三月三十日-->
| + | |
- | <div id="note1">
| + | |
- | <div class="note1h1">2013.3.30</div>
| + | |
- | <div class="note1t1">Chen:Experimental workspace that can automaticly decide whether it is a personal account or business account from the networking and the workspace afford download link of those relevant softwares.Can we get those softwares embedded? How to help our costumers find out the software they want quickly?(keyword search?) It is also important to processing data,generate lab reports and logs in the workspace.</div>
| + | |
- | <div class="note1t1">Future plan:adding softwares in the software library and optimizing the software's functions and landscaping interface. Besides,we want to afford real time data while monitoring on different platforms.And how about sync to the cloud?</div>
| + | |
- | <div class="note1t1">Likai Qiu:easy express. The purpose of design:economize time for researchers, and then they just need to stay on creating new ideas and putting possible idea into practice. Besides, unified expressions get researchers understand other's work easily.Its system's function:drawing,display sequence,dynamic display structure of the plasmid and parts of the experiments,shows the meaning of each graph and table,guiding and help.Question:can we really dynamic display the data? If we standardization the presentation, the software may be reject by other teams for its boredom standardization different kinds of efforts may be impossible.This software told you that you don't need to learn too MAYA and other magic softwares, it can include their funcitions, will it be possible?(perhaps impossible for now) By attach database to the software and afford individuation information search for our users.</div>
| + | |
- | <div class="note1t1">Chuyue Wang:document management and real time monitoring that can help on scientific literature management and take notes and share your ideas.Automatic detection and data recording of streamlined repetition, design shortcut keys to improved operational efficiency. Using graph visualization to understand the data easily.</div>
| + | |
- | <div class="note1t1">Yijuan Zhang:directional optimization of BioBricks.</div>
| + | |
- | <div class="note1t1">Purpose:input enviromental parameters including special loci of genes, the expected expression level and chooses candidate BioBricks. optimize and find out the best sequence under given conditions and setting number of evolutionary (n) chooses the BioBricks, and the systerm will guide the user until the given conditions were met, variation to generates new sequences. Copy,retain or reject BioBricks according to the matched-degree, this step is parallel to natural selection. Circulate</div>
| + | |
- | <div class="note1t1">Stop after circulate n times, output the best sequence. The problems are how to make sure that the genotype equals to its phenotype? How to define the f(x) that we want? And now we need to read some books about genetic algorithm to get the way.</div>
| + | |
- | <div class="note1t1">Summary:Now we have two ideas,build a platform for researchers focusing on synthetic biology (aim to increase their efficency). Already several teams work on it, so it might be a rat race .</div>
| + | |
- | <div class="note1t1">Solve synthetic biology problems with GA. We need to supplement the relevant basic knowledge of GA.So,studying CLOTHO developed by Berkeley and other universities and try to find out some new ideas and make a research to find out what front-line researchers need.We also need to study relevant softwares and GA,protein quaternary structure and knowledge about directional optimization, read more books and literature to make sure the possibility of the idea. For GA is too difficult for some of us, we still need to get come up with some new ideas.</div>
| + | |
- | <div class="note1t1">OK, for this much tasks, work in groups and share new ideas~!</div>
| + | |
- | </br></br>
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- | </div>
| + | |
- | <!--左边小圆-->
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- | <div class="notebook_s3m2p1">
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- | <div id="notebook_s3p1" class="notebook_s3p2" onClick="notebook_s3m2c1();"></div>
| + | |
- | </div>
| + | |
- | <!--左边日期-->
| + | |
- | <div class="notebook_s3m2t1">
| + | |
- | <div class="notebook_s3t5">Meeting </br>Record</div>
| + | |
- | <div class="notebook_s3t4">3.30</div>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- |
| + | |
- | <!--四月-->
| + | |
- | <div id="notebook_s3m2n3" onClick="april();">
| + | |
- | <img src="https://static.igem.org/mediawiki/2013/5/5f/Xmusoftware_notebook_date.png">
| + | |
- | <div class="notebook_s3t1">APRIL</div>
| + | |
- | <div class="notebook_s3t2">2013.4</div>
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- | </div>
| + | |
- | <div id="notebook_s3m2n4">
| + | |
- | <div class="notebook_s3t3">
| + | |
- | <!--四月七日-->
| + | |
- | <div id="note2">
| + | |
- | <div class="note1h1">2013.4.7</div>
| + | |
- | <div class="note1t1">Zhang Yijuan had learn GA & the 《Alteredpeptideligands》,its diameters is in coden,but we need to improve BioBricks,so we need to change it to suit us and increase efficiency.Also ,we read news about Calgary and NewCastle ,SUSTC(calculate terminator efficiency by a score systerm).For coden is linked up with fitness,which influence the secondary structure of protein. For example, the changing of A-tail, stem loop and T-tail, we can also find it in the project of SUSTC.Besides,she also read papers on how to calculate f(x) & take notes when learn new things. SUSTC' fault:just one function, it may not catch everybody' eyes . She plan to change promoter so as to confirm the system efficiency.Huang Jianxing schedule to learn neural network ,after that,he will change the source code to be used on today's system.Huangxin and Huangjian now know just a little about matlab but they think the code can be change easily. Wang Chuyue learn matlab as well.Tangchun read some books about system efficiency and download papers to share on the group.From N-terminal domain rule, he notice when choose parameters is a key point for our project.</div>
| + | |
- | <div class="note1t1">Next week's task had been written on the wall. And we suggest everybody upload and try to explain by powerpoint.</div>
| + | |
- | </br></br>
| + | |
- | </div>
| + | |
- | <!--四月十四日-->
| + | |
- | <div id="note3">
| + | |
- | <div class="note1h1">2013.4.14</div>
| + | |
- | <div class="note1t1">Specific our goals:for most of us aren't familiar with GA, we misunderstand Yijuan's idea at the beginning. we determined to find the best fit BioBrick through genetic recombination and genovariation inside the BioBricks, and we evaluating them by our algorithm.Compare with other team' work:EbolGENTS(2008,Calgary) and Ebolutionary Algorithm(2008,Newcastle University). both of them had used GA, however ,they construct a system with given BioBricks just like build blocks, after which they find the best system in those "structures". as for our group, we focus on genetic recombination and genovariation inside the BioBricks to make new ones, and search for the best with given conditions.</div>
| + | |
- | <div class="note1t1">Reduce the degree of difficulty:it may be a huge project to ensure phenotype and fitness result from mutations of base sequence in the whole BioBricks.so we decided to narrow down and aim at optimize decision of particular bases, promoter, terminator and RBS locus.Yijuan had mentioned that SUSTC had done research on computational efficiency of the terminator's gene sequence.</div>
| + | |
- | <div class="note1t1">Core problem:the core problems of our idea contain two parts:How to ensure phenotype by genotype? How to find the f(x) meet our goal? Fitness function:three ways had been chosen to slove it: first, search for relevant literatures; read the project offered by Professor Fang named " microorganism's choice of the optimal conditions"; if possible, our wet lab should give us a hand on affording real time data and experimental simulation to ensure f(x).</div>
| + | |
- | <div class="note1t1">Current task:check the project of iGEM "calculate terminator’s efficiency by sequence of the terminators" ;all of us need to take a look on SUSTC' work and discuss the next time.Learning Matlab and GA!</div>
| + | |
- | <div class="note1t1">Annotations:we had set sail now!All of us need to learn SUSTC's work on ensuring genotype by phenotype and discuss the next time.We are badly in need of professor's help!</div>
| + | |
- | <div class="note1t1">Try to find more idea! stay hungry!</div>
| + | |
- | </br></br>
| + | |
- | </div>
| + | |
- | <!--四月二十一日-->
| + | |
- | <div id="note4">
| + | |
- | <div class="note1h1">2013.4.21</div>
| + | |
- | <div class="note1t1">This week we had summary the work we had done before and nowadays we need to fix it.GA as a algorithm can work on several biological questions. And several new ways and improvement had been found out to slove the problem. Take an example, GASCO is a new algorithm that improve the answer of GA.</div>
| + | |
- | <div class="note1t1">We start to plan the human practice. That may be of great importance. We had distribute the job and explicit the goal so as to lifting efficiency.</div>
| + | |
- | <div class="note1t1">Neural network can be used in it.</div>
| + | |
- | </br></br></br></br></br></br>
| + | |
- | </div>
| + | |
- | <!--四月二十八-->
| + | |
- | <div id="note5">
| + | |
- | <div class="note1h1">2013.4.28</div>
| + | |
- | <div class="note1t1">Zhang yijuan:after reading several papers and get down to SBOL. She got some new ideas on our program.</div>
| + | |
- | <div class="note1t1">Han tao & Huang Jiang & Huang Xin: they had success got a software that can simulate the situation. However, the software remain some problem to be slove. We had better make a new one, do not use this one, for we can use Matlab.That will be a good idea.</div>
| + | |
- | <div class="note1t1">The platform and relevant work went on well.</div>
| + | |
- | </br></br></br></br></br></br></br>
| + | |
- | </div>
| + | |
- | <div class="notebook_s3m2p2">
| + | |
- | <div id="notebook_s3p2" class="notebook_s3p2" onClick="notebook_s3m2c2();" onmouseover="notebook_s3m2c21();" onmouseout="notebook_s3m2c22();"></div>
| + | |
- | <div id="notebook_s3p3" class="notebook_s3p1" onClick="notebook_s3m2c3();" onmouseover="notebook_s3m2c31();" onmouseout="notebook_s3m2c32();"></div>
| + | |
- | <div id="notebook_s3p4" class="notebook_s3p1" onClick="notebook_s3m2c4();" onmouseover="notebook_s3m2c41();" onmouseout="notebook_s3m2c42();"></div>
| + | |
- | <div id="notebook_s3p5" class="notebook_s3p1" onClick="notebook_s3m2c5();" onmouseover="notebook_s3m2c51();" onmouseout="notebook_s3m2c52();"></div>
| + | |
- | </div>
| + | |
- | <div class="notebook_s3m2t2">
| + | |
- | <div class="notebook_s3t5">Meeting </br>Record</div>
| + | |
- | <div class="notebook_s3t4">4.7</div>
| + | |
- | <div class="notebook_s3t4">4.14</div>
| + | |
- | <div class="notebook_s3t4">4.21</div>
| + | |
- | <div class="notebook_s3t4">4.28</div>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- |
| + | |
- | <!--五月-->
| + | |
- | <div id="notebook_s3m2n5" onClick="may();">
| + | |
- | <img src="https://static.igem.org/mediawiki/2013/5/5f/Xmusoftware_notebook_date.png">
| + | |
- | <div class="notebook_s3t1">MAY</div>
| + | |
- | <div class="notebook_s3t2">2013.5</div>
| + | |
- | </div>
| + | |
- | <div id="notebook_s3m2n6">
| + | |
- | <div class="notebook_s3t3">
| + | |
- | <!--五月五日-->
| + | |
- | <div id="note6">
| + | |
- | <div class="note1h1">2013.5.5</div>
| + | |
- | <div class="note1t1">Most of us take a rest after long hours.</div>
| + | |
- | </br></br></br></br></br></br></br></br></br></br></br></br>
| + | |
- | </div>
| + | |
- | <!--五月十二日-->
| + | |
- | <div id="note7">
| + | |
- | <div class="note1h1">2013.5.12</div>
| + | |
- | <div class="note1t1">From this week,we will be divided into two groups, one named design group and another one Matlab group. For the first group, they need to finish most of work about design. Our logo,clothes and slogan will be their works. Besides,the platform and the wiki to show our achievement require them to try their best to do it. For the second group, they must continue working on the software and try to improve existing algorithm.</div>
| + | |
- | <div class="note1t1">We had got some ideas on human practice and the next step was to check if they can be carried.</div>
| + | |
- | </br></br></br></br></br></br></br></br>
| + | |
- | </div>
| + | |
- | <!--五月十九日-->
| + | |
- | <div id="note8">
| + | |
- | <div class="note1h1">2013.5.19</div>
| + | |
- | <div class="note1t1">Design group:the wiki has been designed and we are now considering combining wet lab's work with us. Han Chen had do a lot work in wet lab and found out what problems they met. We will finish the wiki in the next few days and afford some tools for users.</div>
| + | |
- | <div class="note1t1">Matlab group:already written part of our software and test it. We test it and find that its interface is not friend and difficult for user to master it for the first sight. And we will call for help from the design group. Also,for the semi finals is nearby. We need to take a break.</div>
| + | |
- | </br></br></br></br></br></br></br>
| + | |
- | </div>
| + | |
- | <!--五月二十六日-->
| + | |
- | <div id="note9">
| + | |
- | <div class="note1h1">2013.5.26</div>
| + | |
- | <div class="note1t1">Huang Jiang &Huang Xin: They learn C++ and try to make a program . They learn different kinds of arithmetic and compare them to find what we need.GASCO and some other algorithm are inconsideration.</div>
| + | |
- | <div class="note1t1">Zhang Yijuan:find softwares that can help us to slove those problems.Besides, she also focus on SBOL and find out the way to slove some easy problems we put forward before.</div>
| + | |
- | <div class="note1t1">Zhang Shiqi & Wang Chuyue: already use GA to make a program and test it. But we think they need to make more progress so as to up to standard.</div>
| + | |
- | <div class="note1t1">Qiu Likai & Chen Yuezeng:the software had been finished and they are design the wiki and writing codons. That might be finished in two months.</div>
| + | |
- | <div class="note1t1">Huang Jianxing: read and find some papers about Codon usage bias. He should have been better.</div>
| + | |
- | <div class="note1t1">NCBI is of great importance if we write a software ourselves. And we need to know how to make use of the data in NCBI.</div>
| + | |
- | </br></br>
| + | |
- | </div>
| + | |
- | <div class="notebook_s3m2p2">
| + | |
- | <div class="notebook_s3p2" id="notebook_s3p6" onClick="notebook_s3m2c6();" onmouseover="notebook_s3m2c61();" onmouseout="notebook_s3m2c62();"></div>
| + | |
- | <div class="notebook_s3p1" id="notebook_s3p7" onClick="notebook_s3m2c7();" onmouseover="notebook_s3m2c71();" onmouseout="notebook_s3m2c72();"></div>
| + | |
- | <div class="notebook_s3p1" id="notebook_s3p8" onClick="notebook_s3m2c8();" onmouseover="notebook_s3m2c81();" onmouseout="notebook_s3m2c82();"></div>
| + | |
- | <div class="notebook_s3p1" id="notebook_s3p9" onClick="notebook_s3m2c9();" onmouseover="notebook_s3m2c91();" onmouseout="notebook_s3m2c92();"></div>
| + | |
- | </div>
| + | |
- | <div class="notebook_s3m2t2">
| + | |
- | <div class="notebook_s3t5">Meeting </br>Record</div>
| + | |
- | <div class="notebook_s3t4">5.5</div>
| + | |
- | <div class="notebook_s3t4">5.12</div>
| + | |
- | <div class="notebook_s3t4">5.19</div>
| + | |
- | <div class="notebook_s3t4">5.26</div>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- |
| + | |
- | <!--六月-->
| + | |
- | <div id="notebook_s3m2n7" onClick="june();">
| + | |
- | <img src="https://static.igem.org/mediawiki/2013/5/5f/Xmusoftware_notebook_date.png">
| + | |
- | <div class="notebook_s3t1">JUNE</div>
| + | |
- | <div class="notebook_s3t2">2013.6</div>
| + | |
- | </div>
| + | |
- | <div id="notebook_s3m2n8">
| + | |
- | <div class="notebook_s3t3">
| + | |
- | <!--六月二日-->
| + | |
- | <div id="note10">
| + | |
- | <div class="note1h1">2013.6.2</div>
| + | |
- | <div class="note1t1">Lin shen:codon bias database is important for our works. We need to use Latin to search for the right sequence for the organisms. NCBI had been downloaded and can be imported. PFD(protein folding kinetics), nowdays, 'rotational inertia" as a parameter that affect its folding speed.</div>
| + | |
- | <div class="note1t1">Chen han:everything goes well. He start to prepare for the human practice.</div>
| + | |
- | <div class="note1t1">Zhangyijuan:already explain the meaning of RBS. And figure out the way that how to evaluate it. That idea had been written and be used in our software.</div>
| + | |
- | <div class="note1t1">Hon Yuming: draw something and had got the idea of doing so. The logo design is at the handle. And the logo design influence the next step and we shall finish it ASA possible</div>
| + | |
- | </br></br></br></br></br></br></br>
| + | |
- | </div>
| + | |
- | <!--六月九日-->
| + | |
- | <div id="note11">
| + | |
- | <div class="note1h1">2013.6.9</div>
| + | |
- | <div class="note1t1">Exam week. So call off.</div>
| + | |
- | </br></br></br></br></br></br></br></br></br></br></br></br></br></br></br>
| + | |
- | </div>
| + | |
- | <!--六月十六日-->
| + | |
- | <div id="note12">
| + | |
- | <div class="note1h1">2013.6.16</div>
| + | |
- | <div class="note1t1">Exam week. So call off.</div>
| + | |
- | </br></br></br></br></br></br></br></br></br></br></br></br></br></br></br>
| + | |
- | </div>
| + | |
- | <!--六月二十三日-->
| + | |
- | <div id="note13">
| + | |
- | <div class="note1h1">2013.6.23</div>
| + | |
- | <div class="note1t1">Zhang yijuan had distinguish general transcription factors, recognition of inductivity transcription. Improving by similar softwares.Then she will import the database and check them one by one.So we need to know how to call PWM from the database.On sigma factor, statistic PSFM model by using neural network will be a good way. We know that best length require a certain distance.For not ready-made matrix,we had to written one.She will read papers about RBS following.Huang jianxing & Huang jiang & Lin shen & Han tao had read to know the basic knowledge.Cheng han find papers about sigma 70 & do some work on how to build an experience platform that suits users’s need. He improve and redo the platform to make a new model. </div>
| + | |
- | <div class="note1t1">Team member Yijuan Zhang reported our software project (mainly about evaluating of promoters) to Mrs. Wu , the advisor of wet lab team . We received several suggestions from Mrs. Wu . To enhance the accuracy of our software work, we are supposed to pay attention to the false positives raised during recognition of promoters. And to further improve our promoter-evaluation program, Mrs. Wu suggested that we do some research on some special promoters besides Escherichia coli promoters. On the whole Wu applauded progress we had achieved and encouraged our software team to do our wonderful jobs as always.</div>
| + | |
- | <div class="note1t1">Summer camp,garden party,cathedra of synthetic biology, Card game, Fold it and lantern riddles will help us to introduce iGEM to people.Financial reimbursement including registration fee. Several matters need attention: like travel expense,laboratory items,office supplies,car fare. Printing and copying cost should label amount of money.Qiu likai & Chen yuezhen made the concept map and interface about our software.Huang xin make use of the software that we written before. Then he will look for more papers about sigma 70.</div>
| + | |
- | </br></br>
| + | |
- | </div>
| + | |
- | <!--六月三十日-->
| + | |
- | <div id="note14">
| + | |
- | <div class="note1h1">2013.6.30</div>
| + | |
- | <div class="note1t1">Arithmetic software team on evaluating and optimizing biobircks held a meeting and report our progress and current problems to former iGEMer Mo Youbin. Mo listened to our program with great concern and appreciation and taught one of our team members to us artificial neural net work to build weight position matrix for sigma motifs. We discussed the difficulties in front of us, which is mainly about the refinement of our algorithm and how to store and use the data from database RegulonDB. We decide to focus on improving the algorithm these a few days. In addition, Mo suggested that we start to present our slides in English and make a summary of our theories so as to post them on our wiki.</div>
| + | |
- | <div class="note1t1">Easy Note is the software based on web, which is designed to convenient biosynthetic researchers to do some experimental record and query information. After the registration and login, users can do some basic records, related database and background program and so on. </div>
| + | |
- | <div class="note1t1">Because the interface is too monotonous, and the function is too simple, we plan to design a succinctly and naturally interface and add query information, timing function, set, import and export document in the next month.</div>
| + | |
- | </br></br></br></br>
| + | |
- | </div>
| + | |
- | <div class="notebook_s3m2p2">
| + | |
- | <div class="notebook_s3p2" id="notebook_s3p10" onClick="notebook_s3m2c10();" onmouseover="notebook_s3m2c101();" onmouseout="notebook_s3m2c102();"></div>
| + | |
- | <div class="notebook_s3p1" id="notebook_s3p11" onClick="notebook_s3m2c11();" onmouseover="notebook_s3m2c111();" onmouseout="notebook_s3m2c112();"></div>
| + | |
- | <div class="notebook_s3p1" id="notebook_s3p12" onClick="notebook_s3m2c12();" onmouseover="notebook_s3m2c121();" onmouseout="notebook_s3m2c122();"></div>
| + | |
- | <div class="notebook_s3p1" id="notebook_s3p13" onClick="notebook_s3m2c13();" onmouseover="notebook_s3m2c131();" onmouseout="notebook_s3m2c132();"></div>
| + | |
- | <div class="notebook_s3p1" id="notebook_s3p14" onClick="notebook_s3m2c14();" onmouseover="notebook_s3m2c141();" onmouseout="notebook_s3m2c142();"></div>
| + | |
- | </div>
| + | |
- | <div class="notebook_s3m2t2">
| + | |
- | <div class="notebook_s3t5">Meeting </br>Record</div>
| + | |
- | <div class="notebook_s3t4">6.2</div>
| + | |
- | <div class="notebook_s3t4">6.9</div>
| + | |
- | <div class="notebook_s3t4">6.16</div>
| + | |
- | <div class="notebook_s3t4">6.23</div>
| + | |
- | <div class="notebook_s3t4">6.30</div>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- |
| + | |
- | <!--七月-->
| + | |
- | <div id="notebook_s3m2n9" onClick="july();">
| + | |
- | <img src="https://static.igem.org/mediawiki/2013/5/5f/Xmusoftware_notebook_date.png">
| + | |
- | <div class="notebook_s3t1">JULY</div>
| + | |
- | <div class="notebook_s3t2">2013.7</div>
| + | |
- | </div>
| + | |
- | <div id="notebook_s3m2n10">
| + | |
- | <div class="notebook_s3t3">
| + | |
- | <!--七月七日-->
| + | |
- | <div id="note15">
| + | |
- | <div class="note1h1">2013.7.7</div>
| + | |
- | <div class="note1t1">Han designed small icon so that the interface will be more beautiful. Small icon included add, delete, document, tool, set, text, picture and so on. </div>
| + | |
- | <div class="note1t1">Qiu had successfully realized login in and registry database. At the same time, he coded the data board. Chen had written code for the interface including add, delete, document, tool function. But, it is still not enough perfect because of various reason. What to do next will be discussed at tonight’s meeting.</div>
| + | |
- | <div class="note1t1">Huang Xin learned that we can deal with the data from database using matlab.</div>
| + | |
- | <div class="note1t1">Han Tao refined our algorithm to evaluate promoter strength on java and try to run some existing software designed to improve protein coding sequences.</div>
| + | |
- | <div class="note1t1">Zhang Yijuan started to learn theories on RBS and its prediction. By looking up to literatures, we find several factors which can influence the RBS strength including SD sequence , spacer length, start codon and secondary structure. And we come up with algorithms similar to the algorithms used in the promoter part which take 3 factors, namely, SD sequence, spacer length, start codon into account. And we’ll study the influence of RBS structure on its strength next week.</div>
| + | |
- | <div class="note1t1">Rao Wenjun has built a database in Access containing all the transcription factors’ binding sites and we are now discussing how to use this database in our software.</div>
| + | |
- | </br></br>
| + | |
- | </div>
| + | |
- | <!--七月十四日-->
| + | |
- | <div id="note16">
| + | |
- | <div class="note1h1">2013.7.14</div>
| + | |
- | <div class="note1t1">To improve the login interface and registry interface, Chen designed a new style’s interface which had divided into four section and had used irregular design. When clicking one section, this section enlarged so that the interaction effect was better. Qiu made the great efford to improve the date base. He had finished the add and delete function. Because the date base is difficulty, he spent a lot of time for it so he stayed up late sometimes. Next week, we will improve the function and interface.</div>
| + | |
- | <div class="note1t1">Zhang figured out the algorithm to calculate the free binding energy between RBS mRNA and 16s rRNA and HanTao started to write code for it at once. Now we have a simple program for calculating the free binding energy. So far we have worked out two algorithms to evaluate RBS strength.</div>
| + | |
- | </br></br></br></br></br></br>
| + | |
- | </div>
| + | |
- | <!--七月二十一日-->
| + | |
- | <div id="note17">
| + | |
- | <div class="note1h1">2013.7.21</div>
| + | |
- | <div class="note1t1">ZhangYijuan put forward 2 methods to evaluate RBS strength. The first method is to use the PWM(position weight matrix) of SD sequence and the spacer length between SD sequence and start codon to calculate the relative strength. The second is to calculate the free binding energy between the RBS mRNA and the 16s rRNA in the ribosome. </div>
| + | |
- | <div class="note1t1">HanTao,HuangXin and RaoWenjun is working together on program code.</div>
| + | |
- | <div class="note1t1">Qiu had finished the record module that we can add text, photo, table and so on. Because the record interface isn’t too concise, we should improve in the next week. At the same time, the import and export function had accomplished. In the process of programming, we met with many difficulties. For completing the task better in the next stage, Chen studied the jqery. Next week, we will continue to work hard.</div>
| + | |
- | </br></br></br></br></br>
| + | |
- | </div>
| + | |
- | <!--七月二十八日-->
| + | |
- | <div id="note18">
| + | |
- | <div class="note1h1">2013.7.28</div>
| + | |
- | <div class="note1t1">HanTao began to deal with the GUI of the promoter evaluation part of our project. </div>
| + | |
- | <div class="note1t1">RaoWenjun decide to inlay the biobrick sequence data in our software as txt file.</div>
| + | |
- | <div class="note1t1">ZhangYijuan had put forward the problem of how to determine the weight of motif similarity and spacer length score in the strength evaluation algorithm .After consulting with QiuRuosang, Zhang and QiuRuosang began to design experiments for the data needed to modify as well as validate our algorithm to evaluate both promoter and RBS strength.</div>
| + | |
- | <div class="note1t1">After the end of the third semester in this week, we invest a lot of time for the software production. Qiu had finished and modified the function of adding photograph, table, step and the text. The difficulties in the database exceed we imagine. With increasing a lot of novel effect, login interface had been modified by Chen. Next week, we will tidy up the code for easier to read and improve the existing functionality.s</div>
| + | |
- | </br></br></br></br>
| + | |
- | </div>
| + | |
- | <div class="notebook_s3m2p2">
| + | |
- | <div class="notebook_s3p2" id="notebook_s3p15" onClick="notebook_s3m2c15();" onmouseover="notebook_s3m2c151();" onmouseout="notebook_s3m2c152();"></div>
| + | |
- | <div class="notebook_s3p1" id="notebook_s3p16" onClick="notebook_s3m2c16();" onmouseover="notebook_s3m2c161();" onmouseout="notebook_s3m2c162();"></div>
| + | |
- | <div class="notebook_s3p1" id="notebook_s3p17" onClick="notebook_s3m2c17();" onmouseover="notebook_s3m2c171();" onmouseout="notebook_s3m2c172();"></div>
| + | |
- | <div class="notebook_s3p1" id="notebook_s3p18" onClick="notebook_s3m2c18();" onmouseover="notebook_s3m2c181();" onmouseout="notebook_s3m2c182();"></div>
| + | |
- | </div>
| + | |
- | <div class="notebook_s3m2t2">
| + | |
- | <div class="notebook_s3t5">Meeting </br>Record</div>
| + | |
- | <div class="notebook_s3t4">7.7</div>
| + | |
- | <div class="notebook_s3t4">7.14</div>
| + | |
- | <div class="notebook_s3t4">7.21</div>
| + | |
- | <div class="notebook_s3t4">7.28</div>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- |
| + | |
- | <!--八月-->
| + | |
- | <div id="notebook_s3m2n11" onClick="august();">
| + | |
- | <img src="https://static.igem.org/mediawiki/2013/5/5f/Xmusoftware_notebook_date.png">
| + | |
- | <div class="notebook_s3t1">AUGUST</div>
| + | |
- | <div class="notebook_s3t2">2013.8</div>
| + | |
- | </div>
| + | |
- | <div id="notebook_s3m2n12">
| + | |
- | <div class="notebook_s3t3">Chen:Experimental workspace that can automaticly decide whether it is a personal account or business account from the networking and the workspace afford download link of those relevant softwares.Can we get those softwares embedded? How to help our costumers find out the software they want quickly?(keyword search?) It is also important to processing data,generate lab reports and logs in the workspace.
| + | |
- | </br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br>
| + | |
- | <div class="notebook_s3m2p2">
| + | |
- | <div class="notebook_s3p2"></div>
| + | |
- | <div class="notebook_s3p1"></div>
| + | |
- | <div class="notebook_s3p1"></div>
| + | |
- | <div class="notebook_s3p1"></div>
| + | |
- | </br></br></br>
| + | |
- | <div class="notebook_s3p1"></div>
| + | |
- | <div class="notebook_s3p1"></div>
| + | |
- | <div class="notebook_s3p1"></div>
| + | |
- | <div class="notebook_s3p1"></div>
| + | |
- | <div class="notebook_s3p1"></div>
| + | |
- | </div>
| + | |
- | <div class="notebook_s3m2t2">
| + | |
- | <div class="notebook_s3t5">Meeting </br>Record</div>
| + | |
- | <div class="notebook_s3t4">8.1</div>
| + | |
- | <div class="notebook_s3t4">8.8</div>
| + | |
- | <div class="notebook_s3t4">8.15</div>
| + | |
- | <div class="notebook_s3t4">8.22</div>
| + | |
- | <div class="notebook_s3t5"></br></br>Lab</br> Record</div>
| + | |
- | <div class="notebook_s3t6">3.16</div>
| + | |
- | <div class="notebook_s3t6">3.19</div>
| + | |
- | <div class="notebook_s3t6">3.23</div>
| + | |
- | <div class="notebook_s3t6">3.27</div>
| + | |
- | <div class="notebook_s3t6">3.28</div>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- |
| + | |
- | <!--九月-->
| + | |
- | <div id="notebook_s3m2n13" onClick="september();">
| + | |
- | <img src="https://static.igem.org/mediawiki/2013/5/5f/Xmusoftware_notebook_date.png">
| + | |
- | <div class="notebook_s3t1">SEPTEMBER</div>
| + | |
- | <div class="notebook_s3t2">2013.9</div>
| + | |
- | </div>
| + | |
- | <div id="notebook_s3m2n14">
| + | |
- | <div class="notebook_s3t3">Chen:Experimental workspace that can automaticly decide whether it is a personal account or business account from the networking and the workspace afford download link of those relevant softwares.Can we get those softwares embedded? How to help our costumers find out the software they want quickly?(keyword search?) It is also important to processing data,generate lab reports and logs in the workspace.
| + | |
- | </br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br>
| + | |
- | <div class="notebook_s3m2p2">
| + | |
- | <div class="notebook_s3p2"></div>
| + | |
- | <div class="notebook_s3p1"></div>
| + | |
- | <div class="notebook_s3p1"></div>
| + | |
- | <div class="notebook_s3p1"></div>
| + | |
- | </br></br></br>
| + | |
- | <div class="notebook_s3p1"></div>
| + | |
- | <div class="notebook_s3p1"></div>
| + | |
- | <div class="notebook_s3p1"></div>
| + | |
- | <div class="notebook_s3p1"></div>
| + | |
- | <div class="notebook_s3p1"></div>
| + | |
- | </div>
| + | |
- | <div class="notebook_s3m2t2">
| + | |
- | <div class="notebook_s3t5">Meeting </br>Record</div>
| + | |
- | <div class="notebook_s3t4">3.7</div>
| + | |
- | <div class="notebook_s3t4">3.15</div>
| + | |
- | <div class="notebook_s3t4">3.22</div>
| + | |
- | <div class="notebook_s3t4">3.30</div>
| + | |
- | <div class="notebook_s3t5"></br></br>Lab</br> Record</div>
| + | |
- | <div class="notebook_s3t6">3.16</div>
| + | |
- | <div class="notebook_s3t6">3.19</div>
| + | |
- | <div class="notebook_s3t6">3.23</div>
| + | |
- | <div class="notebook_s3t6">3.27</div>
| + | |
- | <div class="notebook_s3t6">3.28</div>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- |
| + | |
- | <!--十月-->
| + | |
- | <div id="notebook_s3m2n15" onClick="october();">
| + | |
- | <img src="https://static.igem.org/mediawiki/2013/5/5f/Xmusoftware_notebook_date.png">
| + | |
- | <div class="notebook_s3t1">OCTOBER</div>
| + | |
- | <div class="notebook_s3t2">2013.10</div>
| + | |
- | </div>
| + | |
- | <div id="notebook_s3m2n16">
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- | <div class="notebook_s3t3">Chen:Experimental workspace that can automaticly decide whether it is a personal account or business account from the networking and the workspace afford download link of those relevant softwares.Can we get those softwares embedded? How to help our costumers find out the software they want quickly?(keyword search?) It is also important to processing data,generate lab reports and logs in the workspace.
| + | |
- | </br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br></br>
| + | |
- | <div class="notebook_s3m2p2">
| + | |
- | <div class="notebook_s3p2"></div>
| + | |
- | <div class="notebook_s3p1"></div>
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- | <div class="notebook_s3p1"></div>
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- | <div class="notebook_s3p1"></div>
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- | </br></br></br>
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- | <div class="notebook_s3p1"></div>
| + | |
- | <div class="notebook_s3p1"></div>
| + | |
- | <div class="notebook_s3p1"></div>
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- | <div class="notebook_s3p1"></div>
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- | <div class="notebook_s3p1"></div>
| + | |
- | </div>
| + | |
- | <div class="notebook_s3m2t2">
| + | |
- | <div class="notebook_s3t5">Meeting </br>Record</div>
| + | |
- | <div class="notebook_s3t4">3.7</div>
| + | |
- | <div class="notebook_s3t4">3.15</div>
| + | |
- | <div class="notebook_s3t4">3.22</div>
| + | |
- | <div class="notebook_s3t4">3.30</div>
| + | |
- | <div class="notebook_s3t5"></br></br>Lab</br> Record</div>
| + | |
- | <div class="notebook_s3t6">3.16</div>
| + | |
- | <div class="notebook_s3t6">3.19</div>
| + | |
- | <div class="notebook_s3t6">3.23</div>
| + | |
- | <div class="notebook_s3t6">3.27</div>
| + | |
- | <div class="notebook_s3t6">3.28</div>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- |
| + | |
- | <!--镂空圆,下-->
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- | <div id="notebook_s3m2n17">
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- | <div class="notebook_s3p0"></div>
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- | <div class="notebook_s3p00"></div>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- | </div>
| + | |
- | | + | |
- | </div>
| + | |
- | </div>
| + | |
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- | var x = window.innerWidth-1366;
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- | if(x>0){
| + | |
- | x = x / 2;
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- | document.getElementById("xmu_software").style.left= x+"px";
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- | }
| + | |
- | else{
| + | |
- | document.getElementById("xmu_software").style.left="0px";
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- | }
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- | color1=$("#notebook_s3p2").css("background-color");
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- | color2=$("#notebook_s3p3").css("background-color");
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- | | + | |
- | </script>
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- | | + | |
- | </body>
| + | |
- | </html>
| + | |