Difference between revisions of "Team:Tongji-Software/Attributions"

 
(89 intermediate revisions by 4 users not shown)
Line 18: Line 18:
 
#bodyContent h1, #bodyContent h2, #bodyContent h3, #bodyContent h4, #bodyContent h5 { margin-bottom: 0px; }
 
#bodyContent h1, #bodyContent h2, #bodyContent h3, #bodyContent h4, #bodyContent h5 { margin-bottom: 0px; }
  
.judges-will-not-evaluate { border: 4px solid #e4dede; padding: 2% !important; width: 92%!important;}
 
 
body{
 
body{
 
margin: 0;
 
margin: 0;
 
color:#685454;
 
color:#685454;
font-family: "Haas Grot Text R Web", "Helvetica Neue", Helvetica, Arial, sans-serif;
+
font-family: Helvetica, Arial, sans-serif;
 
/* font-family: "Times New Roman", Cambria,  serif;*/
 
/* font-family: "Times New Roman", Cambria,  serif;*/
 
background-color:#fff;
 
background-color:#fff;
Line 31: Line 30:
 
   float: left;
 
   float: left;
 
   top: 0px;
 
   top: 0px;
   background-color: #685454;
+
   background-color: #592e2e;
 
   margin-top:0px;  
 
   margin-top:0px;  
 
   width: 10%;
 
   width: 10%;
Line 69: Line 68:
 
filter: brightness(200%);
 
filter: brightness(200%);
 
transform: scale(1.2);
 
transform: scale(1.2);
 +
}
 +
 +
.line {
 +
  position: fixed;
 +
  float: left;
 +
  top: 0px;
 +
  left:10%;
 +
  background-color: #ffb6bc;
 +
  width: 1%;
 +
  height: 100%;
 +
  padding-right:-20px;
 +
  padding-top:10px;
 
}
 
}
  
Line 77: Line 88:
 
   left:10%;
 
   left:10%;
 
   background-color: #ffb6bc;
 
   background-color: #ffb6bc;
   width: 15%;
+
   width: 16%;
 
   height: 100%;
 
   height: 100%;
 
   padding-right:-20px;
 
   padding-right:-20px;
Line 98: Line 109:
  
 
.left ul li{
 
.left ul li{
 +
  display:block;
 
   color:#685454;
 
   color:#685454;
 
   list-style: none;
 
   list-style: none;
Line 105: Line 117:
 
   border-bottom: 0.5px solid #685454;
 
   border-bottom: 0.5px solid #685454;
 
   transition: 0.3s;
 
   transition: 0.3s;
 +
  font-weight:bold;
 +
  font-size:15px;
 
}
 
}
  
 
.left ul li :hover{
 
.left ul li :hover{
   color: #f47925;
+
   display: inline-block;
   transition: 0.3s;
+
  -webkit-filter: brightness(0%);
 +
filter: brightness(0%);
 +
   transition:all 0.3s;
 +
  transform: scale(1.15);
 +
}
 +
.left li:before {
 +
  content: '';
 +
  height: 100%;
 +
  left: 0;
 +
  position: absolute;
 +
  top: 0;
 +
  -webkit-transition: width 0.2s ease-in;
 +
  transition: width 0.2s ease-in;
 +
  width: 3px;
 +
  z-index: -1;
 +
}
 +
 
 +
.left li:hover:before {
 +
  -webkit-transition: width 0.2s ease-in;
 +
  transition: width 0.2s ease-in;
 +
  width: 100%;
 +
}
  
 +
.left li.open:hover before {
 +
  -webkit-transition: width 0.2s ease-in;
 +
  transition: width 0.2s ease-in;
 +
  width: 100%;
 
}
 
}
  
Line 125: Line 164:
 
top:0px;
 
top:0px;
 
z-index: -1;
 
z-index: -1;
opacity: 0.3;
+
 
 
}
 
}
  
Line 132: Line 171:
 
   position:absolute;
 
   position:absolute;
 
   float: left;
 
   float: left;
   top:85%;
+
   top:25%;
   left:26%;
+
   left:27%;
 
   font-size: 48px;
 
   font-size: 48px;
   color:#c38d8f ;
+
   color:#fc8190 ;
 
   z-index: 2;
 
   z-index: 2;
 
   font-weight: bolder;
 
   font-weight: bolder;
Line 144: Line 183:
 
   float: left;
 
   float: left;
 
   top:110%;
 
   top:110%;
   left:26%;
+
   left:20%;
 
   width:71%;
 
   width:71%;
 
   font-size: 18px;
 
   font-size: 18px;
 
   z-index: 2;
 
   z-index: 2;
  color:#685454;
 
 
   margin-left:50px;
 
   margin-left:50px;
 
  line-height: 35px;
 
  line-height: 35px;
Line 156: Line 194:
 
.content .h1{
 
.content .h1{
 
   margin-top: 20px;
 
   margin-top: 20px;
   font-size: 30px;
+
   font-size: 33px;
 
   font-weight: bold;
 
   font-weight: bold;
   color: #fc8190;
+
   color: #fc8190;  
 
}
 
}
  
 
.content .top{
 
.content .top{
   padding-top: 20px;
+
   padding-top: 23px;
   padding-left: 150px;
+
   padding-left: 90px;
 
   display: table-cell;
 
   display: table-cell;
 
   vertical-align:middle;
 
   vertical-align:middle;
 
   text-align:center;
 
   text-align:center;
 
   font-weight:bold;
 
   font-weight:bold;
   font-size: 20px;
+
   font-size: 25px;
 
   color:#685454;
 
   color:#685454;
 
   padding-bottom: 20px;
 
   padding-bottom: 20px;
Line 176: Line 214:
 
   display: inline-block;
 
   display: inline-block;
 
   text-indent:2em;
 
   text-indent:2em;
   font-size: 20px;
+
   font-size: 18px;
   padding-top: 20px;
+
   padding-top: 10px;
   padding-bottom: 20px;
+
   padding-bottom: 10px;
 +
 
 
}
 
}
  
.content img{
+
.content img{
  padding-left: 50px;
+
 
   display: table-cell;
 
   display: table-cell;
 
   vertical-align:middle;
 
   vertical-align:middle;
 +
  margin:0 auto;
 +
  text-align:center;
 
}
 
}
  
 +
#contact{
 +
  border-radius: 15px;
 +
  width: 90%;
 +
  height:auto;
 +
  background:rgba(255,255,255,0.7);
 +
/* border: 2.5px solid rgba(0,0,0,0.9);*/
 +
  z-index: 5;
 +
  text-align: center;
 +
  display: block;
 +
  margin-bottom: 100px;
 +
}
  
</style>
+
#contact h3{
 +
  font-size: 22px;
 +
  margin-top:35px;
 +
  margin-bottom:10px;
 +
  color : #5b3d3d;
 +
}
  
 +
#contact span{
 +
  margin-top: 15px;
 +
  font-size: 19px;
 +
  color : #826767;
 +
}
 +
 +
#contact img{
 +
  margin-top: 10px;
 +
  transition: all 0.4s;
 +
  margin-bottom: 30px;
 +
}
 +
#contact img:hover{
 +
  transform: scale(1.15);
 +
  transition: all 0.4s;
 +
}
 +
#btn{
 +
display: none;
 +
position: fixed;
 +
left: 90%;
 +
bottom: 40px;
 +
height:80px;
 +
width: 80px;
 +
background: url(https://static.igem.org/mediawiki/2018/d/d1/T--Tongji-Software--top.png) no-repeat left top;
 +
background-size:100% auto;
 +
}
 +
 +
</style>
 +
<link rel="stylesheet" href="https://2018.igem.org/wiki/index.php?title=Template:Tongji-Software/test/css/style.css&action=raw&ctype=text/css">
  
 
<body>
 
<body>
 
<div class="icon">
 
<div class="icon">
 
     <ul>
 
     <ul>
     <a href="https://2018.igem.org/Team:Tongji-Software/project" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/f/fa/T--Tongji-Software--logo.svg" width="55%"  ></li></a>
+
     <a href="https://2018.igem.org/Team:Tongji-Software" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/f/fa/T--Tongji-Software--logo.svg" width="55%"  ></li></a>
  
     <a href="https://2018.igem.org/Team:Tongji-Software/project" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/e/ed/T--Tongji-Software--Pro.svg" width="35%" ></li></a>
+
     <a href="https://2018.igem.org/Team:Tongji-Software/Project" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/e/ed/T--Tongji-Software--Pro.svg" width="35%" ></li></a>
  
     <a href="https://2018.igem.org/Team:Tongji-Software/team" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/1/1f/T--Tongji-Software--Tea.svg" width="35%" ></li></a>
+
     <a href="https://2018.igem.org/Team:Tongji-Software/Team" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/1/1f/T--Tongji-Software--Tea.svg" width="35%" ></li></a>
  
     <a href="https://2018.igem.org/Team:Tongji-Software/attribution" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/8/86/T--Tongji-Software--Att.svg" width="35%" ></li></a>
+
     <a href="https://2018.igem.org/Team:Tongji-Software/Attributions" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/8/86/T--Tongji-Software--Att.svg" width="35%" ></li></a>
  
     <a href="https://2018.igem.org/Team:Tongji-Software/modeling" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/7/77/T--Tongji-Software--Mod.svg" width="35%" ></li></a>
+
     <a href="https://2018.igem.org/Team:Tongji-Software/Model" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/7/77/T--Tongji-Software--Mod.svg" width="35%" ></li></a>
  
     <a href="https://2018.igem.org/Team:Tongji-Software/collaboration" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/d/d3/T--Tongji-Software--Col.svg" width="35%" ></li></a>
+
     <a href="https://2018.igem.org/Team:Tongji-Software/Collaborations" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/d/d3/T--Tongji-Software--Col.svg" width="35%" left="100px"></li></a>
  
 
     <a href="https://2018.igem.org/Team:Tongji-Software/Requirements" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/5/5f/T--Tongji-Software--Req.svg" width="35%" ></li></a>
 
     <a href="https://2018.igem.org/Team:Tongji-Software/Requirements" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/5/5f/T--Tongji-Software--Req.svg" width="35%" ></li></a>
  
     <a href="https://2018.igem.org/Team:Tongji-Software/human-practice" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/c/cc/T--Tongji-Software--Hum.svg" width="35%" ></li></a>
+
     <a href="https://2018.igem.org/Team:Tongji-Software/Human_Practices" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/c/cc/T--Tongji-Software--Hum.svg" width="35%" ></li></a>
  
     <a href="https://2018.igem.org/Team:Tongji-Software/Medal" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/8/8b/T--Tongji-Software--Med.svg" width="35%" ></li></a>
+
     <a href="https://2018.igem.org/Team:Tongji-Software/Measurement" original-title="Project"><li><img src="https://static.igem.org/mediawiki/2018/8/8b/T--Tongji-Software--Med.svg" width="35%" ></li></a>
 
   </ul>
 
   </ul>
 
   </div>
 
   </div>
  
 
+
<div class="line"></div>
<div class="left">
+
<div><a href="javascript:;" id="btn" title="Return to Top"></a></div>
 +
<div id = "wrapper">
 +
<div class="left"  id = "sidebar-wrapper">
 
     <ul>
 
     <ul>
 
       <li><a href="#Overview">Overview</a></li>
 
       <li><a href="#Overview">Overview</a></li>
Line 222: Line 308:
 
       <li><a href="#Search">Search algorithm & Ranking criteria</a></li>
 
       <li><a href="#Search">Search algorithm & Ranking criteria</a></li>
 
       <li><a href="#Additional">Additional Functions</a></li>
 
       <li><a href="#Additional">Additional Functions</a></li>
 +
      <li><a href="#Design">Design</a></li>
 
       <li><a href="#Human">Human Practice and Collaboration</a></li>
 
       <li><a href="#Human">Human Practice and Collaboration</a></li>
       <li><a href="#Financing">Financing</a></li>
+
       <li><a href="#Financing">Financing &</br> Trip planning</a></li>
      <li><a href="#Trip">Trip planning</a></li>
+
       <li><a href="#Advice">Advice and human</br> practice support</a></li>
       <li><a href="#Advice">Advice and human practice support</a></li>
+
     </ul>  
     </ul> //小标题
+
  
 
  </div>
 
  </div>
 
    
 
    
<div class="picture">
+
<div class="picture">
 
     <img src="https://static.igem.org/mediawiki/2018/2/24/T--Tongji-Software--Attribution-background.jpeg"  width="100%" >
 
     <img src="https://static.igem.org/mediawiki/2018/2/24/T--Tongji-Software--Attribution-background.jpeg"  width="100%" >
 
   </div>
 
   </div>
Line 237: Line 323:
 
   </div>
 
   </div>
 
   <div class="title">
 
   <div class="title">
     <span>ATTRIBUTIONS</span> /  /大标题 */ 
+
     <span>ATTRIBUTIONS</span>
 
   </div>
 
   </div>
   
+
   
<div class="content" >     //内容*/
+
<div class="content" id="con">
       <span class="h1" id="Overview">     //小标题
+
<span class="top">
 +
        What makes Alpha Ant meaningful and wonderful is those </br>people’s great work.</br>
 +
       </span>
 +
<span class="detail" >Since we are from different majors, all things can be covered by everyone of us. More information about team members could be found in <a href="https://2018.igem.org/Team:Tongji-Software/Team" target="_blank">Team</a>. Generally, we have three main sessions: biology logic thinking and investigation, programming and modeling, design.</span> </br>
 +
 
 +
<span class="detail" >It’s more like a workflow. At first, everyone is engaged in previous biology research and decide to do a topic about pathway design. Secondly, biology group try to get access to different database and deliver data to programming group. Then data processing and main part programming are followed. At last, design group can figure out how to show our software reasonably and wiki design.</span></br>
 +
 
 +
 +
 
 +
<span class="h1" id="Overview">  
 
         Overview</br>  
 
         Overview</br>  
 
       </span>
 
       </span>
  
 +
    <img src="https://static.igem.org/mediawiki/2018/f/fc/T--Tongji-Software--attribution-graph.png" width="80%" />
 +
</br>
  
  <span>  What makes Alpha Ant meaningful and wonderful is those people’s great work.</br>
+
<span class="h1" id="Previous">  
    Since we are from different majors, all things can be covered by everyone of us. More information about team members could be found in <a href="https://2018.igem.org/Team:Tongji-Software/Team" target="_blank">Team</a>.Generally, we have three main sessions: biology logic thinking and investigation, programming and modeling, design. </br></br>
+
      Previous Research</br>  
 +
      </span>
  
    It’s more like a workflow. At first, everyone is engaged in previous biology research and decide to do a topic about pathway design. Secondly, biology group try to get access to different database and deliver data to programming group. Then data processing and main part programming are followed. At last, design group can figure out how to show our software reasonably and wiki design.</br>
+
<ul>
 +
<li>Haiyan He, Xiaotian Yu, Zhichao Ma and Wei Cao are responsible for learning synthetic biology and mining proper topic.</li>
  
    It’s more like a workflow. At first, everyone is engaged in previous biology research and decide to do a topic about pathway design. Secondly, biology group try to get access to different database and deliver data to programming group. Then data processing and main part programming are followed. At last, design group can figure out how to show our software reasonably and wiki design.</br>
+
<li>Wei Cao investigated the barriers that experimenters could occur in metabolic engineering and interviewed Professor Ping Li for Tongji University for general workflow of metabolic pathway research.</li>
 +
<li>Zhichao Ma communicated with postgraduate students major in bioinformatics.</li>
 +
<li>Xiangzhen Li did some research on graph theoretic algorithm.</li>
 +
</ul>
  
    <span class="b"><b>overview</b></span></br>
 
    <img src="https://static.igem.org/mediawiki/2018/f/fc/T--Tongji-Software--attribution-graph.png" width="600" height="450" />
 
 
</br>
 
</br>
  <span class="b"><b>Previous Research</b></span></br>
 
Haiyan He, Xiaotian Yu, Zhichao Ma and Wei Cao are responsible for learning synthetic biology and mining proper topic.</br>
 
Wei Cao investigated the barriers that experimenters could occur in metabolic engineering and interviewed Professor Ping Li for Tongji University for general workflow of metabolic pathway research. </br>
 
Zhichao Ma communicated with postgraduate students major in bioinformatics.</br>
 
Xiangzhen Li did some research on graph theoretic algorithm.</br></br>
 
  
  <span class="b"><b>Database</b></span></br>
+
<span class="h1" id="Database">  
  Xiaotian Yu, Xiangzhen Li and Zhichao Ma were responsible for getting data from KEGG Database and data processing.</br>
+
      Database</br>  
  Haiyan He and Xiaotian Yu were responsible for calculating thermodynamic data by using equilibrator.</br>
+
      </span>
  Zhichao Ma and Wei Cao was responsible for getting data from Brenda, ChEBI, DrugBank and KnowledgeBase.</br>
+
<ul>
 +
<li>Xiaotian Yu, Xiangzhen Li and Zhichao Ma were responsible for getting data from KEGG Database and data processing.</li>
 +
<li>Haiyan He and Xiaotian Yu were responsible for calculating thermodynamic data by using equilibrator.</li>
 +
<li>Zhichao Ma and Wei Cao was responsible for getting data from Brenda, ChEBI, DrugBank and KnowledgeBase.</li>
 +
</ul>
 +
</br>
  
  <span class="b"><b>Search algorithm & Ranking criteria</b></span></br>
 
  Xiangzhen Li did a lot of research on Graph Theoretic Algorithm and wrote code of DFS.</br>
 
  Xiaotian Yu and Wei Cao read some paper about atom conservation. Then they worked together on coding and model building.</br>
 
  Xiaotian Yu and Zhichao Ma worked on toxicity of compound and added it to ranking criteria.</br></br>
 
  
<span class ="b"><b>Additional Functions</b></span></br>
+
<span class="h1" id="Search">  
 +
      Search algorithm & Ranking criteria</br>  
 +
      </span>
 +
<ul>
 +
<li>Xiangzhen Li did a lot of research on Graph Theoretic Algorithm and wrote code of DFS.</li>
 +
<li> Xiaotian Yu and Wei Cao read some paper about atom conservation. Then they worked together on coding and model building.</li>
 +
<li>Xiaotian Yu and Zhichao Ma worked on toxicity of compound and added it to ranking criteria.</li>
 +
</ul>
 +
</br>
  
<span class ="c"><b>FBA</b></span></br>
+
<span class="h1" id="Additional">  
Wei Cao and Haiyan He learned COBRA toolbox and built FBA model.</br>
+
      Additional Functions</br>  
<span class ="c"><b>Microorganism recommendation</b></span></br>
+
      </span>
  Zhichao Ma and Xiangzhen Li built and optimized microorganism recommendation model.</br>
+
<span class = "c"><b>SMILES Comparison </b></span></br>
+
  Xiaotian Yu learned RDkit toolbox and added SMILES Comparison to our project.</br></br>
+
  
<span class="b"><b>Design</b></span></br>
 
  Yuchen Xing, Yuejia Li were responsible for wiki design. </br>
 
  Yuchen Xing, Wei Cao and Zhichao Ma designed software interface.</br>
 
  YueJia Li also carried poster design work.</br>
 
  
<span class="b"><b>Human Practice and Collaboration</b></span></br>
+
<b>1.Organism recommendation</b></br>
<span class="c"><b>Visiting WuXi AppTec</b></span></br>
+
<span class="detail" >Zhichao Ma and Xiangzhen Li built and optimized microorganism recommendation model.</span></br>
  Wei Cao communicated with WuXi AppTec and made an interview on experts in WuXi AppTec. Haiyan He, Xiaotian Yu, Zhichao Ma and Xiangzhen Li participated this interview and proposed many great ideas. Haiyan He give an excellent speech on this meeting.</br>
+
  
<span class="c"><b>Communicate with programmers</b></span></br>
+
<b>2.Flux Balance Analysis</b></br>
  Zhichao Ma made a speech on a forum in school of life science and technology, Tongji University. There, we got a lot of suggestions on modeling.</br>
+
<span class="detail" >Wei Cao and Haiyan He learned COBRA toolbox and built FBA model.</span></br>
  
<span class="c"><b>Contact with experimenters</b></span></br>
+
<b>3.Atom conservation</b></br>
  Wei Cao made a speech on professor Ping Li’s class and then investigate need of experimenters. </br>
+
<span class="detail" >Wei Cao and Haiyan He learned COBRA toolbox and built FBA model.</span></br>
  
 +
<b>4.SMILES Comparison </b></br>
 +
<span class="detail" >Xiaotian Yu learned RDkit toolbox and added SMILES Comparison to our project.</br></span></br>
  
<span class="c"><b>EuroAsia Meetup</b></span></br>
+
<span class="h1" id="Design">  
  All members attended EuroAsia Meetup in Shenzhen, China. Haiyan took picture for us. Wei Cao and Xiaotian Yu did presentation in this Meetup.</br>
+
      Design</br>  
 +
      </span>
  
 +
<ul>
 +
  <li>Yuchen Xing, Yuejia Li,Wei Cao were responsible for wiki design. </li>
 +
  <li>Yuchen Xing, Wei Cao and Zhichao Ma designed software interface.</li>
 +
  <li>YueJia Li also carried poster design work.</li>
 +
</ul>
 +
</br>
  
 +
<span class="h1" id="Human">
 +
      Human Practices and Collaborations</br>
 +
      </span>
  
<span class="c"><b>CCiC</b></span></br>
+
<b>1.Visiting WuXi AppTec</b></br>
  Xiaotian Yu contacted with Shanghai-tech, who held CCiC in Shanghai.</br>
+
<span class="detail" >Wei Cao communicated with WuXi AppTec and made an interview on experts in WuXi AppTec. Haiyan He, Xiaotian Yu, Zhichao Ma and Xiangzhen Li participated this interview and proposed many great ideas. Haiyan He give an excellent speech on this meeting.</br></span>
  Xiangzhen Li , Xiaotian Yu and Wei Cao gave the committee a great presentation.</br>
+
 
+
  
<span class="c"><b>Meeting with SJTU</b></span></br>
+
<b>2.Communicate with programmers</b></br>
  Wei Cao contacted with SJTU-software and helped arrange meeting with SJTU-software. And rest of the team attended this meeting.</br>
+
<span class="detail" >Zhichao Ma made a speech on a forum in school of life science and technology, Tongji University. There, we got a lot of suggestions on modeling.</br></span>
  
 +
<b>3.Contact with experimenters</b></br>
 +
<span class="detail" >Wei Cao made a speech on professor Ping Li’s class and then investigate need of experimenters. </span></br>
  
<span class="c"><b>Game : “Go Ant!”</b></span></br>
+
<b>4.EuroAsia Meetup</b></br>
  Xiaotian Yu developed the whole game. Of course, the rest of teammates gave him some advice. Yuejia Li designed the magnificent background, which made the game even more fun!</br></br>
+
<span class="detail" > All members attended EuroAsia Meetup in Shenzhen, China. Wei Cao and Xiaotian Yu did presentation in this Meetup. All the member answered questions during the speech.</br></span>
  
 +
<b>5.CCiC</b></br>
 +
<ul>
 +
<li>Xiaotian Yu contacted with Shanghai-tech, who held CCiC in Shanghai.</li>
 +
<li>Xiangzhen Li , Xiaotian Yu and Wei Cao gave the committee a great presentation.</li>
 +
<li>Haiyan He was responsible for poster exhibition part.</li>
 +
<li>Yuejia Li designed the poster.</li>
 +
</ul>
 +
</br>
 +
 
 +
<b>6.Meeting with SJTU & Fudan_China</b></br>
 +
<span class="detail" >Wei Cao contacted with SJTU-software and helped arrange meeting with SJTU-software. Haiyan He contacted with Fudan_China and helped arrange meeting with them. And rest of the team attended this meeting.</br></span>
  
<span class="b"><b>Financing</b></span></br>
+
<b>7.Game : “Go Ant!”</b></br>
Xiaotian Yu is in charge of Financial management.</br></br>
+
<span class="detail" >Xiaotian Yu developed the whole game. Of course, the rest of teammates gave him some advice. Yuejia Li designed the magnificent background, which made the game even more fun!</br></span>
  
<span class="b"><b>Trip planning</b></span></br>
+
<b>8.Visiting Meihua Group</b></br>
  Wei Cao is responsible for flight tickets booking and hotel reservation. The rest of team members help plan the whole trip.</br></br>
+
<span class="detail" >Haiyan He, Xiaotian Yu, Zhichao Ma and Wei Cao participated this visit and proposed many great ideas. Xiaotian Yu gave an excellent speech on this meeting</br></span>
  
<span class="b"><b>Advice and human practice support</b></span></br>
+
<b>9.Visiting Cathay Industrial Biotech</b></br>
  Professor Qi Liu gave us advice on search algorithm and help us contact with WuXi AppTec.</br>
+
<span class="detail" >Haiyan He, Xiaotian Yu, Zhichao Ma and Wei Cao participated this visit and proposed many great ideas. Xiaotian Yu gave an excellent speech on this meeting</br></span>
  Professor Ping Li taught us basic knowledge of synthetic biology and introduced MEIHUA GROUP to us. Then we visited the company and got a lot of useful comments on our software.</br>
+
  Associate professor Ye Len helped us make a speech in The first affiliated middle school of Tongji University.</br></br>
+
  
 +
<b>10.Visiting Key Synthetic Biology Laboratory of CAS</b></br>
 +
<span class="detail" >Xiaotian Yu, Zhichao Ma and Wei Cao participated this visit and proposed many great ideas. Weicao gave an excellent speech on this meeting</br></span>
  
  We are sincerely grateful to everyone who help us in many ways.
+
<b>11.Mini Lectures for High School Students & Freshmen</b></br>
 +
<span class="detail" >Xiangzhen Li and Wei Cao gave these lectures for high school student and freshmen.</br></span></br>
  
  
 +
<span class="h1" id="Financing & Trip planning">
 +
      Financing</br>
 +
      </span>
 +
<ul>
 +
<li>Xiaotian Yu is in charge of Financial management.</li>
 +
<li>Wei Cao is responsible for flight tickets booking and hotel reservation. The rest of team members help plan the whole trip.</li>
 +
</ul>
 +
</br>
  
 +
<span class="h1" id="Advice">
 +
    Advice and human practice support</br>
 +
      </span>
  
 +
<ul>
 +
<li>Professor Qi Liu gave us advice on search algorithm and help us contact with WuXi AppTec.</li>
 +
<li>Professor Ping Li taught us basic knowledge of synthetic biology and introduced MEIHUA GROUP to us. Then we visited the company and got a lot of useful comments on our software.</li>
 +
<li>Associate professor Ye Leng helped us make a speech in The first affiliated middle school of Tongji University.</li>
  
 +
</ul>
 +
</br>
 +
<span class="top">
 +
      We are sincerely grateful to everyone who help us in many ways.</br>
 +
      </span>
  
 +
<div id="contact">
 +
<h3>CONTACT</h3>
 +
<span>annecao@tongji.edu.cn</span><hr/>
 +
<h3>ADDRESS</h3>
 +
<span>1239# Siping Road</br>Tongji University,Shanghai China</span><hr/>
 +
<h3>GET IN TOUCH</h3>
 +
<a href="https://www.facebook.com/tongjiIGEMer/?ref=bookmarks"><img src="https://static.igem.org/mediawiki/2018/8/8c/T--Tongji-Software--facebook.png" width="5%"></a>
 +
</div>
  
 +
</div>
  
  
 
   
 
</span>
 
  
 
</div>
 
</div>
 +
<script src="https://2018.igem.org/wiki/index.php?title=Template:Tongji-Software/test/js/jquery-1.8.3.min.js&action=raw&ctype=text/javascript"></script>
 +
<script src="https://2018.igem.org/wiki/index.php?title=Template:Tongji-Software/test/js/bootstrap.min.js&action=raw&ctype=text/javascript"></script>
 +
<script type="text/javascript">
 +
$(document).ready(function () {
 +
  var trigger = $('.icon'),
 +
    slide = $('.left'),
 +
isClosed = true;
  
 +
trigger.mouseover(function () {
 +
  cross_out();     
 +
});
 +
slide.mouseleave(function () {
 +
  cross_in();     
 +
});
  
 +
function cross_out() {
 +
  if (isClosed == true) {
 +
trigger.removeClass('is-open');
 +
trigger.addClass('is-closed');
 +
 +
$('#wrapper').toggleClass('toggled');
 +
isClosed = false;
 +
  }
 +
}
 +
function cross_in() {
 +
  if (isClosed == false) {
 +
trigger.removeClass('is-closed');
 +
trigger.addClass('is-open');
 +
 +
$('#wrapper').toggleClass('toggled');
 +
isClosed = true;
 +
  }
 +
  }
 +
});
 +
</script>
  
 +
<script>
 +
window.onload = function(){
 +
           
 +
                var mybtn = document.getElementById("btn");
 +
                var Time1 = null;
 +
                var isTop = true;
  
 +
                mybtn.onclick = function(){
 +
                 
 +
                    Time1 = setInterval(function(){
 +
                        var osTop = document.body.scrollTop||document.documentElement.scrollTop;
 +
                       
 +
                        var speed = Math.ceil(osTop/2);
 +
                       
 +
                        document.body.scrollTop = document.documentElement.scrollTop = osTop - speed;
 +
                        if(osTop <= 0){
 +
                           
 +
                            clearInterval(Time1);
 +
                        }
 +
                        isTop = true ;
 +
                    },100)
 +
                }
 +
               
 +
               
 +
                window.onscroll = function(){
 +
                   
 +
                    var osTop = document.body.scrollTop||document.documentElement.scrollTop;
 +
                   
 +
                    var clientHeight = document.documentElement.clientHeight;
 +
                   
 +
                    if (osTop>clientHeight) {
 +
                        mybtn.style.display = "block"
 +
                    }
 +
                    else{
 +
                        mybtn.style.display = "none"
 +
                    }
 +
                    if (!isTop) {
 +
                        clearInterval(Time1);
 +
                    }
 +
                    isTop = false;
 +
                }
 +
            }
  
 +
</script>
  
 
</body>
 
</body>
 
</html>
 
</html>

Latest revision as of 16:28, 17 October 2018

ATTRIBUTIONS
What makes Alpha Ant meaningful and wonderful is those
people’s great work.
Since we are from different majors, all things can be covered by everyone of us. More information about team members could be found in Team. Generally, we have three main sessions: biology logic thinking and investigation, programming and modeling, design.
It’s more like a workflow. At first, everyone is engaged in previous biology research and decide to do a topic about pathway design. Secondly, biology group try to get access to different database and deliver data to programming group. Then data processing and main part programming are followed. At last, design group can figure out how to show our software reasonably and wiki design.
Overview

Previous Research
  • Haiyan He, Xiaotian Yu, Zhichao Ma and Wei Cao are responsible for learning synthetic biology and mining proper topic.
  • Wei Cao investigated the barriers that experimenters could occur in metabolic engineering and interviewed Professor Ping Li for Tongji University for general workflow of metabolic pathway research.
  • Zhichao Ma communicated with postgraduate students major in bioinformatics.
  • Xiangzhen Li did some research on graph theoretic algorithm.

Database
  • Xiaotian Yu, Xiangzhen Li and Zhichao Ma were responsible for getting data from KEGG Database and data processing.
  • Haiyan He and Xiaotian Yu were responsible for calculating thermodynamic data by using equilibrator.
  • Zhichao Ma and Wei Cao was responsible for getting data from Brenda, ChEBI, DrugBank and KnowledgeBase.

Search algorithm & Ranking criteria
  • Xiangzhen Li did a lot of research on Graph Theoretic Algorithm and wrote code of DFS.
  • Xiaotian Yu and Wei Cao read some paper about atom conservation. Then they worked together on coding and model building.
  • Xiaotian Yu and Zhichao Ma worked on toxicity of compound and added it to ranking criteria.

Additional Functions
1.Organism recommendation
Zhichao Ma and Xiangzhen Li built and optimized microorganism recommendation model.
2.Flux Balance Analysis
Wei Cao and Haiyan He learned COBRA toolbox and built FBA model.
3.Atom conservation
Wei Cao and Haiyan He learned COBRA toolbox and built FBA model.
4.SMILES Comparison
Xiaotian Yu learned RDkit toolbox and added SMILES Comparison to our project.

Design
  • Yuchen Xing, Yuejia Li,Wei Cao were responsible for wiki design.
  • Yuchen Xing, Wei Cao and Zhichao Ma designed software interface.
  • YueJia Li also carried poster design work.

Human Practices and Collaborations
1.Visiting WuXi AppTec
Wei Cao communicated with WuXi AppTec and made an interview on experts in WuXi AppTec. Haiyan He, Xiaotian Yu, Zhichao Ma and Xiangzhen Li participated this interview and proposed many great ideas. Haiyan He give an excellent speech on this meeting.
2.Communicate with programmers
Zhichao Ma made a speech on a forum in school of life science and technology, Tongji University. There, we got a lot of suggestions on modeling.
3.Contact with experimenters
Wei Cao made a speech on professor Ping Li’s class and then investigate need of experimenters.
4.EuroAsia Meetup
All members attended EuroAsia Meetup in Shenzhen, China. Wei Cao and Xiaotian Yu did presentation in this Meetup. All the member answered questions during the speech.
5.CCiC
  • Xiaotian Yu contacted with Shanghai-tech, who held CCiC in Shanghai.
  • Xiangzhen Li , Xiaotian Yu and Wei Cao gave the committee a great presentation.
  • Haiyan He was responsible for poster exhibition part.
  • Yuejia Li designed the poster.

6.Meeting with SJTU & Fudan_China
Wei Cao contacted with SJTU-software and helped arrange meeting with SJTU-software. Haiyan He contacted with Fudan_China and helped arrange meeting with them. And rest of the team attended this meeting.
7.Game : “Go Ant!”
Xiaotian Yu developed the whole game. Of course, the rest of teammates gave him some advice. Yuejia Li designed the magnificent background, which made the game even more fun!
8.Visiting Meihua Group
Haiyan He, Xiaotian Yu, Zhichao Ma and Wei Cao participated this visit and proposed many great ideas. Xiaotian Yu gave an excellent speech on this meeting
9.Visiting Cathay Industrial Biotech
Haiyan He, Xiaotian Yu, Zhichao Ma and Wei Cao participated this visit and proposed many great ideas. Xiaotian Yu gave an excellent speech on this meeting
10.Visiting Key Synthetic Biology Laboratory of CAS
Xiaotian Yu, Zhichao Ma and Wei Cao participated this visit and proposed many great ideas. Weicao gave an excellent speech on this meeting
11.Mini Lectures for High School Students & Freshmen
Xiangzhen Li and Wei Cao gave these lectures for high school student and freshmen.

Financing
  • Xiaotian Yu is in charge of Financial management.
  • Wei Cao is responsible for flight tickets booking and hotel reservation. The rest of team members help plan the whole trip.

Advice and human practice support
  • Professor Qi Liu gave us advice on search algorithm and help us contact with WuXi AppTec.
  • Professor Ping Li taught us basic knowledge of synthetic biology and introduced MEIHUA GROUP to us. Then we visited the company and got a lot of useful comments on our software.
  • Associate professor Ye Leng helped us make a speech in The first affiliated middle school of Tongji University.

We are sincerely grateful to everyone who help us in many ways.

CONTACT

annecao@tongji.edu.cn

ADDRESS

1239# Siping Road
Tongji University,Shanghai China

GET IN TOUCH