Team:BostonU

From 2014.igem.org

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{{CSS/Main}}
 
{{Template:Team:BostonU/CSS}}
{{Template:Team:BostonU/CSS}}
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<td style="border:1px solid black;" colspan="3" align="center" height="150px" bgColor=#FF404B>
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<h1 >WELCOME TO iGEM 2014! </h1>
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box-sizing: border-box;
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<p>Your team has been approved and you are ready to start the iGEM season!
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}
-
<br>On this page you can document your project, introduce your team members, document your progress <br> and share your iGEM experience with the rest of the world! </p>
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<br>
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<p style="color:#E7E7E7"> <a href="https://2014.igem.org/wiki/index.php?title=Team:BostonU&action=edit"style="color:#FFFFFF"> Click here  to edit this page!</a> </p>
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h2{
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<a href="https://igem.org/Team.cgi?year=2014&team_name=BostonU"style="color:#000000"> Official Team Profile </a></td>
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<a href="https://2014.igem.org/Team:BostonU/Project"style="color:#000000"> Project</a></td>
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main{
-
<a href="https://2014.igem.org/Team:BostonU/Parts"style="color:#000000"> Parts</a></td>
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<a href="https://2014.igem.org/Team:BostonU/Modeling"style="color:#000000"> Modeling</a></td>
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-
<a href="https://2014.igem.org/Team:BostonU/Notebook"style="color:#000000"> Notebook</a></td>
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 +
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 +
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 +
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<a href="https://2014.igem.org/Team:BostonU/Safety"style=" color:#000000"> Safety </a></td>
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 +
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 +
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 +
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-
<a href="https://2014.igem.org/Team:BostonU/Attributions"style="color:#000000"> Attributions </a></td>
 
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font-size:12pt;
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-
</td>
 
-
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+
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<!--requirements section -->
+
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-
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-
<tr>
+
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-
<td width="45%"  valign="top">
+
width: 100%;
 +
height:100%;
 +
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 +
        background-image:url(https://static.igem.org/mediawiki/2014/0/03/Boston1_bu14.jpg);
 +
font-size: 18px;
 +
text-align: center;
 +
color: rgba(255,255,255,.6);
 +
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 +
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background-size:cover;
 +
min-height:700px;
 +
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 +
}
-
<p> Please be sure to keep these links, your audience will want to find your: </p>
+
.banner .inner {
 +
padding: 160px 0 110px;
 +
}
-
<!-- Links to other team pages -->
+
.banner h1, .banner h2 {
-
<ul>
+
font-size: 40px;
-
<li><a href="https://2014.igem.org/Team:BostonU">Home</a> </li>
+
line-height: 52px;
-
<li><a href="https://2014.igem.org/Team:BostonU/Team">Team</a> </li>
+
color: #fff;
-
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=BostonU">Official Team Profile</a> </li>
+
}
-
<li><a href="https://2014.igem.org/Team:BostonU/Project">Project</a> </li>
+
-
<li><a href="https://2014.igem.org/Team:BostonU/Parts">Parts</a> </li>
+
-
<li><a href="https://2014.igem.org/Team:BostonU/Modeling">Modeling</a> </li>
+
-
<li><a href="https://2014.igem.org/Team:BostonU/Notebook">Notebook</a> </li>
+
-
<li><a href="https://2014.igem.org/Team:BostonU/Safety">Safety</a> </li>
+
-
<li><a href="https://2014.igem.org/Team:BostonU/Attributions">Attributions</a> </li>
+
-
</ul>
+
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 +
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 +
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 +
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 +
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-
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+
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 +
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 +
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 +
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 +
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-
<td > </td>
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-
<td width="45%">
+
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 +
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 +
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 +
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-
<p>There are a few wiki requirements teams must follow:</p>
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.banner .btn, .banner .dot {
-
<ul>
+
-webkit-filter: drop-shadow(0 1px 2px rgba(0,0,0,.3));
-
<li>All pages, images and files must be hosted on the <a href ="https://2014.igem.org/Special:Upload">  2014.igem.org server</a>. </li>
+
-moz-filter: drop-shadow(0 1px 2px rgba(0,0,0,.3));
-
<li>All pages must be created under the team’s name space.</li>
+
-ms-filter: drop-shadow(0 1px 2px rgba(0,0,0,.3));
-
<li>As part of your documentation, keep the links from the menu to the left. </li>
+
-o-filter: drop-shadow(0 1px 2px rgba(0,0,0,.3));
-
<li>Do not use flash in wiki code. </li>
+
filter: drop-shadow(0 1px 2px rgba(0,0,0,.3));
-
<li>The <a href="https://static.igem.org/mediawiki/igem.org/6/60/Igemlogo_300px.png"> iGEM logo </a> should be placed on the upper part of every page and should link to <a href="https://2014.igem.org/Main_Page">2014.igem.org</a>.</li>
+
}
-
</ul>
+
-
<p>Visit the <a href="https://2014.igem.org/Wiki_How-To"> Wiki How To page </a> for a complete list of requirements, tips and other useful information. </p>
+
-
</td>
+
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-
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+
position: absolute;
 +
left: 0;
 +
right: 0;
 +
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 +
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 +
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 +
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 +
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 +
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 +
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 +
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-
<tr> <td colspan="3"  height="15px"> </td></tr>
+
border: 2px solid #fff;
-
<tr><td bgColor="#e7e7e7" colspan="3" height="1"> </tr>
+
border-radius: 6px;
 +
cursor: pointer;
 +
opacity: .4;
-
<!--tips  -->
+
-webkit-transition: background .5s, opacity .5s;
-
<tr><td colspan="3" > <h3> Tips  </h3></td></tr>
+
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 +
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 +
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 +
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 +
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 +
opacity: 1;
 +
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-
<tr>
+
.banner .arrows {
-
<td width="45%" valign="top">
+
position: absolute;
-
<p>We are currently working on providing teams with some easy to use design templates.
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bottom: 20px;
-
<br> In the meantime you can also view other team wikis for inspiration! Here are some very good examples</p>
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right: 20px;
 +
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 +
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 +
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 +
display: inline;
 +
padding-left: 10px;
 +
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 +
}
-
<ul>
+
.wrap {
-
<li> <a href="https://2013.igem.org/Team:SDU-Denmark/"> 2013 SDU Denmark </a> </li>
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margin: 0 auto;
-
<li> <a href="https://2013.igem.org/Team:SYSU-China">2013 SYSU China</a> </li>
+
width: 960px;
-
<li> <a href="https://2013.igem.org/Team:Shenzhen_BGIC_ATCG"> 2013 Shenxhen BGIG ATCG </a></li>
+
}
-
<li> <a href="https://2013.igem.org/Team:Colombia_Uniandes">2013 Colombia Unianades </a></li>
+
-
<li> <a href="https://2013.igem.org/Team:Lethbridge">2013 Lethbridge</a></li>
+
-
</ul>
+
-
<p>For a full wiki list, you can visit <a href="https://igem.org/Team_Wikis?year=2013">iGEM 2013 web sites </a> and <a href="https://igem.org/Team_Wikis?year=2012">iGEM 2012 web sites</a>  lists. </p>
+
.anchor{
-
</td>
+
position:absolute;
 +
top:calc(100% - 125px);
 +
}
-
<td> </td>
+
.topanchor{
-
<td width="45%">
+
position:absolute;
 +
top:calc(0% - 125px);
 +
}
-
<p>This wiki will be your team’s first interaction with the rest of the world, so here are a few tips to help you get started: </p>
+
.lower{
 +
background-image:url(../img_bu14/gradient_bu14.png);
 +
background-color:#FFF;
 +
text-align:center;
 +
background-repeat:repeat-x;
 +
width:100%;
 +
position:absolute;
 +
top:100%;
 +
z-index:10;
 +
}
 +
.content{
 +
text-align:left;
 +
width:100%;
 +
position:relative;
 +
z-index:10;
-
<ul>
+
}
-
<li>State your accomplishments! Tell people what you have achieved from the start. </li>
+
.text{
-
<li>Be clear about what you are doing and what you plan to do.</li>
+
width:75%;
-
<li>You have a global audience! Consider the different backgrounds that your users come from.</li>
+
margin-left:auto;
-
<li>Make sure information is easy to find; nothing should be more than 3 clicks away. </li>
+
margin-right:auto;
-
<li>Avoid using very small fonts and low contrast colors; information should be easy to read. </li>
+
}
-
<li>Start documenting your project as early as possible; don’t leave anything to the last minute before the Wiki Freeze. For a complete list of deadlines visit the <a href="">iGEM 2013 calendar</a> </li>
+
.content1{
-
<li>Have lots of fun! </li>
+
background-image:url(../img_bu14/whitebkgd_bu14.png);
 +
background-repeat:repeat;
 +
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 +
.content2{
 +
background-image:url(../img_bu14/orangemenubkgd_bu14.png);
 +
background-repeat:repeat;
 +
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 +
.content3{
 +
background-image:url(../img_bu14/bluebkgd_bu14.png);
 +
background-repeat:repeat;
 +
}
 +
 
 +
.pagecontent{
 +
position:relative;
 +
left:50px;
 +
top:130px;
 +
width:80%;
 +
text-align:left;
 +
}
 +
 
 +
pageheader{
 +
font-size:28px;
 +
font-weight:700;
 +
text-transform:uppercase;
 +
}
 +
 
 +
.sponsors{
 +
background-color:#FFF;
 +
position:relative;
 +
text-align:center;
 +
bottom:0px;
 +
z-index:10;
 +
}
 +
 
 +
@media only screen and (min-device-width: 320px) and (max-device-width: 480px), (max-width: 900px) {
 +
.wrap {
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    <h1>chimera
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    <h3>an optimized synthetic biology workflow</h3>
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    <h2><br>
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        <th colspan="2" scope="col"><img src="https://static.igem.org/mediawiki/2014/e/ea/Workflow_bu14.png" width="525" height="317" alt="Workflow" style="float:right">Currently in synthetic biology, the creation of novel genetic circuits revolves around a familiar design-build-test cycle. As an increasing number of laboratories become involved in designing newer and more sophisticated constructs, the lack of standardization in production and characterization inhibits workflow efficiency and, by extension, growth of the field. The 2014 Boston University iGEM team seeks to employ a formalized and optimized workflow supported by new bio-design automation applications, with the aim of benefiting synthetic biologists seeking to more efficiently design, build, and characterize complex constructs.
 +
          <br><br>
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          Advancements in bio-design automation (or BDA) have allowed for the implementation of a variety of software and automation tools that help improve the design-build-test efficiency in a synthetic biology laboratory. We will take a novel approach to the design-build-test cycle by using software tools to formalize our workflows, thus making us one of the first BDA iGEM teams. Using basic parts from the <a href="http://cidarlab.org/" target="_blank">CIDAR</a> MoClo library (built by the <a href="https://2012.igem.org/Team:BostonU" target="_blank">2012</a> and <a href="https://2013.igem.org/Team:BostonU" target="_blank">2013</a> BU iGEM teams), we will build complex constructs using our formalized workflow, in addition to providing comprehensive characterization data for all new parts and improving data for existing parts in the <a href="http://parts.igem.org/Main_Page" target="_blank">Registry of Standard Biological Parts</a>. <br><br>
 +
          Our BDA approach will include utilizing various software tools throughout the design-build-test cycle in our wet lab work, including Eugene, Raven, and the TASBE flow cytometry tool.
 +
          <br><br>
 +
          The design of our genetic devices will be facilitated by <a href="http://eugenecad.org/" target="_blank">Eugene</a>, a language specifically designed for the description of genetic networks. Eugene allows for a very efficient design process for new parts by providing an exhaustive list of possible transcriptional units that can be made with available genetic parts, while following a set of rules to ensure the viability of the final designs. <br><br>
 +
          The building process will be facilitated by <a href="http://cidarlab.org/raven/" target="_blank">Raven</a>, a web-based tool that generates an assembly plan for genetic devices. Our team plans to build devices using the MoClo method employed by previous BU iGEM teams, in addition to multiplexing in order to build many variations on one design in an efficient one-pot reaction. <br><br>
 +
          We will use flow cytometry in conjunction with the <a href="https://synbiotools.bbn.com/" target="_blank">TASBE Tools</a> to test the functionality of new constructs and enhance the documentation available for existing parts in the Registry. Additionally, we will contribute several new parts and their characterization data to the Registry including hybrid promoters, fusion proteins, and a variety of new vectors.&nbsp;</th>
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Revision as of 03:36, 18 June 2014

 

Start


chimera

an optimized synthetic biology workflow


WorkflowCurrently in synthetic biology, the creation of novel genetic circuits revolves around a familiar design-build-test cycle. As an increasing number of laboratories become involved in designing newer and more sophisticated constructs, the lack of standardization in production and characterization inhibits workflow efficiency and, by extension, growth of the field. The 2014 Boston University iGEM team seeks to employ a formalized and optimized workflow supported by new bio-design automation applications, with the aim of benefiting synthetic biologists seeking to more efficiently design, build, and characterize complex constructs.

Advancements in bio-design automation (or BDA) have allowed for the implementation of a variety of software and automation tools that help improve the design-build-test efficiency in a synthetic biology laboratory. We will take a novel approach to the design-build-test cycle by using software tools to formalize our workflows, thus making us one of the first BDA iGEM teams. Using basic parts from the CIDAR MoClo library (built by the 2012 and 2013 BU iGEM teams), we will build complex constructs using our formalized workflow, in addition to providing comprehensive characterization data for all new parts and improving data for existing parts in the Registry of Standard Biological Parts.

Our BDA approach will include utilizing various software tools throughout the design-build-test cycle in our wet lab work, including Eugene, Raven, and the TASBE flow cytometry tool.

The design of our genetic devices will be facilitated by Eugene, a language specifically designed for the description of genetic networks. Eugene allows for a very efficient design process for new parts by providing an exhaustive list of possible transcriptional units that can be made with available genetic parts, while following a set of rules to ensure the viability of the final designs.

The building process will be facilitated by Raven, a web-based tool that generates an assembly plan for genetic devices. Our team plans to build devices using the MoClo method employed by previous BU iGEM teams, in addition to multiplexing in order to build many variations on one design in an efficient one-pot reaction.

We will use flow cytometry in conjunction with the TASBE Tools to test the functionality of new constructs and enhance the documentation available for existing parts in the Registry. Additionally, we will contribute several new parts and their characterization data to the Registry including hybrid promoters, fusion proteins, and a variety of new vectors. 

 
 




Our Sponsors


Retrieved from "http://2014.igem.org/Team:BostonU"