Team:Michigan Software

From 2014.igem.org

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<p class="sciencedescription">Experimental reproducibility is hindered by current protocols.</p>
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<p>Choosing reliable protocols is a recurrent problem in scientific research. Experimental practices may vary immensely across different laboratories, diminishing both the reproducibility of procedures and overall scientific method.</p>
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<a href="https://2014.igem.org/Team:Michigan_Software/Project#Description">Learn more about problem</a>
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<h1 >WELCOME TO iGEM 2014! </h1>
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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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<p style="color:#E7E7E7"> <a href="https://2014.igem.org/wiki/index.php?title=Team:Michigan_Software&action=edit"style="color:#FFFFFF"> Click here  to edit this page!</a> </p>
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<a href="https://2014.igem.org/Team:Michigan_Software"style="color:#000000">Home </a> </td>
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<a href="https://2014.igem.org/Team:Michigan_Software/Team"style="color:#000000"> Team </a> </td>
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<a href="https://igem.org/Team.cgi?year=2014&team_name=Michigan_Software"style="color:#000000"> Official Team Profile </a></td>
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<a href="https://2014.igem.org/Team:Michigan_Software/Project"style="color:#000000"> Project</a></td>
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<a href="https://2014.igem.org/Team:Michigan_Software/Attributions"style="color:#000000"> Attributions </a></td>
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<td align ="center"> <a href="https://2014.igem.org/Main_Page"> <img src="https://static.igem.org/mediawiki/igem.org/6/60/Igemlogo_300px.png" width="55px"></a> </td>
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Choosing apt and reliable protocols for new experiments is a problem that productive wet labs routinely face. However, it is difficult to know in detail which protocols will produce the best results. Experimental practices may differ immensely across laboratories, and precise details of these practices may be lost or forgotten as skilled faculty or students leave the lab to pursue other endeavors. These two realities give rise to a vast number of experimental protocols of which many are left with undocumented experiential knowledge. Furthermore, no tool yet exists to allow wet lab investigators to measure and compare the efficacy of protocols before executing them forthright.
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Such fragmentation in protocol methods and their documentation may to some degree hamper scientific progress. From the immense number of protocols currently in use, there are few well-defined protocols that are generally agreed upon by the scientific community, in part due to the lack of a system that can supply a measure of a protocol’s acceptance compared to its variants. In turn, the lack of commonly accepted protocols and their inadequate documentation has the potential to affect experimental reproducibility through method inconsistencies across laboratories and across succession of investigators.
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In order to address these problems, we set out to build a database that integrates a crowdsourced ratings and comments system to clearly document, rate, elaborate, review, and organize variants of experimental protocols. Such a tool serves as a curator for protocol variants and enables wet lab investigators to compare protocol efficacies. Furthermore, the crowdsourced ratings system quantifies a protocol’s acceptance within the scientific community and can serve as a useful criterion to assist with finding and selecting from common protocols. In addition, a protocol comments system provides an avenue through which experiential knowledge can be passed along. As an extension to the protocol database, we will also develop a dynamic calculator that can run user-defined theoretical calculations for any protocol, such as limiting reagent, yield, or even the monetary cost of the materials used. The calculator further assists investigators in comparing and performing protocols. In all, these tools will help wet lab investigators to document, organize, and compare protocols to assist with scientific experimentation.
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<p> Please be sure to keep these links, your audience will want to find your: </p>
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<li><a href="https://2014.igem.org/Team:Michigan_Software">Home</a> </li>
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<li><a href="https://2014.igem.org/Team:Michigan_Software/Team">Team</a> </li>
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<li><a href="https://igem.org/Team.cgi?year=2013&team_name=Michigan_Software">Official Team Profile</a> </li>
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<li><a href="https://2014.igem.org/Team:Michigan_Software/Project">Project</a> </li>
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<li><a href="https://2014.igem.org/Team:Michigan_Software/Parts">Parts</a> </li>
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<li><a href="https://2014.igem.org/Team:Michigan_Software/Modeling">Modeling</a> </li>
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<li><a href="https://2014.igem.org/Team:Michigan_Software/Notebook">Notebook</a> </li>
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<li><a href="https://2014.igem.org/Team:Michigan_Software/Safety">Safety</a> </li>
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<li><a href="https://2014.igem.org/Team:Michigan_Software/Attributions">Attributions</a> </li>
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<p>There are a few wiki requirements teams must follow:</p>
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<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>
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<li>All pages must be created under the team’s name space.</li>
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<li>As part of your documentation, keep the links from the menu to the left. </li>
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<li>Do not use flash in wiki code. </li>
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<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>
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<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>
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<tr><td colspan="3" > <h3> Tips  </h3></td></tr>
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<p>We are currently working on providing teams with some easy to use design templates.
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<br> In the meantime you can also view other team wikis for inspiration! Here are some very good examples</p>
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<li> <a href="https://2013.igem.org/Team:SDU-Denmark/"> 2013 SDU Denmark </a> </li>
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<li> <a href="https://2013.igem.org/Team:SYSU-China">2013 SYSU China</a> </li>
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<li> <a href="https://2013.igem.org/Team:Shenzhen_BGIC_ATCG"> 2013 Shenxhen BGIG ATCG </a></li>
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<li> <a href="https://2013.igem.org/Team:Colombia_Uniandes">2013 Colombia Unianades </a></li>
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<li> <a href="https://2013.igem.org/Team:Lethbridge">2013 Lethbridge</a></li>
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<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>
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<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>
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<p> In response, we developed ProtoCat, a free online catalog of laboratory protocols. Our software condenses the vast array of protocols into a single location, giving users access to top-rated procedures from across the globe. </p>
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<a href="https://2014.igem.org/Team:Michigan_Software/Protocat">Check out our software</a>
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<li>State your accomplishments! Tell people what you have achieved from the start. </li>
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<li>Be clear about what you are doing and what you plan to do.</li>
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<li>You have a global audience! Consider the different backgrounds that your users come from.</li>
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<li>Make sure information is easy to find; nothing should be more than 3 clicks away. </li>
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<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>
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Latest revision as of 03:05, 18 October 2014

Michigan Software

Experimental reproducibility is hindered by current protocols.

Choosing reliable protocols is a recurrent problem in scientific research. Experimental practices may vary immensely across different laboratories, diminishing both the reproducibility of procedures and overall scientific method.

Learn more about problem

In response, we developed ProtoCat, a free online catalog of laboratory protocols. Our software condenses the vast array of protocols into a single location, giving users access to top-rated procedures from across the globe.

Check out our software

                                                                 

contact info: igemsoftware-requests@umich.edu.

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