Latest revision as of 20:44, 5 September 2017

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Partner Special Offers for iGEM Teams

Complimentary software and technical support from MathWorks!

MathWorks is pleased to sponsor the 2017 iGEM competition. As an iGEM partner, MathWorks will provide complimentary software and technical support to all iGEM teams for use in the competition.

The complimentary software kit is designed specifically to cater to the needs of iGEM teams with the following 12 products:

MATLAB

Simulink

SimBiology

Curve Fitting Toolbox

Symbolic Math Toolbox

Optimization Toolbox

Global Optimization Toolbox

Bioinformatics Toolbox

Statistics and Machine Learning Toolbox

Partial Differential Equation Toolbox

Image Processing Toolbox

Computer Vision Toolbox

Getting Started!

Interested in using MATLAB for your in silico projects?
We have put together a few video tutorials to help you get started.

For more resources, check out the competition page, product pages, webinars, and additional tutorials.

MATLAB and SimBiology in Past iGEMs

See how former iGEMers used MathWorks tools, such as MATLAB and SimBiology, for a variety of modeling and simulation projects. A few examples from previous years!

Team Imperial College used SimBiology to model their gene circuit in order to optimize their design and to predict system behavior under different conditions, such as different promoter strength or copy number.
Team Sydney Australia used SimBiology to develop a gene regulation pathway model of their ethylene biosensor and to run sensitivity analysis in order to identify processes that have the most significant impact on biosensor output.
Team TU Delft modeled 3D printing of their bacterial biofilm using MATLAB in order to determine the factors that have a strong influence on the biofilm strength.
Team Oxford built stochastic and deterministic models of genetic circuits in order to tackle environmental pollution by developing a device for the detection and degradation of the hazardous yet indispensable solvent dichloromethane (DCM).
Team KU Leuven modelled the pathway leading to Methyl Salicylate (MeS) production and performed sensitivity analysis, in order to predict MeS production and find the rate limiting steps.
Team Carnegie Mellon derived an ODE model and used it with experimental time-course data to estimate key parameters like transcriptional and translational efficiency.
Team Slovenia performed parameter scans to better characterize the effects of the parameters space on the behavior their bistable system, Switch IT.

Technical Mentoring

Can't find what you are looking for? Have a specific question about using MATLAB tools for your iGEM work? We are here to help.
Feel free to contact Fulden Buyukozturk, SimBiology Technical Expert, to request assistance via email at fulden.buyukozturk@mathworks.com

Follow Fulden on Twitter @fulden_b

@@ Line 6: / Line 6: @@
 <center><h1>Partner Special Offers for iGEM Teams</h1></center>
 <br>
-<img src="https://static.igem.org/mediawiki/2012/c/c0/MathWorks_logo_small.png" width="200px">
+<img src="https://static.igem.org/mediawiki/2012/c/c0/MathWorks_logo_small.png" width="300px">
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 <ul>
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 <br>
 <br>
-<cneter><b>The complementary software kit includes the following 12 products:</b></center>
+<cneter><b>The complimentary software kit is designed specifically to cater to the needs of iGEM teams with the following 12 products:</b></center>
-</div><ul><ul>
+</div><ul><ul><ul><ul><ul>
 <div class="column half_size">
 <li>MATLAB</li>
@@ Line 33: / Line 33: @@
 <li>Computer Vision Toolbox</li>
 </div>
-</ul></ul>
+</ul></ul></ul></ul></ul>
 <br><br>
 </p>
 <div class="clear"></div>
 <div class="column full_size">
-<br><br>
+<a href="http://www.mathworks.com/academia/student-competitions/software-request-registration-igem.html">
-<h3>Request Your Free Kit</h3><br>
+<div class="highlight gray turquoise_top link_box">
-<p>To request your Free Software Kit, please complete the <a href="https://www.mathworks.com/academia/student-competitions/software-request-registration-igem.html"> Software Request Form </a>(must be completed by faculty advisor) to request the complimentary software kit.
+<center>
+<h2>Request Your Free Kit</h2>
-</p>
+<p>To request your Free Software Kit, please complete the Software Request Form.<br>Must be completed by team leader or faculty advisor. </p>
+</center>
+</div>
+</a>
 <div class="clear"></div>
-<div class="clear"></div><div class="clear"></div>
+<br>
-<h2> Getting Started! </h2>
+<div class="column half_size">
+<h3> Getting Started! </h3>
-<p>
+<p>Interested in using MATLAB for your <i> in silico </i> projects? <br>
-Interested in using MATLAB for your <i> in silico </i> projects?
 We have put together a few <u> video tutorials</u> to help you get started. </p>
 <ul>
+<li style="padding-bottom:5px;" > <a href="http://www.mathworks.com/videos/introduction-to-data-analysis-in-matlab-for-life-scientists-81712.html" style="text-decoration: none">  Introduction to Data Analysis in MATLAB for Life Scientists  </a></li>
+<li style="padding-bottom:5px;" > <a href="http://www.mathworks.com/videos/data-driven-fitting-with-matlab-81809.html" style="text-decoration: none">  Data Driven Fitting with MATLAB </a></li>
+<li style="padding-bottom:5px;" > <a href=" http://www.mathworks.com/academia/student_center/tutorials/computational-math-tutorial-launchpad.html" style="text-decoration: none"> MATLAB with Interactive Computational Mathematics</a></li>
 <li style="padding-bottom:5px;" > <a href="http://www.mathworks.com/videos/modeling-synthetic-biology-systems-with-matlab-and-simbiology-101691.html"  style="text-decoration: none">SimBiology and MATLAB for Modeling Synthetic Biology Systems</a>
+<li style="padding-bottom:5px;" > <a href="http://www.mathworks.com/academia/student_center/tutorials/register.html"  style="text-decoration: none"> Getting started with MATLAB </a></li>
-<li style="padding-bottom:5px;" > <a href="http://www.mathworks.com/academia/student_center/tutorials/register.html"  style="text-decoration: none"> Getting started with MATLAB </a>
+<li style="padding-bottom:5px;"> <a href="http://www.mathworks.com/videos/building-a-model-in-simbiology-68960.html"  style="text-decoration: none"> Drag-and-drop model-building in SimBiology </a></li>
-</li>
+<li style="padding-bottom:5px;"> <a href="http://www.mathworks.com/videos/modeling-biology-with-simbiology-an-introduction-for-igem-teams-81817.html"  style="text-decoration: none"> SimBiology for modeling and simulating dynamics of synthetic biology systems </a></li>
-<li style="padding-bottom:5px;"> <a href="http://www.mathworks.com/videos/building-a-model-in-simbiology-68960.html"  style="text-decoration: none"> Drag-and-drop model-building in SimBiology </a>
+<li style="padding-bottom:5px;"> <a href="http://www.mathworks.com/videos/simulating-a-model-in-simbiology-117245.html" style="text-decoration: none"> Simulating a Model in SimBiology </a></li>
-</li>
-<li style="padding-bottom:5px;"> <a href="http://www.mathworks.com/academia/student_center/tutorials/computational-math/solving-ordinary-diff-equations/player.html"  style="text-decoration: none">
-	 Solving nonlinear differential equations in MATLAB </a>
-</li>
-<li style="padding-bottom:5px;"> <a href="http://www.mathworks.com/videos/modeling-biology-with-simbiology-an-introduction-for-igem-teams-81817.html"  style="text-decoration: none"> SimBiology for modeling and simulating dynamics of synthetic biology systems </a>
-</li>
-<li style="padding-bottom:5px;"> <a href="http://www.mathworks.com/videos/simulating-a-model-in-simbiology-117245.html" style="text-decoration: none"> Simulating a Model in SimBiology </a>
-</li>
 </ul>
@@ Line 76: / Line 75: @@
 </p>
 <br>
-<h3> Technical Mentoring </h3>
+</div>
+<div class="column half_size">
+<h3> MATLAB and SimBiology in Past iGEMs </h3>
+<p>See how former iGEMers used MathWorks tools, such as MATLAB and SimBiology, for a variety of modeling and simulation projects. A few examples from previous years!
+<ul>
-<p>
+<li> <span style="font-weight:bold; color: #d77600"> Team Imperial College </span> <a href="https://2016.igem.org/Team:Imperial_Collegestyle="Font-Weight:" >used SimBiology to model their gene circuit </a> in order to optimize their design and to predict system behavior under different conditions, such as different promoter strength or copy number.</li>
-Can't find what you are looking for? Have a specific question about using MATLAB tools for your iGEM work? We are here to help. Feel free to
+<li> <span style="font-weight:bold; color: #d77600"> Team Sydney Australia </span> used SimBiology to develop a gene regulation pathway model of their ethylene biosensor and <a href="https://2016.igem.org/Team:Sydney_Australia" style="Font-Weight:" > to run sensitivity analysis </a> in order to identify processes that have the most significant impact on biosensor output.</li>
-contact Fulden Buyukozturk, SimBiology Technical Expert, to request assistance via email at <a href="mailto:fulden.buyukozturk@mathworks.com" style="color:#005fce;">fulden.buyukozturk@mathworks.com</a>
+<li> <span style="font-weight:bold; color: #d77600"> Team TU Delft </span> <a href="https://2015.igem.org/Team:TU_Delft" style="Font-Weight:" > modeled 3D printing of their bacterial biofilm</a> using MATLAB in order to determine the factors that have a strong influence on the biofilm strength.</li>
-<br><br>
+<li> <span style="font-weight:bold; color: #d77600"> Team Oxford </span> built<a href="https://2014.igem.org/Team:Oxford/Modelling" style="Font-Weight:" > stochastic and deterministic models</a> of genetic circuits in order to tackle environmental pollution by developing a device for the detection and degradation of the hazardous yet indispensable solvent dichloromethane (DCM).</li>
-Follow Fulden on Twitter <a href="https://twitter.com/fulden_b">@fulden_b</a></p>
+<li> <span style="font-weight:bold; color: #d77600"> Team KU Leuven </span> <a href="https://2013.igem.org/Team:KU_Leuven/Project/modelling" style="Font-Weight:" > modelled</a> the pathway leading to Methyl Salicylate (MeS) production and performed sensitivity analysis, in order to predict MeS production and find the rate limiting steps. </li>
+<li> <span style="font-weight:bold; color: #d77600"> Team Carnegie Mellon </span> derived an <a href =  "https://2012.igem.org/Team:Carnegie_Mellon/Mod-Overview" style="Font-Weight:"> ODE model</a> and used it with experimental time-course data to estimate key parameters like transcriptional and translational efficiency.</li>
+<li> <span style="font-weight:bold; color: #d77600"> Team Slovenia  </span>performed <a href =  "https://2012.igem.org/Team:Slovenia/ModelingPositiveFeedbackLoopSwitch" style="Font-Weight:"> parameter scans</a>  to better characterize the effects of the parameters space on the behavior their bistable system, Switch IT.</li>
+</ul></p>
+</div>
+<div class="column ful_size">
+<h3> Technical Mentoring </h3>
+<p>Can't find what you are looking for? Have a specific question about using MATLAB tools for your iGEM work? We are here to help. <br>
+Feel free to contact Fulden Buyukozturk, SimBiology Technical Expert, to request assistance via email at <a href="mailto:fulden.buyukozturk@mathworks.com" style="color:#005fce;">fulden.buyukozturk@mathworks.com</a><br>
 <br>
-<p> <b> Good luck with your projects! </b> </p>
+Follow Fulden on Twitter <a href="http://twitter.com/fulden_b">@fulden_b</a>
+<br>
+<br>
+<p> <h2> Good luck with your projects! </h2> </p>
 </ul>
 </div>
@@ Line 96: / Line 109: @@
 <ul><ul><ul><ul>
-<h3> MATLAB and SimBiology in Past iGEMs </h3>
-See how former iGEMers used MathWorks tools, such as MATLAB and SimBiology, for a variety of modeling and simulation projects. A few examples from previous years!
-<ul><ul>
-<li> <span style="font-weight:bold; color: #d77600"> Team TU Delft </span> <a href="https://2015.igem.org/Team:TU_Delft" style="Font-Weight:" > modeled 3D printing of their bacterial biofilm</a> using MATLAB in order to determine the factors that have a strong influence on the biofilm strength.</li>
-<li> <span style="font-weight:bold; color: #d77600"> Team Oxford </span> built
-<a href="https://2014.igem.org/Team:Oxford/Modelling" style="Font-Weight:" > stochastic and deterministic models</a>
-of genetic circuits in order to tackle environmental pollution by developing a device for the detection and degradation of the hazardous yet indispensable solvent dichloromethane (DCM).
-</li>
-<li> <span style="font-weight:bold; color: #d77600"> Team KU Leuven </span>
-<a href="https://2013.igem.org/Team:KU_Leuven/Project/modelling" style="Font-Weight:" > modelled</a>
-the pathway leading to Methyl Salicylate (MeS) production and performed sensitivity analysis, in order to predict MeS production and find the rate limiting steps.
-</li>
-<li> <span style="font-weight:bold; color: #d77600"> Team Carnegie Mellon </span> derived an <a href =  "https://2012.igem.org/Team:Carnegie_Mellon/Mod-Overview" style="Font-Weight:"> ODE model</a> and used it with experimental time-course data to estimate key parameters like transcriptional and translational efficiency.
-</li>
-<li> <span style="font-weight:bold; color: #d77600"> Team Slovenia  </span>performed <a href =  "https://2012.igem.org/Team:Slovenia/ModelingPositiveFeedbackLoopSwitch" style="Font-Weight:"> parameter scans</a>  to better characterize the effects of the parameters space on the behavior their bistable system, Switch IT.
-</li>
-</ul>
-</div>

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