Difference between revisions of "Sponsors/MathWorks"

Latest revision as of 18:02, 10 June 2016

MathWorks is pleased to sponsor the 2016 iGEM competition. As an iGEM partner, MathWorks will provide complimentary software and technical support to all iGEM teams for use in the competition. Please complete the Software Request Form (must be completed by faculty advisor) to request the complimentary software kit. In order to learn more about our sponsorship and to request complimentary software for use in the competition, visit our iGEM competition page.

The complementary software kit includes 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.

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

Good luck with your projects!

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 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.

@@ Line 4: / Line 4: @@
 <p> MathWorks is pleased to sponsor the 2016 iGEM competition. As an iGEM partner, MathWorks will provide complimentary software and technical support to all iGEM teams for use in the competition. Please complete the <a href="http://www.mathworks.com/academia/student-competitions/software-request-registration-igem.html" > <b>Software Request Form</b></a> (must be completed by faculty advisor) to request the complimentary software kit.
-Learn more about our sponsorship and request complimentary software for use in the competition <a href="http://www.mathworks.com/academia/student-competitions/igem/">here </a> or visit us at
+In order to learn more about our sponsorship and to request complimentary software for use in the competition, visit our <a href="http://www.mathworks.com/academia/student-competitions/igem/" style="color:#005fce; text-decoration:none;">iGEM competition page</a>.</p>
-http://www.mathworks.com/academia/student-competitions/igem/ </p>
 <br>
-<p> The complementary software kit includes the following 11 products:</p>
+<p> The complementary software kit includes the following 12 products:</p>
 <div class="clear"></div>
 <div style="border-top:3px solid #c0c0c0;">
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-<div style="margin-left:40px;width:30%;float:left;">
+<div style="margin-left:30px;width:30%;float:left;">
 <ul style="padding-right:30px; font-family: Verdana; color:#000000; margin:5px ">
 <li style="padding-bottom:5px">  MATLAB
@@ Line 20: / Line 19: @@
 <li style="padding-bottom:5px">  SimBiology
 <li style="padding-bottom:2px">  Curve Fitting Toolbox
 </ul>
 </div>
@@ Line 30: / Line 30: @@
 </ul>
 </div>
-<div style="width:30%;float:left;">
+<div style="width:35%;float:left;">
 <ul style="padding-right:30px; font-family: Verdana;  color:#000000; margin:5px; ">
 <li style="padding-bottom:5px">  Statistics and Machine Learning Toolbox
@@ Line 52: / Line 52: @@
 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>
+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/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>
@@ Line 63: / Line 65: @@
 </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>
@@ Line 79: / Line 83: @@
 <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. Feel free to
-contact Fulden Buyukozturk via email at <u> fulden.buyukozturk AT mathworks.com</u> to request assistance.
+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>
-</p>
+<br><br>
+Follow Fulden on Twitter <a href="https://twitter.com/fulden_b">@fulden_b</a></p>
 <br>
 <p> <b> Good luck with your projects! </b> </p>
@@ Line 93: / Line 98: @@
 <div style="float:right;width:350px; background-color: #f2f2f2; border-radius: 5px; border:2px solid gray; padding-left: 15px; padding-top:10px; padding-bottom:10px;">
-<hx1 style="font-size:120%; color:#000000; font-weight:bold"> Webinar </hx1>
-<p style="padding-right:20px"> <u> SimBiology and MATLAB for Modeling Synthetic Biology Systems </u>
-<p style="padding-right:20px"> This webinar provides iGEM teams with an introduction to modeling, simulation and analysis with MATLAB and SimBiology using an example from synthetic biology literature.
-<p style="padding-right:20px"> <a href="http://www.mathworks.com/videos/modeling-synthetic-biology-systems-with-matlab-and-simbiology-101691.html" style="Font-Weight:" > Watch Recorded Webinar Here! </a>
-</p>
-<br>
 <hx1 style="font-size:120%; color:#000000; font-weight:bold"> MATLAB and SimBiology in Past iGEMs </hx1>
@@ Line 107: / Line 104: @@
 <ul style="padding-left:-10px; padding-right: 10px;">
-<li> <span style="font-weight:bold; color: #00cc00"> Team Oxford </span> built
+<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: #00cc00"> Team KU Leuven </span>
+<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: #00cc00"> 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> <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: #00cc00"> 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> <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>