Team:Newcastle/Outreach/Workshop

From 2013.igem.org

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{{Team:Newcastle}}
{{Team:Newcastle}}
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=Modelling Workshop at the U.K. meet up=
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=Modelling Workshop at the UK meet up=
==Overview==
==Overview==
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On Friday the 12th of July our team was at UCL for the iGEM U.K. meet up. We delivered a workshop about Mathematical modelling and using the rule-based modelling language BioNetGen.  
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On Friday the 12th of July our team was at UCL for the iGEM UK meet up. We delivered a workshop about Mathematical modelling and using the rule-based modelling language BioNetGen. We believe the workshop presentation and handouts we developed are a great resource for those new to biological modelling.
We first gave a presentation covering the following areas:
We first gave a presentation covering the following areas:
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• What is modelling?
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*What is modelling?
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*The benefits of rule-based modelling.
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• The benefits of rule-based modelling.
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*The difference between deterministic and stochastic modelling.
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*How to build a Michaelis-Menten model with BioNetGen.
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• The difference between deterministic and stochastic modelling.
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-
 
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• How to build a Michaelis-Menten model with BioNetGen.
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NB. Information about modelling the Subtilin system is included in our lecture slides on our wiki for the extra keen but was not covered in our talk.
NB. Information about modelling the Subtilin system is included in our lecture slides on our wiki for the extra keen but was not covered in our talk.
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We then ran a practice session in which we helped people get to grips with the BioNetGen language and the software required to produce models (Rulebender). We provided a hand-out guiding people in how to build a Michaelis-Menten model and a simplified Lac operon model. We were also happy to help build models for attendees own iGEM projects.
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We then ran a practice session in which we helped people get to grips with the BioNetGen language and the software required to produce models ([https://2013.igem.org/Team:Newcastle/Modelling/RuleBender RuleBender]). We provided a hand-out guiding people in how to build a Michaelis-Menten model and a simplified Lac operon model. This workshop also introduced [https://2013.igem.org/Team:Leeds/Modeling Team:Leeds] to BioNetGen which they then used in their project.
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[[File:Workshop2.jpg|600px]]
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[[File:Workshop2.jpg|500px]]
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==Slides and handouts==
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Links to our slides, hand-outs and feedback form are listed below:
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==Presentation==
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These are the slides from our modelling presentation:
<html>
<html>
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<iframe src="https://skydrive.live.com/embed?cid=A67E48B91B122E55&resid=A67E48B91B122E55%21112&authkey=AKt313lzFLi-ZsQ&em=2" width="402" height="327" frameborder="0" scrolling="no"></iframe>
<iframe src="https://skydrive.live.com/embed?cid=A67E48B91B122E55&resid=A67E48B91B122E55%21112&authkey=AKt313lzFLi-ZsQ&em=2" width="402" height="327" frameborder="0" scrolling="no"></iframe>
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<p style="text-align:center;">Download pdf version <a href="https://static.igem.org/mediawiki/2013/9/96/BareCillus_Workshop_Presentation.pdf">here</a></p>
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<p style="text-align:center;">A downloadable version can be found <a href="https://static.igem.org/mediawiki/2013/9/96/BareCillus_Workshop_Presentation.pdf">here</a>.</p>
</div>
</div>
</html>
</html>
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==Handouts==
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This is the handout from our modelling workshop:
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[https://static.igem.org/mediawiki/2013/7/7a/Workshop_Handout%281%29.pdf Workshop handout (incl. information about BioNetGen syntax)]
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<html>
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<div style="text-align:center;">
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<iframe src="https://skydrive.live.com/embed?cid=7825331CA7243819&resid=7825331CA7243819%21110&authkey=AFI9n46tTkAQ2ts&em=2" width="476" height="288" frameborder="0" scrolling="no"></iframe>
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<p style="text-align:center">
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A downloadable version can be found <a href="https://static.igem.org/mediawiki/2013/b/ba/Workshop_Handout.pdf">here</a>.
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</p>
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</div>
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</html>
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==Feedback==
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This is the feedback form from our modelling workshop:
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==Workshop Feedback==
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<html>
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Feedback form used in the workshop is here [https://static.igem.org/mediawiki/2013/a/af/Workshop_Feedback.pdf Feedback Form]
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<div style="text-align:center">
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<iframe src="https://skydrive.live.com/embed?cid=7825331CA7243819&resid=7825331CA7243819%21115&authkey=AIH4ftVLvZTEsy0&em=2" width="476" height="288" frameborder="0" scrolling="no"></iframe>
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<p style="text-align:center">
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A downloadable version can be found <a href="https://static.igem.org/mediawiki/2013/a/af/Workshop_Feedback.pdf">here</a>.
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</p>
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</div>
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</html>
After we presented our workshop, attendees filled in their feedback forms scoring different aspects of the workshop between 1 (strongly disagree) and 5 (strongly agree). The mean results from these forms are listed below:
After we presented our workshop, attendees filled in their feedback forms scoring different aspects of the workshop between 1 (strongly disagree) and 5 (strongly agree). The mean results from these forms are listed below:
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1. The workshop talk was:
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<table class="data">
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<tr>
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<th colspan="2">The workshop talk was:</th>
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</tr>
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<tr class="odd">
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<td class="text">Relevant</td>
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<td class="data">4.6</td>
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</tr>
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<tr class="even">
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<td class="text">Easy to understand</td>
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<td class="data">4.3</td>
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</tr>
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<tr class="odd">
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<td class="text">Well-paced</td>
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<td class="data">4.3</td>
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</tr>
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</table>
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<table class="data">
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<tr>
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<th colspan="2">The BioNetGen practice was:</th>
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</tr>
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<tr class="odd">
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<td class="text">Useful</td>
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<td class="data">4.1</td>
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</tr>
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<tr class="even">
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<td class="text">Complemented the talk</td>
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<td class="data">4.4</td>
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</tr>
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</table>
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<table class="data">
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<tr>
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<th colspan="2">The workshop overall:</th>
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</tr>
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<tr class="odd">
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<td class="text">Was well structured</td>
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<td class="data">4.2</td>
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</tr>
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<tr class="even">
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<td class="text">Will help you build your own models</td>
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<td class="data">3.9</td>
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</tr>
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<tr class="odd">
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<td class="text">Interesting</td>
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<td class="data">4.6</td>
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</tr>
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</table>
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<table class="data">
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<tr>
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<th colspan="2">Workshop handouts:</th>
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</tr>
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<tr class="odd">
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<td class="text">Supported presentation material</td>
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<td class="data">4.1</td>
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</tr>
 +
<tr class="even">
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<td class="text">Aided you in building a model</td>
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<td class="data">4.0</td>
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</tr>
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<tr class="odd">
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<td class="text">Were clear and well-organized</td>
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<td class="data">4.1</td>
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</tr>
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</table>
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<table class="data">
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<tr>
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<th colspan="2">The presenters were:</th>
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</tr>
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<tr class="odd">
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<td class="text">Knowledgeable</td>
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<td class="data">4.3</td>
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</tr>
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<tr class="even">
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<td class="text">Well-prepared</td>
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<td class="data">4.5</td>
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</tr>
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<tr class="odd">
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<td class="text">Responsive to participants’ questions</td>
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<td class="data">4.6</td>
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</tr>
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</table>
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*Relevant 4.6
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The feedback we received suggests that people found our workshop interesting and well structured. The part of feedback we scored lowest on was for helping people build their own model, possibly because they are using different software to build models. We also think we could improve the clarity of our handouts to guide people through our prepared exercises more effectively. We enjoyed delivering this workshop and feel the feedback shows our workshop was a success.  We believe the workshop presentation and handouts we developed are a great resource for those new to biological modelling.  We were happy to hear that [https://2013.igem.org/Team:Leeds/Modeling Team:Leeds] began using BioNetGen after some of their team members attended our workshop.
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*Easy to understand 4.33
 
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*Well-paced 4.27     
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==Gallery==
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2. The BioNetGen practice was:
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<style>
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    #wrapgal {
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    margin: 0px 50px;
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<script src="http://code.jquery.com/jquery-1.10.2.min.js"></script> <!-- 32 KB -->
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*Useful 4.13   
 
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*Complemented the talk 4.4
 
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3. The workshop overall:
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<link  href="http://fotorama.s3.amazonaws.com/4.2.3/fotorama.css" rel="stylesheet"> <!-- 3 KB -->
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<script src="http://fotorama.s3.amazonaws.com/4.2.3/fotorama.js"></script> <!-- 12 KB -->
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*Was well structured 4.2   
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<div id="wrapgal">
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<div class="fotorama" data-ratio="1.5" data-hash="true" data-nav="thumbs" data-fit="cover" data-allow-full-screen="native" data-thumb-height="48" data-width="640" data-height="480" data-keyboard="true">
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*Will help you build your own models 3.87
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  <img src="https://static.igem.org/mediawiki/2013/f/f1/BareCillus_mod%284%29.JPG">
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  <img src="https://static.igem.org/mediawiki/2013/b/b0/BareCillus_mod%285%29.JPG">
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*Interesting 4.6 
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  <img src="https://static.igem.org/mediawiki/2013/9/9f/BareCillus_mod%287%29.JPG">
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  <img src="https://static.igem.org/mediawiki/2013/9/9f/BareCillus_mod%287%29.JPG">
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  <img src="https://static.igem.org/mediawiki/2013/4/47/BareCillus_mod%289%29.JPG">
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4. Workshop handouts:  
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  <img src="https://static.igem.org/mediawiki/2013/b/b4/BareCillus_mod%2810%29.JPG">
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  <img src="https://static.igem.org/mediawiki/2013/f/f5/BareCillus_mod%2811%29.JPG">
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*Supported presentation material 4.13   
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  <img src="https://static.igem.org/mediawiki/2013/1/19/BareCillus_mod%2812%29.JPG">
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  <img src="https://static.igem.org/mediawiki/2013/b/b2/BareCillus_mod(13).JPG">
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*Aided you in building a model 4   
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  <img src="https://static.igem.org/mediawiki/2013/1/1a/BareCillus_mod%2815%29.JPG">
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  <img src="https://static.igem.org/mediawiki/2013/b/bf/BareCillus_mod%2818%29.JPG">
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*Were clear and well-organized 4.07   
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  <img src="https://static.igem.org/mediawiki/2013/b/be/BareCillus_mod%2820%29.JPG">
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  <img src="https://static.igem.org/mediawiki/2013/e/eb/BareCillus_mod%2822%29.JPG">
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5. The presenters were:
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  <img src="https://static.igem.org/mediawiki/2013/9/9d/BareCillus_mod%2825%29.JPG">
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  <img src="https://static.igem.org/mediawiki/2013/7/74/BareCillus_mod%2826%29.JPG">
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*Knowledgeable 4.33     
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  <img src="https://static.igem.org/mediawiki/2013/e/e8/BareCillus_mod%2827%29.jpg">
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  <img src="https://static.igem.org/mediawiki/2013/1/1a/BareCillus_mod%2828%29.JPG">
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*Well-prepared 4.47   
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  <img src="https://static.igem.org/mediawiki/2013/0/09/BareCillus_mod%2832%29.JPG">
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  <img src="https://static.igem.org/mediawiki/2013/c/c7/BareCillus_mod%2834%29.jpg">
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*Responsive to participants’ questions 4.6
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  <img src="https://static.igem.org/mediawiki/2013/5/58/BareCillus_mod%2835%29.JPG">
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  <img src="https://static.igem.org/mediawiki/2013/b/b4/BareCillus_mod%2836%29.JPG">
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  <img src="https://static.igem.org/mediawiki/2013/d/d7/BareCillus_mod%2837%29.jpg">
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  <img src="https://static.igem.org/mediawiki/2013/f/f3/BareCillus_mod%2838%29.jpg">
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  <img src="https://static.igem.org/mediawiki/2013/d/d9/BareCillus_mod%2839%29.jpg">
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  <img src="https://static.igem.org/mediawiki/2013/b/b1/BareCillus_mod%2840%29.JPG">
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  <img src="https://static.igem.org/mediawiki/2013/0/03/BareCillus_mod%2841%29.jpg">
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  <img src="https://static.igem.org/mediawiki/2013/5/56/BareCillus_mod%2842%29.jpg">
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  <img src="https://static.igem.org/mediawiki/2013/d/d6/BareCillus_mod%2843%29.JPG">
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  <img src="https://static.igem.org/mediawiki/2013/0/01/BareCillus_mod%2845%29.jpg">
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  <img src="https://static.igem.org/mediawiki/2013/0/07/BareCillus_mod%2848%29.jpg">
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  <img src="https://static.igem.org/mediawiki/2013/2/23/BareCillus_mod%2849%29.jpg">
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  <img src="https://static.igem.org/mediawiki/2013/4/41/BareCillus_mod%2850%29.jpg">
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  <img src="https://static.igem.org/mediawiki/2013/9/9b/BareCillus_mod%2851%29.jpg">
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  <img src="https://static.igem.org/mediawiki/2013/4/46/BareCillus_mod%2853%29.jpg">
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  <img src="https://static.igem.org/mediawiki/2013/0/0e/BareCillus_mod%2855%29.jpg">
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  <img src="https://static.igem.org/mediawiki/2013/1/13/BareCillus_mod%2856%29.jpg">
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  <img src="https://static.igem.org/mediawiki/2013/0/05/BareCillus_mod%2859%29.JPG">
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  <img src="https://static.igem.org/mediawiki/2013/6/60/BareCillus_mod%2860%29.JPG">
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  <img src="https://static.igem.org/mediawiki/2013/7/79/BareCillus_mod%2861%29.JPG">
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  <img src="">
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  <img src="">
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</div>
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</div>
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</html>
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The feedback we received suggests that people found our workshop interesting and well structured. The part of feedback we scored lowest on was for helping people build their own model, possibly because they are using different software to build models. We also think we could improve the clarity of our handouts to guide people through our prepared exercises more effectively. We enjoyed delivering this workshop and feel the feedback shows our workshop was a success.
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{{Team:Newcastle/Sponsors}}

Latest revision as of 18:57, 28 October 2013

 
X
 
IGEM Home Newcastle University

Contents

Modelling Workshop at the UK meet up

Overview

On Friday the 12th of July our team was at UCL for the iGEM UK meet up. We delivered a workshop about Mathematical modelling and using the rule-based modelling language BioNetGen. We believe the workshop presentation and handouts we developed are a great resource for those new to biological modelling.

We first gave a presentation covering the following areas:

  • What is modelling?
  • The benefits of rule-based modelling.
  • The difference between deterministic and stochastic modelling.
  • How to build a Michaelis-Menten model with BioNetGen.

NB. Information about modelling the Subtilin system is included in our lecture slides on our wiki for the extra keen but was not covered in our talk.

We then ran a practice session in which we helped people get to grips with the BioNetGen language and the software required to produce models (RuleBender). We provided a hand-out guiding people in how to build a Michaelis-Menten model and a simplified Lac operon model. This workshop also introduced Team:Leeds to BioNetGen which they then used in their project. Workshop2.jpg

Presentation

These are the slides from our modelling presentation:

A downloadable version can be found here.

Handouts

This is the handout from our modelling workshop:

A downloadable version can be found here.

Feedback

This is the feedback form from our modelling workshop:

A downloadable version can be found here.

After we presented our workshop, attendees filled in their feedback forms scoring different aspects of the workshop between 1 (strongly disagree) and 5 (strongly agree). The mean results from these forms are listed below:

The workshop talk was:
Relevant 4.6
Easy to understand 4.3
Well-paced 4.3
The BioNetGen practice was:
Useful 4.1
Complemented the talk 4.4
The workshop overall:
Was well structured 4.2
Will help you build your own models 3.9
Interesting 4.6
Workshop handouts:
Supported presentation material 4.1
Aided you in building a model 4.0
Were clear and well-organized 4.1
The presenters were:
Knowledgeable 4.3
Well-prepared 4.5
Responsive to participants’ questions 4.6

The feedback we received suggests that people found our workshop interesting and well structured. The part of feedback we scored lowest on was for helping people build their own model, possibly because they are using different software to build models. We also think we could improve the clarity of our handouts to guide people through our prepared exercises more effectively. We enjoyed delivering this workshop and feel the feedback shows our workshop was a success. We believe the workshop presentation and handouts we developed are a great resource for those new to biological modelling. We were happy to hear that Team:Leeds began using BioNetGen after some of their team members attended our workshop.


Gallery


Newcastle University The Centre for Bacterial Cell Biology Newcastle Biomedicine The School of Computing Science The School of Computing Science

Retrieved from "http://2013.igem.org/Team:Newcastle/Outreach/Workshop"