Latest revision as of 20:35, 4 October 2013

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Collaborations

During our project we were able to collaborate with other iGEMers. This page details the help we gave to other teams. If you would like to see how we contributed to other teams please click on the appropriate University logo's.

Edinburgh

We were able to help Team Edinburgh with their modelling by supplying them with some Bacillus subtilis parameters:

Definition	Value	Source
Cell division rate, growth rate	30-73mins	http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106920/pdf/jb000547.pdf
Genome equivalents of DNA per cell	1.6 - 3.3	http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106920/pdf/jb000547.pdf
Replication time of chromosome, "C period"	50-58	http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106920/pdf/jb000547.pdf
Delay before cell division, "D period"	21-34	http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106920/pdf/jb000547.pdf
Number of replicating forks	2	-
Number of replicating origins	0.43-1.7	http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106920/pdf/jb000547.pdf
Cell volume	0.85±0.38 μm^3	http://www.ncbi.nlm.nih.gov/pubmed/21395229
Minimal replication time of chromosome	55min	http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106920/pdf/jb000547.pdf
Numbe of rrn operons per chomosome	10 operons	http://www.ncbi.nlm.nih.gov/pubmed/12644506

Leeds

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, including teaching the basics of using the rule-based modelling language BioNetGen. We also supplied attendees with all the software needed to produce BioNetGen models on a handy USB. This workshop introduced the Leeds iGEM team to BioNetGen, who went on to use BioNetGen to model the Cpx pathway in their project.

These are the slides from our modelling presentation:

A downloadable version can be found here.

This is the handout from our modelling workshop:

A downloadable version can be found here.

Manchester

We have helped the Manchester team with their 'introduction to modelling', giving ideas on how this could be achieved and producing a tutorial video giving a brief introduction to modelling using BioNetGen.

NRP-UEA-Norwich

We supplied a soil sample for the Norwich team to be used in their project. As a part of their Outreach activities, we filled in a questionaire about the differences between the iGEM experience and degree subject learning experince.

Greensboro-Austin

Our team filled in a questionaire about the current BioBrick assembly standards and submission, in order to help the Texas at Austin team modernise the standards.

@@ Line 2: / Line 2: @@
 = Collaborations =
+During our project we were able to collaborate with other iGEMers. This page details the help we gave to other teams. If you would like to see how we contributed to other teams please click on the appropriate University logo's.
 ==<div id="title" style=" display: none;">Edinburgh</div>==
 <html>
-<img src="https://static.igem.org/mediawiki/2013/a/ae/BareCillus_Edinburgh_logo.jpg" alt="Edinburgh University">
+<a href="https://2013.igem.org/Team:Edinburgh/Collaboration">
+<img src="https://static.igem.org/mediawiki/2013/a/ae/BareCillus_Edinburgh_logo.jpg" alt="Edinburgh University">
+</a>
 </html>
-We were able to supply Team Edinburgh with some ''Bacillus subtilis'' parameters:
+We were able to help Team Edinburgh with their modelling by supplying them with some ''Bacillus subtilis'' parameters:
-==Leeds==
+<table class="data">
+	<tr>
+		<th>Definition</th>
+                <th>Value</th>
+                <th>Source</th>
+	</tr>
+	<tr class="odd">
+		<td class="data">Cell division rate, growth rate</td>
+		<td class="data">30-73mins</td>
+                <td class="data">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106920/pdf/jb000547.pdf</td>
-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 taught the basics of using the rule-based modelling language BioNetGen. This workshop introduced the Leeds iGEM team to BioNetGen. [https://2013.igem.org/Team:Leeds/Modeling Team Leeds went on to use BioNetGen to model the Cpx pathway in their project].
+	</tr>
+	<tr class="even">
+		<td class="data">Genome equivalents of DNA per cell</td>
+		<td class="data">1.6 - 3.3</td>
+                <td class="data">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106920/pdf/jb000547.pdf</td>
+	</tr>
+	<tr class="odd">
+		<td class="data">Replication time of chromosome, "C period"</td>
+		<td class="data">50-58</td>
+                <td class="data">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106920/pdf/jb000547.pdf</td>
+	</tr>
+	<tr class="even">
+		<td class="data">Delay before cell division, "D period"</td>
+		<td class="data">21-34</td>
+                <td class="data">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106920/pdf/jb000547.pdf</td>
+	</tr>
+	<tr class="odd">
+		<td class="data">Number of replicating forks</td>
+		<td class="data">2</td>
+                <td class="data">-</td>
+	</tr>
+	<tr class="even">
+		<td class="data">Number of replicating origins</td>
+		<td class="data">0.43-1.7</td>
+                <td class="data">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106920/pdf/jb000547.pdf</td>
+	</tr>
+	<tr class="odd">
+		<td class="data">Cell volume</td>
+		<td class="data">0.85±0.38 μm^3 </td>
+                <td class="data">http://www.ncbi.nlm.nih.gov/pubmed/21395229</td>
+	</tr>
+	<tr class="even">
+		<td class="data">Minimal replication time of chromosome</td>
+		<td class="data">55min</td>
+                <td class="data">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC106920/pdf/jb000547.pdf</td>
+	</tr>
+	<tr class="odd">
+		<td class="data">Numbe of rrn operons per chomosome</td>
+		<td class="data">10 operons</td>
+                <td class="data">http://www.ncbi.nlm.nih.gov/pubmed/12644506</td>
+	</tr>
+</table>
+==<div id="title" style=" display: none;">Leeds</div>==
+<html>
+<a href="https://2013.igem.org/Team:Leeds/Attributions">
+<img src="https://static.igem.org/mediawiki/2013/0/0d/BareCillus_Leeds_logo.jpg" alt="Leeds University" width= "40%">
+</a>
+</html>
+On Friday the 12th of July our team was at UCL for the [https://2013.igem.org/Team:Newcastle/Outreach/uk_meet iGEM U.K. meet up]. We delivered a [https://2013.igem.org/Team:Newcastle/Outreach/Workshop workshop about Mathematical modelling], including teaching the basics of using the rule-based modelling language BioNetGen. We also supplied attendees with all the software needed to produce BioNetGen models on a handy USB. This workshop introduced the Leeds iGEM team to BioNetGen, [https://2013.igem.org/Team:Leeds/Attributions who went on to use BioNetGen to model the Cpx pathway in their project].
+These are the slides from our modelling presentation:
+<html>
+<div style="text-align:center;">
+<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>
+<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>
+</html>
+This is the handout from our modelling workshop:
+<html>
+<div style="text-align:center;">
+<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>
+<p style="text-align:center">
+A downloadable version can be found <a href="https://static.igem.org/mediawiki/2013/b/ba/Workshop_Handout.pdf">here</a>.
+</p>
+</div>
+</html>
+==<div id="title" style=" display: none;">Manchester</div>==
+<html>
+<style type="text/css">
+#video {
+   margin-left:10px;
+}
+</style>
+<a href="https://2013.igem.org/Team:Manchester/Collaboration">
+<img src="https://static.igem.org/mediawiki/2013/4/40/BareCillus_Manchester_logo.jpg" alt="Manchester University"  width= "40%"></a>
+<p>We have helped the Manchester team with their 'introduction to modelling', giving ideas on how this could be achieved and producing a tutorial video giving a brief introduction to modelling using BioNetGen.</p>
+<div id="video">
+<video src="https://static.igem.org/mediawiki/2013/4/47/BioNetGen_Tutorial.mp4" width="480" height="260" controls preload></video>
+</div>
+</html>
+==<div id="title" style=" display: none;">NRP-UEA-Norwich</div>==
+<html>
+<a href="https://2013.igem.org/Team:NRP-UEA-Norwich/HumanPractice/SoilSamples/31-45">
+<img src="https://static.igem.org/mediawiki/2013/e/e9/BareCillus_UEA_logo.png"width= "200px" height="100px">
+</a>
+</html>
+We supplied a [https://2013.igem.org/Team:NRP-UEA-Norwich/HumanPractice/SoilSamples/31-45 soil sample] for the Norwich team to be used in their project. As a part of their Outreach activities, we filled in a questionaire about the differences between the iGEM experience and degree subject learning experince.
+[[File:BareCillus_Norwich_1.jpg|600px]]
+==<div id="title" style=" display: none;">Greensboro-Austin</div>==
+<html>
+<a href="https://2013.igem.org/Team:Greensboro-Austin">
+<img src="https://static.igem.org/mediawiki/2013/d/d9/BareCillus_University_of_Texas_at_Austin_logo.png" alt="Texas at Austin"width= "40%">
+</a>
+</html>
-==Manchester==
+Our team filled in a questionaire about the current BioBrick assembly standards and submission, in order to help the Texas at Austin team modernise the standards.
-Collaboration3 with ------
+[[File:BareCillus_Austin_1.jpg]]
 {{Team:Newcastle/Sponsors}}

Team:Newcastle/Collaborations

From 2013.igem.org