Difference between revisions of "Team:Duke/Notebook"

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{{Duke}}
 
{{Duke}}
 
<html>
 
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<style>
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table.group,table.group td{
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border: 0 !important;
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.group .name{
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</style>
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<article>
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<section>
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<h2>Notebook</h2>
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<div class="split collapse-h4">
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<div class="left fltwo">
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<h4 id="week-1">Week 1: Jan 10 – Jan 16</h4>
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<table class="group">
 +
<tr><td class="name">General</td><td>team forming (14.1.2016)</td></tr>
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</table>
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</div>
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<div class="right flone">
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<img src="https://static.igem.org/mediawiki/2016/thumb/0/0e/T--Groningen--Notebook-Notification-First-Meeting.jpg/730px-T--Groningen--Notebook-Notification-First-Meeting.jpg" />
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</div>
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</div>
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<div class="week collapse-h4">
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<h4 id="week-2">Week 2: Jan 17 – Jan 23</h4>
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 +
<table class="group">
 +
<tr><td class="name">General</td><td>write motivation letter</td></tr>
 +
</table>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
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<h4 id="week-4">Week 4: Jan 31 – Feb 6</h4>
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 +
<table class="group">
 +
<tr><td class="name">General</td><td>weekly meeting: team forming</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/b/b9/T--Groningen--team-team.jpg" />
 +
</div>
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</div>
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<div class="week collapse-h4">
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<h4 id="week-5">Week 5: Feb 7 – Feb 13</h4>
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 +
<table class="group">
 +
<tr><td class="name">General</td><td>weekly meeting: team forming</td></tr>
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</table>
 +
</div>
 +
<div class="split collapse-h4">
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<div class="left fltwo">
 +
<h4 id="week-6">Week 6: Feb 14 – Feb 20</h4>
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 +
<table class="group">
 +
<tr><td class="name">General</td><td>weekly meeting: team forming</td></tr>
 +
</table>
 +
</div>
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<div class="right flone">
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<img src="https://static.igem.org/mediawiki/2016/thumb/5/51/T--Groningen--week6.jpg/800px-T--Groningen--week6.jpg" />
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</div>
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</div>
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<div class="week collapse-h4">
 +
<h4 id="week-8">Week 8: Feb 28 – Mar 5</h4>
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 +
<table class="group">
 +
<tr><td class="name">General</td><td>weekly meeting: project brainstorming</td></tr>
 +
</table>
 +
</div>
 +
<div class="week collapse-h4">
 +
<h4 id="week-9">Week 9: Mar 6 – Mar 12</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">General</td><td>weekly meeting: project brainstorming</td></tr>
 +
</table>
 +
</div>
 +
<div class="week collapse-h4">
 +
<h4 id="week-10">Week 10: Mar 13 – Mar 19</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">General</td><td>weekly meeting: project brainstorming</td></tr>
 +
</table>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-11">Week 11: Mar 20 – Mar 26</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">General</td><td>weekly meeting: project brainstorming</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/5/5d/T--Groningen--Notebook-MeetingiGEM2016.jpg/800px-T--Groningen--Notebook-MeetingiGEM2016.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-12">Week 12: Mar 27 – Apr 2</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">General</td><td>weekly meeting: decide on project</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/e/ee/T--Groningen--CriminalDude.png/489px-T--Groningen--CriminalDude.png" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-13">Week 13: Apr 3 – Apr 9</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">HP</td><td>Preparations for NBC</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/9/92/T--Groningen--week13.jpg/800px-T--Groningen--week13.jpg" />
 +
</div>
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</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-14">Week 14: Apr 10 – Apr 16</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">HP</td><td>NBC Wageningen</td></tr>
 +
<tr><td class="name">Coding/Wiki</td><td>Start with DNA encoder</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/4/45/T--Groningen--First-Presentation-at-NBC-0Wageningen.jpg/800px-T--Groningen--First-Presentation-at-NBC-0Wageningen.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-15">Week 15: Apr 17 – Apr 23</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">Coding/Wiki</td><td>DNA encoder</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/9/97/T--Groningen--week15.jpg" />
 +
</div>
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</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-16">Week 16: Apr 24 – Apr 30</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">Coding/Wiki</td><td>First version of encoder done</td></tr>
 +
<tr><td class="name">General lab</td><td>starting of setting up the lab</td></tr>
 +
</table>
 +
</div>
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<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/5/56/T--Groningen--SetupLab.jpg/800px-T--Groningen--SetupLab.jpg" />
 +
</div>
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</div>
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<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-17">Week 17: May 1 – May 7</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">General lab</td><td>setting up the lab</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/2/28/T--Groningen--week17.jpg/800px-T--Groningen--week17.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-18">Week 18: May 8 – May 14</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">HP</td><td>Preparation for Meeting of Dutch Teams Wageningen</td></tr>
 +
<tr><td class="name">Modelling/Coding</td><td>Start with MultiAgent System Model</td></tr>
 +
<tr><td class="name">Coding/Wiki</td><td>DNA encoder</td></tr>
 +
<tr><td class="name">General lab</td><td>setting up the lab</td></tr>
 +
<tr><td class="name">Integration/Lab</td><td>plan integration cloning</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/0/0c/T--Groningen--week18.jpg/800px-T--Groningen--week18.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-19">Week 19: May 15 – May 21</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">HP</td><td>Meeting of Dutch Teams - Wageningen</td></tr>
 +
<tr><td class="name">Modelling/Coding</td><td>Literature MAS</td></tr>
 +
<tr><td class="name">Coding/Wiki</td><td>DNA encoder</td></tr>
 +
<tr><td class="name">General lab</td><td>setting up the lab, free license from eLab journal received</td></tr>
 +
<tr><td class="name">Integration/Lab</td><td>plan integration cloning</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/e/e9/T--Wageningen_UR--National2.jpg/800px-T--Wageningen_UR--National2.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-20">Week 20: May 22 – May 28</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">HP</td><td>Campus Party Attendance</td></tr>
 +
<tr><td class="name">Modelling/Coding</td><td>Literature MAS</td></tr>
 +
<tr><td class="name">General lab</td><td>setting up the lab</td></tr>
 +
<tr><td class="name">Integration/Lab</td><td>plan integration cloning</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/2/2e/T--Groningen--week20.jpeg/800px-T--Groningen--week20.jpeg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-21">Week 21: May 29 – Jun 4</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">HP</td><td>Night of Art and Sciences Participation (ScienceLinx)</td></tr>
 +
<tr><td class="name">Modelling/Coding</td><td>Literature MAS</td></tr>
 +
<tr><td class="name">Integration/Lab</td><td>plan integration cloning</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/2/2d/T--Groningen--week21.jpg/799px-T--Groningen--week21.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-22">Week 22: Jun 5 – Jun 11</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">Modelling/Coding</td><td>
 +
</td></tr>
 +
<tr><td class="name">Integration/Lab</td><td>plan integration cloning, prepare medium for <em>Bacillus subtilis</em> transformation,</td></tr>
 +
<tr><td class="name">Antibiotics/Lab</td><td>Preparing sporulation medium</td></tr>
 +
<tr><td class="name">RIVM - Safe by Design</td><td>First Phone call with RIVM</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/2/24/T--Groningen--Notebook-prep-lb.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-23">Week 23: Jun 12 – Jun 18</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">Modelling/Coding</td><td>Start MAS Coding</td></tr>
 +
<tr><td class="name">General lab</td><td>16.6. first order of lab needs</td></tr>
 +
<tr><td class="name">Integration/Lab</td><td>plan integration cloning</td></tr>
 +
<tr><td class="name">Antibiotics/Lab</td><td>Sporulation of <em>B. subtilis</em> 168</td></tr>
 +
<tr><td class="name">RIVM - Safe by Design</td><td>Working on proposal Safe by Design</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/1/1a/T--Groningen--week23.jpg/800px-T--Groningen--week23.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-24">Week 24: Jun 19 – Jun 25</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">Modelling/Coding</td><td>Coding</td></tr>
 +
<tr><td class="name">Coding/Wiki</td><td>Start with wiki</td></tr>
 +
<tr><td class="name">Integration/Lab</td><td>plan integration cloning</td></tr>
 +
<tr><td class="name">Antibiotics/Lab</td><td>Testing UV resistance of spores</td></tr>
 +
<tr><td class="name">Collaboration Wageningen</td><td>skype with Wageningen</td></tr>
 +
<tr><td class="name">RIVM - Safe by Design</td><td>Working on proposal Safe by Design</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/8/84/T--Groningen--Notebook-Working-On-The-Wiki-Marco.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-25">Week 25: Jun 26 – Jul 2</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">HP</td><td>Research National regulations for Sending</td></tr>
 +
<tr><td class="name">Modelling/Coding</td><td>Coding</td></tr>
 +
<tr><td class="name">Integration/Lab</td><td>plan integration cloning</td></tr>
 +
<tr><td class="name">RIVM - Safe by Design</td><td>Working on proposal Safe by Design</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/3/3b/T--Groningen--week25.jpg/800px-T--Groningen--week25.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-26">Week 26: Jul 3 – Jul 9</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">HP</td><td>Research National Regulations for Sending</td></tr>
 +
<tr><td class="name">Modelling/Coding</td><td>Genetic Algorithm finished</td></tr>
 +
<tr><td class="name">Coding/Wiki</td><td>DNA encoder</td></tr>
 +
<tr><td class="name">Integration/Lab</td><td>plan integration cloning</td></tr>
 +
<tr><td class="name">Antibiotics/Lab</td><td>Determining optimal plating dilution, MIC of ciprofloxacin</td></tr>
 +
<tr><td class="name">RIVM - Safe by Design</td><td>First Meeting with RIVM</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/d/d1/T--Groningen--Notebook-1stMeeting-RIVM.jpg/800px-T--Groningen--Notebook-1stMeeting-RIVM.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-27">Week 27: Jul 10 – Jul 16</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">HP</td><td>Contact National Cyber Security Center and RIVM for orientation in regulations</td></tr>
 +
<tr><td class="name">Modelling/Coding</td><td>Coding</td></tr>
 +
<tr><td class="name">Coding/Wiki</td><td>DNA format finalized</td></tr>
 +
<tr><td class="name">General lab</td><td>13.7. first order of the gBlocks</td></tr>
 +
<tr><td class="name">Integration/Lab</td><td>message and key gBlock order</td></tr>
 +
<tr><td class="name">Antibiotics/Lab</td><td>Ciprofloxacin MIC and MBC, patterning experiment</td></tr>
 +
<tr><td class="name">RIVM - Safe by Design</td><td>Working on product of Proposal (booklet) Safe by Design</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/5/54/T--Groningen--week27.jpg/800px-T--Groningen--week27.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-28">Week 28: Jul 17 – Jul 23</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">HP</td><td>Research International Regulations for Sending/Planning Future Scenearios/Collaboration with iGEM Teams for International Survey</td></tr>
 +
<tr><td class="name">Modelling/Coding</td><td>Coding</td></tr>
 +
<tr><td class="name">General lab</td><td>19.7.clone manager tutorial by Bara, 22.7. half of the gBlocks received, 21.7. competent cells preparation, digestion of linearized plasmid backbones </td></tr>
 +
<tr><td class="name">Integration/Lab</td><td>message gBlock received -> start of the cloning process</td></tr>
 +
<tr><td class="name">Kill switch/Lab</td><td>E.coli top10 competent cell preparation, basic layout of kill switches</td></tr>
 +
<tr><td class="name">Antibiotics/Lab</td><td>Spirofloxacin MIC tests and Photoswitch test</td></tr>
 +
<tr><td class="name">RIVM - Safe by Design</td><td>Working on product of Proposal (booklet) Safe by Design</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/5/50/T--Groningen--week28.jpg/800px-T--Groningen--week28.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-29">Week 29: Jul 24 – Jul 30</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">HP</td><td>Release of the Survey to social Media/Planning Future Scnearios</td></tr>
 +
<tr><td class="name">Modelling/Coding</td><td>First Results Sender</td></tr>
 +
<tr><td class="name">General lab</td><td>second half of the gBlocks received, preparation of agarose for the gels, amplifying of gBlocks</td></tr>
 +
<tr><td class="name">Integration/Lab</td><td>cloning procedure of the message into pdr111 (E.coli TOP10)</td></tr>
 +
<tr><td class="name">Kill switch/Lab</td><td>Primer design, Detailed kill switch layout; nuclease biobrick order</td></tr>
 +
<tr><td class="name">Antibiotics/Lab</td><td>Spirofloxacin MIC tests</td></tr>
 +
<tr><td class="name">Spores/Lab</td><td>Test Tonia's and Daniel's protocols</td></tr>
 +
<tr><td class="name">RIVM - Safe by Design</td><td>Working on product of Proposal (booklet) Safe by Design</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/d/d4/T--Groningen--Notebook-Gblocks.jpeg/450px-T--Groningen--Notebook-Gblocks.jpeg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-30">Week 30: Jul 31 – Aug 6</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">HP</td><td>Interview JanJaap and visit to Groninger Archieven/RADIO PARTICIPATION</td></tr>
 +
<tr><td class="name">Modelling/Coding</td><td>First Results Criminal</td></tr>
 +
<tr><td class="name">Integration/Lab</td><td>pDR111+message transformation to <em>Bacillus subtilis</em> trp+, starch test to verify right colonies, samples for sequencing</td></tr>
 +
<tr><td class="name">Kill switch/Lab</td><td>Cloning - RBS (34), tetR and 2terminator; Cloning repeat - RBS (34)</td></tr>
 +
<tr><td class="name">Antibiotics/Lab</td><td>Spirofloxacin MIC tests with E. coli</td></tr>
 +
<tr><td class="name">Spores/Lab</td><td>Test Tonia's and Daniel's protocols</td></tr>
 +
<tr><td class="name">RIVM - Safe by Design</td><td>Working on product of Proposal (booklet) Safe by Design</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/e/e2/T--Groningen--Notebook-sambit.gif" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-31">Week 31: Aug 7 – Aug 13</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">HP</td><td>Planning Future Scenarios/Working on presentation for ScienceLinX Day</td></tr>
 +
<tr><td class="name">Modelling/Coding</td><td>MAS Paper + Wiki</td></tr>
 +
<tr><td class="name">General lab</td><td>amplification of gBlocks</td></tr>
 +
<tr><td class="name">Integration/Lab</td><td>cloning procedure of pDR111+message+sfGFP and pdr111+sfGFP</td></tr>
 +
<tr><td class="name">Kill switch/Lab</td><td>Cloning - RBS (34)</td></tr>
 +
<tr><td class="name">Antibiotics/Lab</td><td>Spirofloxacin MIC tests with E. coli</td></tr>
 +
<tr><td class="name">Spores/Lab</td><td>Daniel's protocol worked best and fastest</td></tr>
 +
<tr><td class="name">Collaboration Wageningen</td><td>vitamin b12 and guanine stock, recive biobrick</td></tr>
 +
<tr><td class="name">RIVM - Safe by Design</td><td>Second Phone Call RIVM</td></tr>
 +
<tr><td class="name">CRISPR/CAS9</td><td>Starting a new idea (using CRISPR/Cas 9)</td></tr>
 +
<tr><td class="name">decoy/sfGFP</td><td>cloning plan sfGFP</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/8/85/T--Groningen--week35.jpg/800px-T--Groningen--week35.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-32">Week 32: Aug 14 – Aug 20</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">HP</td><td>Elaboration of Proposal of Labelling of GMOs</td></tr>
 +
<tr><td class="name">Modelling/Coding</td><td>Start of Random Mutation Model</td></tr>
 +
<tr><td class="name">Integration/Lab</td><td>problems with gBlock</td></tr>
 +
<tr><td class="name">Kill switch/Lab</td><td>Genomic DNA for nuclease; pimer design for nuclease</td></tr>
 +
<tr><td class="name">Antibiotics/Lab</td><td>Ciprofloxacin-resistant B. sub. by directed evolution</td></tr>
 +
<tr><td class="name">Collaboration Wageningen</td><td>plan plate reader experiment</td></tr>
 +
<tr><td class="name">RIVM - Safe by Design</td><td>Working on product of Proposal (booklet) Safe by Design</td></tr>
 +
<tr><td class="name">CRISPR/CAS9</td><td>Worked on design plan (e.g. primers, plasmids, labwork) </td></tr>
 +
<tr><td class="name">decoy/sfGFP</td><td>cloning sfGFP in pDR111/ sequencing validation</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/2/21/T--Groningen--Notebook-plate-reader.jpg/800px-T--Groningen--Notebook-plate-reader.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-33">Week 33: Aug 21 – Aug 27</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">HP</td><td>Planning Future Scenarios/Working on presentation for ScienceLinX Day/Prepairing Lab equipment etc for SienceLinX Day</td></tr>
 +
<tr><td class="name">Modelling/Coding</td><td>Literature Model 2</td></tr>
 +
<tr><td class="name">Coding/Wiki</td><td>Wiki</td></tr>
 +
<tr><td class="name">General lab</td><td>22.8. second order of the gBlocks</td></tr>
 +
<tr><td class="name">Integration/Lab</td><td>problems with gBlock, ordering of the new key sequence as a gBlock</td></tr>
 +
<tr><td class="name">Kill switch/Lab</td><td>Cloning - RBS (30); nuclease biobrick recieved</td></tr>
 +
<tr><td class="name">Antibiotics/Lab</td><td>Ciprofloxacin-resistant B. sub. by directed evolution</td></tr>
 +
<tr><td class="name">Collaboration Wageningen</td><td>microscopy, repeat plate reader experiment</td></tr>
 +
<tr><td class="name">RIVM - Safe by Design</td><td>Working on product of Proposal (booklet) Safe by Design</td></tr>
 +
<tr><td class="name">CRISPR/CAS9</td><td>Worked on design plan (e.g. primers, plasmids, labwork) </td></tr>
 +
<tr><td class="name">decoy/sfGFP</td><td>integration of sfGFP pDR111 into the genome of <em>B. subtilis</em></td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/1/16/T--Groningen--week33.jpeg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-34">Week 34: Aug 28 – Sep 3</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">HP</td><td>ScienceLinX Day/BioART with students/GBB Meeting</td></tr>
 +
<tr><td class="name">Modelling/Coding</td><td>Coding + Results</td></tr>
 +
<tr><td class="name">Coding/Wiki</td><td>Wiki</td></tr>
 +
<tr><td class="name">General lab</td><td>2.9. second order of lab needs, gBlock received</td></tr>
 +
<tr><td class="name">Integration/Lab</td><td>key gBlock received -> start of the cloning process, cloning procedure of the key into pdr111 (E.coli TOP10)</td></tr>
 +
<tr><td class="name">Kill switch/Lab</td><td>Cloning - RBS (30) + nuclease, tetR + RBS (30) + nuclease </td></tr>
 +
<tr><td class="name">Antibiotics/Lab</td><td>Ciprofloxacin-resistant B. sub. by directed evolution</td></tr>
 +
<tr><td class="name">Collaboration Wageningen</td><td>repeat plate reader experiment</td></tr>
 +
<tr><td class="name">RIVM - Safe by Design</td><td>Third Phone Call RIVM</td></tr>
 +
<tr><td class="name">CRISPR/CAS9</td><td>Worked on design plan (e.g. primers, plasmids, labwork) </td></tr>
 +
<tr><td class="name">decoy/sfGFP</td><td>microscopy of <em>B.subtilis</em>+sfGFP</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/a/a4/T--Groningen--Notebook-gbb-1.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-35">Week 35: Sep 4 – Sep 10</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">HP</td><td>Future Scenarios were completed/Meeting with Simone from the university paper</td></tr>
 +
<tr><td class="name">Modelling/Coding</td><td>More Literature + Autocorrecting Codes</td></tr>
 +
<tr><td class="name">Coding/Wiki</td><td>Wiki</td></tr>
 +
<tr><td class="name">Integration/Lab</td><td>transform pDR111+key to <em>Bacillus subtilis</em>, sequence the message obtained from spores, send spores to Wageningen and Eindhoven, time-lapse movie (germination of spores)</td></tr>
 +
<tr><td class="name">Kill switch/Lab</td><td>Cloning - tetR + RBS (30) + nuclease, tetR + RBS (30) + nuclease + 2terminator</td></tr>
 +
<tr><td class="name">Antibiotics/Lab</td><td>Ciprofloxacin-resistant B. sub. by directed evolution (experiment 1)</td></tr>
 +
<tr><td class="name">RIVM - Safe by Design</td><td>Working on product of Proposal (booklet) Safe by Design</td></tr>
 +
<tr><td class="name">CRISPR/CAS9</td><td>Worked on design plan (e.g. primers, plasmids, labwork) </td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/e/e8/T--Groningen--week35-2.jpg/450px-T--Groningen--week35-2.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-36">Week 36: Sep 11 – Sep 17</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">HP</td><td>BBQ/Auction/ New Scientist interview/Shooting Unifocus movie</td></tr>
 +
<tr><td class="name">Modelling/Coding</td><td>Final Fixes everywhere for Wiki</td></tr>
 +
<tr><td class="name">Coding/Wiki</td><td>Wiki</td></tr>
 +
<tr><td class="name">Kill switch/Lab</td><td>Sequencing</td></tr>
 +
<tr><td class="name">Antibiotics/Lab</td><td>Ciprofloxacin-resistant B. sub. by directed evolution</td></tr>
 +
<tr><td class="name">RIVM - Safe by Design</td><td>Working on product of Proposal (booklet) Safe by Design</td></tr>
 +
<tr><td class="name">CRISPR/CAS9</td><td>Start cloning first steps in lab</td></tr>
 +
<tr><td class="name">decoy/sfGFP</td><td>plan sfGFP biobrick</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/2/2d/T--Groningen--Notebook-sfgfp-ecoli.jpg/800px-T--Groningen--Notebook-sfgfp-ecoli.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-37">Week 37: Sep 18 – Sep 24</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">Coding/Wiki</td><td>Wiki</td></tr>
 +
<tr><td class="name">Antibiotics/Lab</td><td>Ciprofloxacin-resistant B. sub. by directed evolution (experiment 2)</td></tr>
 +
<tr><td class="name">RIVM - Safe by Design</td><td>RIVM Meeting, Den Haag > Presentation of Product, Safe by Design</td></tr>
 +
<tr><td class="name">CRISPR/CAS9</td><td>Start cloning first steps in lab</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/0/09/T--Groningen--week37.jpg/800px-T--Groningen--week37.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-38">Week 38: Sep 25 – Oct 1</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">General</td><td>Portrait Picture</td></tr>
 +
<tr><td class="name">Coding/Wiki</td><td>Wiki</td></tr>
 +
<tr><td class="name">Integration/Lab</td><td>K823023 BioBrick received from iGEM headquarters</td></tr>
 +
<tr><td class="name">Kill switch/Lab</td><td>Start over clone RBS+nucA in pSB1C3,</td></tr>
 +
<tr><td class="name">Antibiotics/Lab</td><td>decoy experiment, clone PatpI promoter from gblock in pSB1C3</td></tr>
 +
<tr><td class="name">Collaboration Wageningen</td><td>final plate reader experiment</td></tr>
 +
<tr><td class="name">CRISPR/CAS9</td><td>The practialside is withdrawn</td></tr>
 +
<tr><td class="name">decoy/sfGFP</td><td>clone sfGFP in pSB1C3, sequencing</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/9/98/T--Groningen--Notebook-take-pic.jpg/800px-T--Groningen--Notebook-take-pic.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-39">Week 39: Oct 2 – Oct 8</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">HP</td><td>Students from High School in NL BioART</td></tr>
 +
<tr><td class="name">Coding/Wiki</td><td>Wiki chill</td></tr>
 +
<tr><td class="name">Integration/Lab</td><td>clone key, message in pSB1C3, and K823023</td></tr>
 +
<tr><td class="name">Kill switch/Lab</td><td>clone tetR+RBS+nucA in pSB1C3, send RBSnucA for sequencing</td></tr>
 +
<tr><td class="name">Antibiotics/Lab</td><td>sequence PatpI</td></tr>
 +
<tr><td class="name">decoy/sfGFP</td><td>decoy experiment FACS, microscopy</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/c/cf/T--Groningen--week39.jpg/800px-T--Groningen--week39.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-40">Week 40: Oct 9 – Oct 15</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">General</td><td>New team photo</td></tr>
 +
<tr><td class="name">HP</td><td>Publication in the national news (NOS)</td></tr>
 +
<tr><td class="name">Coding/Wiki</td><td>Wiki cool</td></tr>
 +
<tr><td class="name">Integration/Lab</td><td>integrate message, key in B. subtili 168, strach test</td></tr>
 +
<tr><td class="name">Kill switch/Lab</td><td>clone tetR+RBS+nucA+TER2 in pSB1C3, find incorrect suffix  in nucA K729004, order primer nucA correct prefix, suffix</td></tr>
 +
<tr><td class="name">Antibiotics/Lab</td><td>MIC test - E. coli wt vs qnrS1</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/b/b4/T--Groningen--Notebook-bara-eike-lab.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-41">Week 41: Oct 16 – Oct 22</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">HP</td><td>Interview Dagblad van het Noorden (local newspaper)</td></tr>
 +
<tr><td class="name">Coding/Wiki</td><td>Wiki freeze!</td></tr>
 +
<tr><td class="name">Kill switch/Lab</td><td>improve nucA clone it in pSB1C3 with correct prefix and suffix</td></tr>
 +
<tr><td class="name">Antibiotics/Lab</td><td>MIC tests - B. subtilis 168 (wt) vs (qnrS1) vs (resistant isolate)</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/0/0d/T--Groningen--Notebook-biobricks.jpg/450px-T--Groningen--Notebook-biobricks.jpg" />
 +
</div>
 +
</div>
 +
<div class="split collapse-h4">
 +
<div class="left fltwo">
 +
<h4 id="week-42">Week 42: Oct 23 – Oct 29</h4>
 +
 +
<table class="group">
 +
<tr><td class="name">General</td><td>Jamboree!</td></tr>
 +
</table>
 +
</div>
 +
<div class="right flone">
 +
<img src="https://static.igem.org/mediawiki/2016/thumb/a/ad/T--Groningen--week42.jpg/800px-T--Groningen--week42.jpg" />
 +
</div>
 +
</div>
 +
</section>
 +
<section>
 +
<h2>From our iGEM lab to the office</h2>
 +
<figure>
 +
<video controls preload="metadata">
 +
<source src="https://static.igem.org/mediawiki/2016/3/3b/T--Groningen--Results-labtooffice.mp4" />
 +
</video>
 +
 +
<figcaption>From our iGEM lab to the office</figcaption>
 +
</figure>
 +
</section>
 +
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Revision as of 17:22, 12 October 2017

Notebook

Week 1: Jan 10 – Jan 16

Generalteam forming (14.1.2016)

Week 2: Jan 17 – Jan 23

Generalwrite motivation letter

Week 4: Jan 31 – Feb 6

Generalweekly meeting: team forming

Week 5: Feb 7 – Feb 13

Generalweekly meeting: team forming

Week 6: Feb 14 – Feb 20

Generalweekly meeting: team forming

Week 8: Feb 28 – Mar 5

Generalweekly meeting: project brainstorming

Week 9: Mar 6 – Mar 12

Generalweekly meeting: project brainstorming

Week 10: Mar 13 – Mar 19

Generalweekly meeting: project brainstorming

Week 11: Mar 20 – Mar 26

Generalweekly meeting: project brainstorming

Week 12: Mar 27 – Apr 2

Generalweekly meeting: decide on project

Week 13: Apr 3 – Apr 9

HPPreparations for NBC

Week 14: Apr 10 – Apr 16

HPNBC Wageningen
Coding/WikiStart with DNA encoder

Week 15: Apr 17 – Apr 23

Coding/WikiDNA encoder

Week 16: Apr 24 – Apr 30

Coding/WikiFirst version of encoder done
General labstarting of setting up the lab

Week 17: May 1 – May 7

General labsetting up the lab

Week 18: May 8 – May 14

HPPreparation for Meeting of Dutch Teams Wageningen
Modelling/CodingStart with MultiAgent System Model
Coding/WikiDNA encoder
General labsetting up the lab
Integration/Labplan integration cloning

Week 19: May 15 – May 21

HPMeeting of Dutch Teams - Wageningen
Modelling/CodingLiterature MAS
Coding/WikiDNA encoder
General labsetting up the lab, free license from eLab journal received
Integration/Labplan integration cloning

Week 20: May 22 – May 28

HPCampus Party Attendance
Modelling/CodingLiterature MAS
General labsetting up the lab
Integration/Labplan integration cloning

Week 21: May 29 – Jun 4

HPNight of Art and Sciences Participation (ScienceLinx)
Modelling/CodingLiterature MAS
Integration/Labplan integration cloning

Week 22: Jun 5 – Jun 11

Modelling/Coding
Integration/Labplan integration cloning, prepare medium for Bacillus subtilis transformation,
Antibiotics/LabPreparing sporulation medium
RIVM - Safe by DesignFirst Phone call with RIVM

Week 23: Jun 12 – Jun 18

Modelling/CodingStart MAS Coding
General lab16.6. first order of lab needs
Integration/Labplan integration cloning
Antibiotics/LabSporulation of B. subtilis 168
RIVM - Safe by DesignWorking on proposal Safe by Design

Week 24: Jun 19 – Jun 25

Modelling/CodingCoding
Coding/WikiStart with wiki
Integration/Labplan integration cloning
Antibiotics/LabTesting UV resistance of spores
Collaboration Wageningenskype with Wageningen
RIVM - Safe by DesignWorking on proposal Safe by Design

Week 25: Jun 26 – Jul 2

HPResearch National regulations for Sending
Modelling/CodingCoding
Integration/Labplan integration cloning
RIVM - Safe by DesignWorking on proposal Safe by Design

Week 26: Jul 3 – Jul 9

HPResearch National Regulations for Sending
Modelling/CodingGenetic Algorithm finished
Coding/WikiDNA encoder
Integration/Labplan integration cloning
Antibiotics/LabDetermining optimal plating dilution, MIC of ciprofloxacin
RIVM - Safe by DesignFirst Meeting with RIVM

Week 27: Jul 10 – Jul 16

HPContact National Cyber Security Center and RIVM for orientation in regulations
Modelling/CodingCoding
Coding/WikiDNA format finalized
General lab13.7. first order of the gBlocks
Integration/Labmessage and key gBlock order
Antibiotics/LabCiprofloxacin MIC and MBC, patterning experiment
RIVM - Safe by DesignWorking on product of Proposal (booklet) Safe by Design

Week 28: Jul 17 – Jul 23

HPResearch International Regulations for Sending/Planning Future Scenearios/Collaboration with iGEM Teams for International Survey
Modelling/CodingCoding
General lab19.7.clone manager tutorial by Bara, 22.7. half of the gBlocks received, 21.7. competent cells preparation, digestion of linearized plasmid backbones
Integration/Labmessage gBlock received -> start of the cloning process
Kill switch/LabE.coli top10 competent cell preparation, basic layout of kill switches
Antibiotics/LabSpirofloxacin MIC tests and Photoswitch test
RIVM - Safe by DesignWorking on product of Proposal (booklet) Safe by Design

Week 29: Jul 24 – Jul 30

HPRelease of the Survey to social Media/Planning Future Scnearios
Modelling/CodingFirst Results Sender
General labsecond half of the gBlocks received, preparation of agarose for the gels, amplifying of gBlocks
Integration/Labcloning procedure of the message into pdr111 (E.coli TOP10)
Kill switch/LabPrimer design, Detailed kill switch layout; nuclease biobrick order
Antibiotics/LabSpirofloxacin MIC tests
Spores/LabTest Tonia's and Daniel's protocols
RIVM - Safe by DesignWorking on product of Proposal (booklet) Safe by Design

Week 30: Jul 31 – Aug 6

HPInterview JanJaap and visit to Groninger Archieven/RADIO PARTICIPATION
Modelling/CodingFirst Results Criminal
Integration/LabpDR111+message transformation to Bacillus subtilis trp+, starch test to verify right colonies, samples for sequencing
Kill switch/LabCloning - RBS (34), tetR and 2terminator; Cloning repeat - RBS (34)
Antibiotics/LabSpirofloxacin MIC tests with E. coli
Spores/LabTest Tonia's and Daniel's protocols
RIVM - Safe by DesignWorking on product of Proposal (booklet) Safe by Design

Week 31: Aug 7 – Aug 13

HPPlanning Future Scenarios/Working on presentation for ScienceLinX Day
Modelling/CodingMAS Paper + Wiki
General labamplification of gBlocks
Integration/Labcloning procedure of pDR111+message+sfGFP and pdr111+sfGFP
Kill switch/LabCloning - RBS (34)
Antibiotics/LabSpirofloxacin MIC tests with E. coli
Spores/LabDaniel's protocol worked best and fastest
Collaboration Wageningenvitamin b12 and guanine stock, recive biobrick
RIVM - Safe by DesignSecond Phone Call RIVM
CRISPR/CAS9Starting a new idea (using CRISPR/Cas 9)
decoy/sfGFPcloning plan sfGFP

Week 32: Aug 14 – Aug 20

HPElaboration of Proposal of Labelling of GMOs
Modelling/CodingStart of Random Mutation Model
Integration/Labproblems with gBlock
Kill switch/LabGenomic DNA for nuclease; pimer design for nuclease
Antibiotics/LabCiprofloxacin-resistant B. sub. by directed evolution
Collaboration Wageningenplan plate reader experiment
RIVM - Safe by DesignWorking on product of Proposal (booklet) Safe by Design
CRISPR/CAS9Worked on design plan (e.g. primers, plasmids, labwork)
decoy/sfGFPcloning sfGFP in pDR111/ sequencing validation

Week 33: Aug 21 – Aug 27

HPPlanning Future Scenarios/Working on presentation for ScienceLinX Day/Prepairing Lab equipment etc for SienceLinX Day
Modelling/CodingLiterature Model 2
Coding/WikiWiki
General lab22.8. second order of the gBlocks
Integration/Labproblems with gBlock, ordering of the new key sequence as a gBlock
Kill switch/LabCloning - RBS (30); nuclease biobrick recieved
Antibiotics/LabCiprofloxacin-resistant B. sub. by directed evolution
Collaboration Wageningenmicroscopy, repeat plate reader experiment
RIVM - Safe by DesignWorking on product of Proposal (booklet) Safe by Design
CRISPR/CAS9Worked on design plan (e.g. primers, plasmids, labwork)
decoy/sfGFPintegration of sfGFP pDR111 into the genome of B. subtilis

Week 34: Aug 28 – Sep 3

HPScienceLinX Day/BioART with students/GBB Meeting
Modelling/CodingCoding + Results
Coding/WikiWiki
General lab2.9. second order of lab needs, gBlock received
Integration/Labkey gBlock received -> start of the cloning process, cloning procedure of the key into pdr111 (E.coli TOP10)
Kill switch/LabCloning - RBS (30) + nuclease, tetR + RBS (30) + nuclease 
Antibiotics/LabCiprofloxacin-resistant B. sub. by directed evolution
Collaboration Wageningenrepeat plate reader experiment
RIVM - Safe by DesignThird Phone Call RIVM
CRISPR/CAS9Worked on design plan (e.g. primers, plasmids, labwork)
decoy/sfGFPmicroscopy of B.subtilis+sfGFP

Week 35: Sep 4 – Sep 10

HPFuture Scenarios were completed/Meeting with Simone from the university paper
Modelling/CodingMore Literature + Autocorrecting Codes
Coding/WikiWiki
Integration/Labtransform pDR111+key to Bacillus subtilis, sequence the message obtained from spores, send spores to Wageningen and Eindhoven, time-lapse movie (germination of spores)
Kill switch/LabCloning - tetR + RBS (30) + nuclease, tetR + RBS (30) + nuclease + 2terminator
Antibiotics/LabCiprofloxacin-resistant B. sub. by directed evolution (experiment 1)
RIVM - Safe by DesignWorking on product of Proposal (booklet) Safe by Design
CRISPR/CAS9Worked on design plan (e.g. primers, plasmids, labwork)

Week 36: Sep 11 – Sep 17

HPBBQ/Auction/ New Scientist interview/Shooting Unifocus movie
Modelling/CodingFinal Fixes everywhere for Wiki
Coding/WikiWiki
Kill switch/LabSequencing
Antibiotics/LabCiprofloxacin-resistant B. sub. by directed evolution
RIVM - Safe by DesignWorking on product of Proposal (booklet) Safe by Design
CRISPR/CAS9Start cloning first steps in lab
decoy/sfGFPplan sfGFP biobrick

Week 37: Sep 18 – Sep 24

Coding/WikiWiki
Antibiotics/LabCiprofloxacin-resistant B. sub. by directed evolution (experiment 2)
RIVM - Safe by DesignRIVM Meeting, Den Haag > Presentation of Product, Safe by Design
CRISPR/CAS9Start cloning first steps in lab

Week 38: Sep 25 – Oct 1

GeneralPortrait Picture
Coding/WikiWiki
Integration/LabK823023 BioBrick received from iGEM headquarters
Kill switch/LabStart over clone RBS+nucA in pSB1C3,
Antibiotics/Labdecoy experiment, clone PatpI promoter from gblock in pSB1C3
Collaboration Wageningenfinal plate reader experiment
CRISPR/CAS9The practialside is withdrawn
decoy/sfGFPclone sfGFP in pSB1C3, sequencing

Week 39: Oct 2 – Oct 8

HPStudents from High School in NL BioART
Coding/WikiWiki chill
Integration/Labclone key, message in pSB1C3, and K823023
Kill switch/Labclone tetR+RBS+nucA in pSB1C3, send RBSnucA for sequencing
Antibiotics/Labsequence PatpI
decoy/sfGFPdecoy experiment FACS, microscopy

Week 40: Oct 9 – Oct 15

GeneralNew team photo
HPPublication in the national news (NOS)
Coding/WikiWiki cool
Integration/Labintegrate message, key in B. subtili 168, strach test
Kill switch/Labclone tetR+RBS+nucA+TER2 in pSB1C3, find incorrect suffix in nucA K729004, order primer nucA correct prefix, suffix
Antibiotics/LabMIC test - E. coli wt vs qnrS1

Week 41: Oct 16 – Oct 22

HPInterview Dagblad van het Noorden (local newspaper)
Coding/WikiWiki freeze!
Kill switch/Labimprove nucA clone it in pSB1C3 with correct prefix and suffix
Antibiotics/LabMIC tests - B. subtilis 168 (wt) vs (qnrS1) vs (resistant isolate)

Week 42: Oct 23 – Oct 29

GeneralJamboree!

From our iGEM lab to the office

From our iGEM lab to the office