ETHZ/Internal

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< ETHZ(Difference between revisions)
('''.::Plasmid 3 ''(pacyc177km)''::.'')
(Introduction)
 
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<center>[[ETHZ | Main Page]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Model | System Modeling]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Simulation | Simulations]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Biology | System Implementation]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Biology/Lab| Lab Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Meet_the_team | Meet the Team]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Internal | Team Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Pictures | Pictures!]]</center><br>
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<center>[[ETHZ/Main_page | Main Page]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Biology | Biology Pespective]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Engineering | Engineering Perspective]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Meet_the_team | Meet the Team]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Internal | Team Notes]] &nbsp;&nbsp;&nbsp;&nbsp; [[ETHZ/Pictures | Pictures!]]</center>
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<center><font size = '+2'><b> .:: ETH Zurich - EducatETH ''E. coli'' ::. </b></font></center><br>
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<div id="colortab" class="ddcolortabs">
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<ul>
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<li><a href="https://2007.igem.org/wiki/index.php?title=ETHZ" title="Home" rel="dropmenu_home"><span>Home</span></a></li>
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<li><a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Model" title="Modeling" rel="dropmenu_modeling"><span>System Modeling</span></a></li>
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<li><a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Simulation" title="Simulations" rel="dropmenu_simulation"><span>Simulations</span></a></li>
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<li><a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Biology" title="System Implementation" rel="dropmenu_biology"><span>System Implementation</span></a></li>
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<li><a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Meet_the_team" title="Meet the team" rel="dropmenu_meettheteam"><span>Meet the team</span></a></li>
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<li><a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Pictures" title="Pictures!" rel="dropmenu_pictures"><span>Pictures!</span></a></li>
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</ul>
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</div>
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<div class="ddcolortabsline">&nbsp;</div>
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====='''.:: Task List ::.'''=====
 
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The things to do, from the most pressing (timewise), to the least pressing (timewise) is below. Please put your name next to the task that you believe that you can undertake.
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<!--1st drop down menu -->
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<div id="dropmenu_home" class="dropmenudiv_a">
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ#Introduction">Introduction</a>
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ#Team_Members">Team Members</a>
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ#Acknowledgments">Acknowledgments</a>
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ#Site_Map">Site map</a>
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</div>
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# '''Team descriptions (overdue) and team photograph''' <br> ''Christian'': I guess I am the only semiprofessional photographer of the group. I can do some group pictures etc. but for this we need some ideas... - I would like to do something special. I also made the group-pics of the Synth. Biology 3.0 conference. Some references  ;-)  : [http://www.fotocommunity.de/pc/pc/mypics/461397] <br> ''Raphael'': What about a short movie of us?
 
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# '''Team rosters due (1.9.)'''<br> ''Martin'': Does somebody know, what exactly should be done here? <br> ''Nan'': A list of team members, including some basic personal info.? (e.g. nationality, background, pet peeves...? )<br>''Katerina'': Guys, to make this easier, either write things about you on your personal page on the wiki or link to a page about you. This way it'll be easy to put it all together afterwards.
 
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# '''Labwork (parts have to be at the registry in Boston on 26.10.)''' <br> ''Joe'': I can be in the lab at least 2 evenings a week and some times through the weekdays. <br> ''Martin'': From Monday I can work every day for the whole day. At the moment I only work for several hours... <br> ''Rico'': I have my exam on Tuesday. Afterwards I can assist.<br> ''Christian'': I can do the introduction of the polylinker into the vectors beside my normal labwork on the Hoenggerberg. I could also do the whole biobrick assembly if you want this (I will go on holiday from the 5.10-24.10.07) <br> ''Raphael'': That's the part where I will mainly contribute, from 14.09. on I can work several days/week<br> ''Christos'': I can assist at the afternoons, if needed. <br> ''Katerina'': 7.09 - 30.09 generally plenty of time, apart from when I do my semester project presentation, will keep you posted when that is. <br> ''Sylke'': I'll not be available until 14th of October but from then on I can work several days per week fulltime.
 
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# '''Testing/ Analysis/ Detection (due to 02.11.)''' <br> ''Sylke'': Meeting with Alfredo Franco-Obregon (FACS guy from center) on 18.09. concerning devices available for detection of GFP/ derivatives.
 
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# '''Simulation and sensitivity analysis'''<br> ''Martin'': From 10. Sept. I've got plenty time to work on it. I think Markus would join here too ;-)  <br> ''Tim'': I can contribute in running stuff and help identify parameters from literature <br> ''Rico'': I can do simulations, sensitivity analysis. <br> ''Nan'': I would like to do simulations and sensitivity analysis. <br> ''Christos'': Yeap, I guess I can be here too. I will check some toolboxes to automate things, this weekend. <br> ''Katerina'': Want to help (parameter identification, programming, sensitivity analysis). Discuss in upcoming meeting tasks, versioning and ask Christian about parameters.
 
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# '''Presentation''' <br> ''Joe'': I'm American... I can sale anything.<br> ''Martin'': I'm bad in Layout stuff, but maybe I can help as an idea supplier or so. <br> ''Rico'': I like giving presentations. For preparation we will need a mixture of different background and excellent pictures!!! <br> ''Christian'': I can provide the molecular biology knowledge and part. <br> ''Nan'': I can work on the slides. <br> ''Christos'': I like this part, I guess everyone will contribute anyway...<br> ''Katerina'': I believe I can be of help in structure, layout and fancy stuff. Could help train a bit the people we decide to do the presentation (question answering, style). I also think that Joe and Christos could be good for doing the presentation (structured, pleasant voices and lively), can discuss this in a meeting. <br> ''Sylke'': I can help with the bio-part and I'm good at doing graphics and stuff. Can be a help when it needs to look good :-)
 
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#''' Poster''' <br> ''Joe'': See 5. above <br> ''Rico'': I can help. <br> ''Christian'': I can provide the molecular biology knowledge and part. <br> ''Nan'': Partly art. I will help. <br> ''Christos'': You can sell, but can you trick? lol :)<br> ''Katerina'': Not my strong point, but have an eye for typos, fonts, layout etc, so can help in final checking. <br> ''Sylke'': See above. Good at layout.
 
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# '''Wiki (Project and part documentation due on 26.10)''' <br> ''Martin'': See the points above, from next Monday I will give everything, now I'm doing my best... <br> ''Rico'': I can help. I guess this will have to contain the materials that we will also use for poster and presenttion anyway. <br> ''Nan'': Shouldn't it be updated with every going on process? <br> ''Christos'': I am trying to put stuff in, as it comes along. I will update the bio pages with the presentation material, this weekend (I hope). <br> ''Katerina'': You guys have done a great job so far, will help with whatever needed.
 
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# '''T-Shirts''' <br> ''Sylke'': in print (2007-09-24)
 
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====='''.:: Lab Log ::.'''=====
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<div id="dropmenu_modeling" class="dropmenudiv_a" style="width: 150px;">
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Model#Introduction">Introduction</a>
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Model#Model_Overview">Model Overview</a>
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Model#Detailed_Model">Detailed Model</a>
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Model#Final_Model">Final Model</a>
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Modeling_Basics">Modeling Basics Page</a>
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Model#Mathematical_Model">Mathematical Model</a>
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/FSM">FSM View Page</a>
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/FlipFlop">Flip-Flop View Page</a>
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Parameters">Parameters Page</a>
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</div>
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The following are the numbering of the parts/plasmids that we use in the lab. Please use the same numberings if you label something when working in the lab. Extend the list for new concatenated parts.
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<div id="dropmenu_simulation" class="dropmenudiv_a" style="width: 150px;">
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Simulation#Introduction">Introduction</a>
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Simulation#Simulation_of_Test_Cases">Test Cases</a>
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Simulation#Sensitivity_Analysis">Sensitivity Analysis</a>
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</div>
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# [http://partsregistry.org/Part:BBa_B0034 B0034]
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# [http://partsregistry.org/Part:BBa_R0062 R0062]
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<div id="dropmenu_biology" class="dropmenudiv_a" style="width: 150px;">
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# [http://partsregistry.org/Part:BBa_R0053 R0053]
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Biology#Introduction">Introduction</a>
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# [http://partsregistry.org/Part:BBa_J23100 J23100]
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Biology#The_Complete_System">The Complete System</a>
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# [http://partsregistry.org/Part:BBa_J37033 J37033]
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Biology#System_Phases">System Phases</a>
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# [http://partsregistry.org/Part:BBa_E0434 E0434]
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Biology#Current_Cloning_Status">Current Cloning Status</a>
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# [http://partsregistry.org/Part:BBa_B0015 B0015]
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Biology/parts">System Parts Page</a>
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# [http://partsregistry.org/Part:BBa_Q04400 Q04400]
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Biology/Lab">Lab Notes Page</a>
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# [http://partsregistry.org/Part:BBa_R0010 R0010]
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</div>
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# [http://partsregistry.org/Part:BBa_E0422 E0422]
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# [http://partsregistry.org/Part:BBa_R0040 R0040]
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# [http://partsregistry.org/Part:BBa_R0051 R0051]
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# [http://partsregistry.org/Part:BBa_Q04121 Q04121]
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# [http://partsregistry.org/Part:BBa_C0053 C0053]
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# [http://partsregistry.org/Part:BBa_Q04510 Q4510]
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====='''.:: Week 1 ::.'''=====
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<div id="dropmenu_meettheteam" class="dropmenudiv_a" style="width: 150px;">
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Meet_the_team#The_ETH_Zurich_07_Team">The ETH Zurich 07 Team</a>
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Meet_the_team#Team_Description">Team Description</a>
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<a href="https://2007.igem.org/wiki/index.php?title=ETHZ/Internal">Brainstorming Page</a>
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</div>
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<script type="text/javascript">
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! Date                       
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//SYNTAX: tabdropdown.init("menu_id", [integer OR "auto"])
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! TODO's             
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! Completed             
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! People
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| Mon, 06. Aug. 2007         
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* Preparing the Solutions                     
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| Sylke, Raphael, Stefan, Markus, Martin, Christos, Joe
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| Tue, 07. Aug. 2007         
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* Prepare competent cells for all parts
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* Transformation of all the parts                     
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| Sylke, Raphael, Stefan, Markus, Martin, Christos, Joe
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| Wed, 08. Aug. 2007         
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* Preparing the grown cultures (12) for the MINIPREP <br> (o/n cultures)                     
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| Raphael, Stefan
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| Thu, 09. Aug. 2007         
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* MINIPREP of the grown (10) o/n cultures
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* Gelelectrophoresis of the grown cultures (step: 0.8% Agarose)                     
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| Raphael, Stefan, Martin, Christos, Joe
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| Fri, 10. Aug. 2007         
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* 7 working parts/plasmids (step after "DIGESTS"): <br> (B0034, R0062, R0053, E0434, B0015, R0010, E0422)
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* 4 parts/plasmids minipreped: <br> (R0040, R0051, Q04121, C0053)
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Christos <br> Markus <br> Stefan
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| Sat, 11. Aug. 2007         
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| no labwork                     
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| Sun, 12. Aug. 2007       
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| labwork cancelled
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====='''.:: Week 2 ::.'''=====
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</html>
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__NOTOC__
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=Introduction=
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! Date                       
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! TODO's             
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! Completed             
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! People
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| Mon, 13. Aug. 2007 <br> start at 3 pm       
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* Prepare competent cells
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* Transformations of J23100, J37033, Q04400, Q04510
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* Control Restrictions (step after "MINIPREP") <br>R0040, R0051, Q04121, C0053
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* o/n culture (E.Coli Top10)
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* Control Restrictions (didn't work)
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|  Martin<br> Markus <br> Christos <br> Tim <br>
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| Tue, 14. Aug. 2007         
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| Morning Shift: <br>
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* Start Preparing competent cells (for J23100, J37033, Q04400, Q04510) <br>                   
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Evening Shift: <br>
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* Transformations of J23100, J37033, Q04400, Q04510
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| Morning Shift: <br>
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* Prepared competent cells (stored in the -80°C freezer in the basement)    <br>
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Evening Shift: <br>
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* Transformation of J23100, J37033, Q04400, Q04510 and R0040, R0051, Q04121, C0053 (in the 37°C incubator until Wednesday)
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* Prepared new Liquid LB, LB Agar (both in the autoclave), Agarose Gel with concentrations of 0.8% and 2.4%                   
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|Morning Shift (9am-1pm?): <br> Markus, Tim <br> <br> Evening Shift (5pm-...):<br> Martin, Christos
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| Wed, 15. Aug. 2007         
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* Ligation (step: "LINK ASSEMBLY"): <br> R0053 + E0422 <br> R0010 + E0422 <br> R0010 + E0434 <br> S/P: R0053, R0010 <br> X/P: E0422, E0434
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* Ligation didn't work due to bad quality of enzymes (probably)                       
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| From 12:<br> Martin, Markus<br><br>
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| Thu, 16. Aug. 2007         
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* Miniprep (J23100, J37033, Q04400, Q04510, R0040, R0051, Q04121, C0053)
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* Transformation of #13 and #14
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* Miniprep of #4 (J23100), #5 (J37033), #8 (Q04400), #11 (R0040), #12 (R0051), #15 (Q04510) <br> One batch is miniprepped (after step 19 in the miniprep procedure) and a second batch is frozen as a backup (which is to be miniprepped from step 3 on)
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* Transformation of #13 (Q04121) and #14 (C0053) <br> Numbers #13 and #14 are now growing in the 37°C incubator (step 13 in the transformation procedure)
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Markus, Christos, (Martin)
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| Fri, 17. Aug. 2007         
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* o/n of #13 and #14
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* Check whether miniprep of parts #4 #5 #8 #11 #12 (#13 #14) #15 was successful
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* #13 and #14 didn't grow
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* # 4, 8 and 11 had the plasmid, they were streaked out new on plates, that we have them now on plates
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* New white pipette tips prepared (autoclave)
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* New bottles of Liquid LB and LB Agar prepared (autoclave)
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| Martin
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| Sat, 18. Aug. 2007         
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| Sun, 19. Aug. 2007         
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====='''.:: Week 3 ::.'''=====
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This page documents the process of coming up with a suitable idea for this year's iGEM contest. It is only intended to be a loose gathering of remarks and ideas, instead of a well ordered part of our project documentation. Still, if you are interested in getting a glimpse on our first weeks, you are more than welcome to go on. But beware: afterwards, you might end up with more open questions than answers ...
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Little rearrangements of the parts. Planning of the sequences to order them.
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Have fun!
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== Brainstorming ==
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====='''.:: Week 4 ::.'''=====
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During the first two weeks of July, the team tries to come up with a set of ideas for a project. The team is divided into three groups, which will brainstorm individually. Sven and Joerg are available on the 4th and 5th of July in case groups need to consult them. The objective is that each group comes up with many fancy ideas (it is not yet important that they can be realized at all). To facilitate this, keep in mind the following "brainstorming rules":
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# Defer judgment – “the rules of physics don't apply” & “cells behave exactly as they are supposed to”
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! Date                       
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# Encourage wild ideas
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! TODO's             
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# Build on the ideas of others
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! Completed             
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# Be visual
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! People
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# Go for quantity
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# Stay focused on topic
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| Mon, 27. Aug. 2007         
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| Tue, 28. Aug. 2007         
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| Wed, 29. Aug. 2007         
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| Thu, 30. Aug. 2007         
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| Fri, 31. Aug. 2007         
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| Sat, 01. Sept. 2007         
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* Transform pbr322, pcyc177 and pck01                   
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* Transform pbr322, pcyc177 and pck01 and plated them                     
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| Sun, 02. Sept. 2007       
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* Prepare o/n of pbr322, pcyc177, pck01
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* o/n of pcyc177, pck01
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* the plates of pcyc177 and pck01 are in the fridge
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* transformed pbr322 because the culture didn't grow on the plate
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| Stefan
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====='''.:: Week 5 ::.'''=====
 
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<p>
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! Date                       
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[[Image:Brainstorming.jpg|left|thumb|300px|Brainstorming on the learning system]]
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! TODO's             
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[[Image:Brainstorming2.jpg|center|thumb|300px|Brainstorming on the learning system]]
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! Completed             
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</p>
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! People
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<br>
-
|-
+
=== Preliminary ideas ===
-
| Mon, 03. Sept. 2007         
+
-
|
+
-
* Prepare new competent cells
+
-
* Miniprep pcyc177 and pcK01
+
-
* prepare new o/n culture of pbr322
+
-
* Run agarose gel of Minipreped plasmids
+
-
|
+
-
* New competent cells prepared, they are now in the -80° Frezzer in the basement, column #17, dark orange box (we have now 30-35 EDTs of competent cells...)
+
-
* Minipreped pcyc177 and pck01 (in the -18° freezer, where the antibiotics are)
+
-
* pbr322 didn't grow again, so no o/n could be prepared, but we get a culture from Andy on tuesday
+
-
* new o/n of pcyc177 and pck01 prepared (3 Falcons each), because we need to have more plasmids
+
-
* 2 boxes of blue pipette tips are in the autoclave
+
-
* Stefan ran the agarose gel (?)                   
+
-
| Martin, Stefan
+
-
|-
+
-
| Tue, 04. Sept. 2007         
+
-
|
+
-
* Miniprep pcyc177 and pck01
+
-
* cut the prepped plasmids to test if we've got the right ones
+
-
* run agarose gel to test the cut and uncut ones
+
-
* prepare new o/n of pbr322 (from Andy)                   
+
-
|
+
-
* Miniprep of pcyc177 and pck01 (but not yet tested)
+
-
* Prepared 3 o/ns of pbr322 (finally ;-) and each 1 o/n of pcyc177 and pck01, just in case there are problems with the miniprep
+
-
| Martin, Christian
+
-
|-
+
-
| Wed, 05. Sept. 2007         
+
-
|         
+
-
* Miniprep of pbr322
+
-
* Test-Digest of pcyc177 and pck01 and agarose gel...
+
-
* Streak out all three plasmids on new plates, so we have them in reserve         
+
-
|
+
-
* New Plate of pbr322.
+
-
* Minipreps and Agarose Gels will be done tomorrow
+
-
| Martin
+
-
|-
+
-
| Thu, 06. Sept. 2007         
+
-
|
+
-
* Miniprep of pbr322, pacyc177, pck01
+
-
* Test with agarose gel                   
+
-
|
+
-
* Gel of the older plasmids -> plasmid present
+
-
| Christian
+
-
|-
+
-
| Fri, 07. Sept. 2007         
+
-
|
+
-
* Miniprep of pbr322, pacyc177, pck01                   
+
-
|
+
-
* Plasmids miniprepped
+
-
| Martin
+
-
|-
+
-
| Sat, 08. Sept. 2007         
+
-
|                   
+
-
|                       
+
-
|
+
-
|-
+
-
| Sun, 09. Sept. 2007       
+
-
|
+
-
|
+
-
|
+
-
|}
+
-
====='''.:: Week 6 ::.'''=====
+
* '''PID Controller''': Design a PID controller out of biological elements. The P component can be a simple output to a regulatory protein, and the I component can be the overall protein production at a time period. What can the D component be?
 +
* '''Motion Detector''': Cells are grown on a petri dish. Below the dish, moving images are displayed. A 3-state automaton is proposed. Output A is created when light is present. Output B is created when light is absent. Moving patterns will cause some cells to create both outputs over time. This will result in some “inspector” cells producing output C, by collecting outputs A and B.
 +
* '''Analog-to-Digital Converter''': Compare the level of protein concentration with thresholds, and digitize the output.
 +
* '''Neural Network''': Create a sort of biological neural network with bacteria. We should address the issue of learning, and find a way to incorporate the feedback in the cell decision making process. Directed evolution can be a sort of feedback, but we want to avoid this. (This idea was the basis for the “learning project”)
 +
* '''Paramedic Cells''': Some cells are able to detect signals coming from other cells, and create food for them, or create proteins in order to save them and make them function better.
 +
* '''Cell Batteries''': Cells are able to create and store large quantities of ATP, during a “storing process”. Afterwards, they can detect a signal and give back all the energy they stored, in a short burst, like a capacitor. Other ideas are that the cells can “blow up” and emit large amounts of GFP, based on the ATP that they have accumulated.
 +
* '''Flashing Bacteria''': Cells are grown on a light pattern. The cells that are on the bright parts of the image are oscillating in phase, while the others are remaining dark. This results in the observation of a flashing pattern.
 +
* '''Biocam''': Visible to Fluorescent light converter.
 +
* '''BioCD''': “Print” cells on a film, then read them out and “reconstruct” the original data. Basically, it is an analog to digital converter, followed by a system that can interpret the digitized data. (This idea was the basis for the “Music of life project”, where cells would produce fluorescent proteins based on an analog input. Then, the amount and type of fluorescence would code some music).
 +
* '''Clock''': A follow-the-leader system. We have two groups of cells. The first group creates something that repels the second group. The second group creates a protein that attracts the first group. This way, the first group tries to “catch” the second group, whereas the second group tries to “evade” the first group. This results in them moving around. We can say that the second group is the leader, and the first group exhibits a "follow-the-leader” behavior. Emitting GFP, the groups then act as a sort of analog watch.
 +
* '''Sensors''': Various systems that can sense PH, pressure, temperature, meat quality, moisture, etc. have been proposed.
-
{| class="wikitable" border="1" cellspacing="0" cellpadding="2" style="text-align:left; margin: 1em 1em 1em 0; background: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;"
+
=== Preferred projects===
-
! Date                       
+
Two ideas of the above are chosen for further examination. The team will be again split up in two groups (different ones than before to make sure that new ideas come up with mixing of people). Each group has to come up with a prototype model of the initial system, remarks on its feasibility and coolness. Our results
-
! TODO's             
+
will be presented to all team members, so that potential projects may be limited to a final project. The preferred projects are:
-
! Completed             
+
-
! People
+
-
|-
+
-
| Mon, 10. Sept. 2007
+
-
|       
+
-
* Miniprep pBR322
+
-
* annealing of different MCSs
+
-
* Digest of pCK01 with BamHI+AseI
+
-
* digest of pACYC177 with BamHI+PstI
+
-
* digest of pBR322 with EcoRI+PstI
+
-
  all digests o/n
+
-
|
+
-
|
+
-
Christian
+
-
|  |
+
-
|-
+
-
| Tue, 11. Sept. 2007         
+
-
|
+
-
* Gelextraction of backbones pBR322, pCK01, pACYC digest did NOT work
+
-
* 1x ligation of MCS inside backbones o/d, Trafo
+
-
* 1x ligation of MCS inside backbones o/n
+
-
|
+
-
* plate all 3 plasmids for new minipreps
+
-
|
+
-
Christian
+
-
|-
+
-
| Wed, 12. Sept. 2007         
+
-
|
+
-
* Trafo of o/n ligations
+
-
* o/n cultures of putative clones         
+
-
|
+
-
|
+
-
Christian
+
-
|-
+
-
| Thu, 13. Sept. 2007         
+
-
|
+
-
* Minipreps of putative clones pCK01-MCS and pBR322-MCS
+
-
* control digests of putative clones
+
-
* new o/n cultures of the putative clones of o/n ligations
+
-
|
+
-
|
+
-
Christian
+
-
|-
+
-
| Fri, 14. Sept. 2007         
+
-
|
+
-
*separation of control digests of putative clones                   
+
-
|
+
-
'''*pBR322-MCS (Tet-selection) clone2 positive'''
+
-
|
+
-
Christian
+
-
|-
+
-
| Sat, 15. Sept. 2007         
+
-
|                   
+
-
|                       
+
-
|
+
-
|-
+
-
| Sun, 16. Sept. 2007       
+
-
|
+
-
|
+
-
|
+
-
|}
+
-
====='''.:: Week 7 ::.'''=====
+
# '''Music of Life''': The basic idea is that instead of having an analog-to-digital converter with four outputs (three fluorescent proteins, and no output), we can have two switches. When switch A is on, RFP is produced. When switch B is on, GFP is produced. When both switches A and B are on, a yellowish output is observed. By recording these outputs, we can later create music, by assigning each fluorescent protein to a chord. For example, RFP would correspond to a G chord. The strength of the fluorescence can signify the strength of the chord. If the cells are placed on a spinning disk, we can have something like a vinyl player. A camera is observing the cells, and music is created on the fly.
 +
# '''Learning''': Based on the idea of the neural network, we want to create a biological system where the cells can learn a specific behavior. In order to simplify the system, we decided that the cells can learn to recognize a specific type of other cells. We divide the process in a learning phase and a recognition phase. First, cells A are put together with cells B. Then, cells A are “learning” to recognize cells B. If afterwards they are put in a petri dish with cells B, they will emit GFP. Otherwise, they will stay dark.
-
{| class="wikitable" border="1" cellspacing="0" cellpadding="2" style="text-align:left; margin: 1em 1em 1em 0; background: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;"
+
=== Final project===
-
! Date                       
+
-
! TODO's             
+
-
! Completed             
+
-
! People
+
-
|-
+
-
| Mon, 17. Sept. 2007         
+
-
|
+
-
Hönggerberg:
+
-
* new digest of pACYC177 with BamHI+PstI o/n
+
-
Zentrum:
+
-
* digest of pACYC177, pBR322 AP
+
-
* ligation of 177 and 322AP
+
-
|
+
-
Zentrum:
+
-
* digest of pBR322 AP (the concentration of DNA was too low for pacyc177...)
+
-
* ligation of pBR322 o/n
+
-
* 100 ml o/n culture to MAXIprep pacyc177
+
-
* Transformation of pBR322 AP to have it on plates (because andy only miniprepped them)
+
-
|
+
-
Hönngerberg:<br> Christian <br> Zentrum:<br> Martin, Raphael
+
-
|-
+
-
| Tue, 18. Sept. 2007         
+
-
|
+
-
Hönggerberg:
+
-
* different control digests of pBR322-MCS (Tet) (see last week)
+
-
* separation of pACYC177 digest
+
-
Zentrum:
+
-
* Test Digests of pck01 with XbaI, SpeI, PstI, Xba/Pst, Xba/Spe (because all of them should be in the plasmid due to the sequence, and if they are it would be crap!!!)
+
-
* Transformation of the ligated pbr322 AP (MCS)
+
-
* Prep pacyc177
+
-
* Digest prepped pacyc177
+
-
|
+
-
Hönggerberg:<br>
+
-
> no DNA on pACYC177 digest-gel, only degradation smear<br> <br>
+
-
Zentrum:
+
-
* Plates of pbr322 AP grew
+
-
* No Digest of pck01 worked due to too low DNA concentration... (che cazzo di low copy plasmids !!!!)
+
-
* Miniprepped only 20 ml of the pacyc o/n culture with Quiagen Kit, the results were great! We have loads of DNA! (thank god! )
+
-
* Digest of pacyc177 with BamHI (45 µl), then precipitated, in the gel was still very much DNA, but there were still 3 bands, so we guess, that it hasn't cut, maybe because the BamHI in the center is very old, perhaps we should Digest it in Höngg again.
+
-
* Digest of pacyc177 with PstI o/n (pray that it will work!)
+
-
* New o/n cultures of pck01 (to prep it like pacyc177), pbr322 AP (to prep it too, to have something on stock again, if the ligation didn't work), top10 (to make new competent cells)
+
-
* test digest of pck01 with notI, but due to the low DNA concentration I don't think it will work. I took glooves, if it now work, then we have caught some DNases in the earlier test digests
+
-
  |
+
-
Höngg:<br>
+
-
Christian <br>
+
-
Zentrum:<br>
+
-
Martin, Raphael
+
-
|-
+
-
| Wed, 19. Sept. 2007         
+
-
|
+
-
Zentrum:
+
-
* o/n culture of pbr322 AP (MCS), then test digest and see if it is ligated
+
-
* Prep of pck01 and test digests (xba, pst, spe, pvuI, notI)
+
-
* check the digests of pacyc177 (pst) and pck01 (notI)
+
-
* design new linkers for pck01, design primers for PCR for the extraction of SpeI from pck01         
+
-
|
+
-
|
+
-
|-
+
-
| Thu, 20. Sept. 2007         
+
-
|
+
-
|
+
-
|
+
-
|-
+
-
| Fri, 21. Sept. 2007         
+
-
|                   
+
-
|
+
-
|
+
-
|-
+
-
| Sat, 22. Sept. 2007         
+
-
|                   
+
-
|                       
+
-
|
+
-
|-
+
-
| Sun, 23. Sept. 2007       
+
-
|
+
-
|
+
-
|
+
-
|}
+
-
====='''.:: Week 8 ::.'''=====
+
The chosen project is a modified version of Learning which was presented at the last meeting. The system proposed is modified, as in its current state may be implemented with two switches only, something which is really smashing. Keeping the idea of learning, training, and testing phases, we have come up with educatETH <i>E.coli</i>.
-
 
+
-
{| class="wikitable" border="1" cellspacing="0" cellpadding="2" style="text-align:left; margin: 1em 1em 1em 0; background: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;"
+
-
! Date                       
+
-
! TODO's             
+
-
! Completed             
+
-
! People
+
-
|-
+
-
| Mon, 24. Sept. 2007         
+
-
|
+
-
|
+
-
|
+
-
|-
+
-
| Tue, 25. Sept. 2007         
+
-
|
+
-
|
+
-
|
+
-
|-
+
-
| Wed, 26. Sept. 2007         
+
-
|         
+
-
|
+
-
|
+
-
|-
+
-
| Thu, 27. Sept. 2007         
+
-
|
+
-
|
+
-
|
+
-
|-
+
-
| Fri, 28. Sept. 2007         
+
-
|                   
+
-
|
+
-
|
+
-
|-
+
-
| Sat, 29. Sept. 2007         
+
-
|                   
+
-
|                       
+
-
|
+
-
|-
+
-
| Sun, 30. Sept. 2007       
+
-
|
+
-
|
+
-
|
+
-
|}
+
-
 
+
-
==== '''.::Plasmid 1 ''(pbr322ap)''::.''' ====
+
-
 
+
-
# Put parts 1,2,3 in pbr322ap plasmids.
+
-
# Merge plasmid containing part '''2''' ''(donor)'' with plasmid containing part '''3''' ''(acceptor)''. You should get a plasmid containing a '''2.3''' composite part.
+
-
# Merge plasmid containing part '''1''' ''(donor)'' with plasmid containing composite part '''2.3'''  ''(acceptor)''. You should get a plasmid containing a '''1.2.3''' composite part.
+
-
 
+
-
==== '''.::Plasmid 2 ''(pck01cm)''::.''' ====
+
-
 
+
-
# Put parts 4,5,8,9 in  pck01cm plasmids.  
+
-
# Merge plasmid containing part '''4''' ''(donor)'' with plasmid containing part '''5''' ''(acceptor)''. You should get a plasmid containing a '''4.5''' composite part.
+
-
# Merge plasmid containing part '''8''' ''(donor)'' with plasmid containing part '''9''' ''(acceptor)''. You should get a plasmid containing a '''8.9''' composite part. ''Note'': this step can be done simultaneously with the above.
+
-
# Merge plasmid containing composite part '''4.5''' ''(donor)'' with plasmid containing composite part '''8.9''' ''(acceptor)''. You should get a plasmid containing a '''4.5.8.9''' composite part.
+
-
 
+
-
==== '''.::Plasmid 3 ''(pacyc177km)''::.''' ====
+
-
 
+
-
# Put parts 6,7,10,11 in  pacyc177km plasmids.
+
-
# Merge plasmid containing part '''6''' ''(donor)'' with plasmid containing part '''7''' ''(acceptor)''. You should get a plasmid containing a '''6.7''' composite part.
+
-
# Merge plasmid containing part '''10''' ''(donor)'' with plasmid containing part '''11''' ''(acceptor)''. You should get a plasmid containing a '''10.11''' composite part. ''Note'': this step can be done simultaneously with the above.
+
-
# Merge plasmid containing composite part '''6.7''' ''(donor)'' with plasmid containing composite part '''10.11''' ''(acceptor)''. You should get a plasmid containing a '''6.7.10.11''' composite part.
+
-
 
+
-
==== '''.::Linkers::.''' ====
+
-
 
+
-
# [[ETHZ/pCK01-1| pck01-1]]
+
-
# [[ETHZ/pCK01-2| pck01-2]]
+
-
# [[ETHZ/pacyc177-1| pacyc177-1]]
+
-
# [[ETHZ/pacyc177-2| pacyc177-2]]
+
-
# [[ETHZ/pbr322-1| pbr322-1]]
+
-
# [[ETHZ/pbr322-2| pbr322-2]]
+
-
# [[ETHZ/pbr322-3| pbr322-3]]
+
-
# [[ETHZ/pbr322-4| pbr322-4]]
+
-
 
+
-
We have got 4 linkers for pbr322, because there are two for the tetracycline version of pbr333 and two for the ampicillin version.
+

Latest revision as of 20:36, 26 October 2007

ETHZ banner.png

 


Introduction

This page documents the process of coming up with a suitable idea for this year's iGEM contest. It is only intended to be a loose gathering of remarks and ideas, instead of a well ordered part of our project documentation. Still, if you are interested in getting a glimpse on our first weeks, you are more than welcome to go on. But beware: afterwards, you might end up with more open questions than answers ...

Have fun!

Brainstorming

During the first two weeks of July, the team tries to come up with a set of ideas for a project. The team is divided into three groups, which will brainstorm individually. Sven and Joerg are available on the 4th and 5th of July in case groups need to consult them. The objective is that each group comes up with many fancy ideas (it is not yet important that they can be realized at all). To facilitate this, keep in mind the following "brainstorming rules":

  1. Defer judgment – “the rules of physics don't apply” & “cells behave exactly as they are supposed to”
  2. Encourage wild ideas
  3. Build on the ideas of others
  4. Be visual
  5. Go for quantity
  6. Stay focused on topic


Brainstorming on the learning system
Brainstorming on the learning system


Preliminary ideas

  • PID Controller: Design a PID controller out of biological elements. The P component can be a simple output to a regulatory protein, and the I component can be the overall protein production at a time period. What can the D component be?
  • Motion Detector: Cells are grown on a petri dish. Below the dish, moving images are displayed. A 3-state automaton is proposed. Output A is created when light is present. Output B is created when light is absent. Moving patterns will cause some cells to create both outputs over time. This will result in some “inspector” cells producing output C, by collecting outputs A and B.
  • Analog-to-Digital Converter: Compare the level of protein concentration with thresholds, and digitize the output.
  • Neural Network: Create a sort of biological neural network with bacteria. We should address the issue of learning, and find a way to incorporate the feedback in the cell decision making process. Directed evolution can be a sort of feedback, but we want to avoid this. (This idea was the basis for the “learning project”)
  • Paramedic Cells: Some cells are able to detect signals coming from other cells, and create food for them, or create proteins in order to save them and make them function better.
  • Cell Batteries: Cells are able to create and store large quantities of ATP, during a “storing process”. Afterwards, they can detect a signal and give back all the energy they stored, in a short burst, like a capacitor. Other ideas are that the cells can “blow up” and emit large amounts of GFP, based on the ATP that they have accumulated.
  • Flashing Bacteria: Cells are grown on a light pattern. The cells that are on the bright parts of the image are oscillating in phase, while the others are remaining dark. This results in the observation of a flashing pattern.
  • Biocam: Visible to Fluorescent light converter.
  • BioCD: “Print” cells on a film, then read them out and “reconstruct” the original data. Basically, it is an analog to digital converter, followed by a system that can interpret the digitized data. (This idea was the basis for the “Music of life project”, where cells would produce fluorescent proteins based on an analog input. Then, the amount and type of fluorescence would code some music).
  • Clock: A follow-the-leader system. We have two groups of cells. The first group creates something that repels the second group. The second group creates a protein that attracts the first group. This way, the first group tries to “catch” the second group, whereas the second group tries to “evade” the first group. This results in them moving around. We can say that the second group is the leader, and the first group exhibits a "follow-the-leader” behavior. Emitting GFP, the groups then act as a sort of analog watch.
  • Sensors: Various systems that can sense PH, pressure, temperature, meat quality, moisture, etc. have been proposed.

Preferred projects

Two ideas of the above are chosen for further examination. The team will be again split up in two groups (different ones than before to make sure that new ideas come up with mixing of people). Each group has to come up with a prototype model of the initial system, remarks on its feasibility and coolness. Our results will be presented to all team members, so that potential projects may be limited to a final project. The preferred projects are:

  1. Music of Life: The basic idea is that instead of having an analog-to-digital converter with four outputs (three fluorescent proteins, and no output), we can have two switches. When switch A is on, RFP is produced. When switch B is on, GFP is produced. When both switches A and B are on, a yellowish output is observed. By recording these outputs, we can later create music, by assigning each fluorescent protein to a chord. For example, RFP would correspond to a G chord. The strength of the fluorescence can signify the strength of the chord. If the cells are placed on a spinning disk, we can have something like a vinyl player. A camera is observing the cells, and music is created on the fly.
  2. Learning: Based on the idea of the neural network, we want to create a biological system where the cells can learn a specific behavior. In order to simplify the system, we decided that the cells can learn to recognize a specific type of other cells. We divide the process in a learning phase and a recognition phase. First, cells A are put together with cells B. Then, cells A are “learning” to recognize cells B. If afterwards they are put in a petri dish with cells B, they will emit GFP. Otherwise, they will stay dark.

Final project

The chosen project is a modified version of Learning which was presented at the last meeting. The system proposed is modified, as in its current state may be implemented with two switches only, something which is really smashing. Keeping the idea of learning, training, and testing phases, we have come up with educatETH E.coli.