Difference between revisions of "Team:Groningen/Notebook"

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<h4>Week 1: Jan 10 – Jan 16</h4>
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<h4>Week 2: Jan 17 – Jan 23</h4>
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<h4>Week 4: Jan 31 – Feb 6</h4>
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<h4>Week 5: Feb 7 – Feb 13</h4>
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<h4>Week 6: Feb 14 – Feb 20</h4>
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<h4>Week 8: Feb 28 – Mar 5</h4>
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<h4>Week 9: Mar 6 – Mar 12</h4>
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<h4>Week 10: Mar 13 – Mar 19</h4>
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<h4 id="week-10">Week 10: Mar 13 – Mar 19</h4>
 
 
 
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<h4>Week 11: Mar 20 – Mar 26</h4>
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<h4 id="week-11">Week 11: Mar 20 – Mar 26</h4>
 
 
 
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<h4>Week 12: Mar 27 – Apr 2</h4>
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<h4 id="week-12">Week 12: Mar 27 – Apr 2</h4>
 
 
 
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<h4>Week 13: Apr 3 – Apr 9</h4>
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<h4 id="week-13">Week 13: Apr 3 – Apr 9</h4>
 
 
 
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<h4>Week 14: Apr 10 – Apr 16</h4>
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<h4 id="week-14">Week 14: Apr 10 – Apr 16</h4>
 
 
 
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<h4>Week 15: Apr 17 – Apr 23</h4>
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<h4 id="week-15">Week 15: Apr 17 – Apr 23</h4>
 
 
 
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<h4>Week 16: Apr 24 – Apr 30</h4>
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<h4 id="week-16">Week 16: Apr 24 – Apr 30</h4>
 
 
 
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<h4>Week 17: May 1 – May 7</h4>
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<h4 id="week-17">Week 17: May 1 – May 7</h4>
 
 
 
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<h4>Week 18: May 8 – May 14</h4>
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<h4 id="week-18">Week 18: May 8 – May 14</h4>
 
 
 
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<h4>Week 19: May 15 – May 21</h4>
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<h4 id="week-19">Week 19: May 15 – May 21</h4>
 
 
 
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<h4>Week 20: May 22 – May 28</h4>
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<h4 id="week-20">Week 20: May 22 – May 28</h4>
 
 
 
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<h4>Week 21: May 29 – Jun 4</h4>
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<h4 id="week-21">Week 21: May 29 – Jun 4</h4>
 
 
 
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<h4>Week 22: Jun 5 – Jun 11</h4>
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<h4 id="week-22">Week 22: Jun 5 – Jun 11</h4>
 
 
 
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<h4>Week 23: Jun 12 – Jun 18</h4>
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<h4 id="week-23">Week 23: Jun 12 – Jun 18</h4>
 
 
 
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<h4>Week 24: Jun 19 – Jun 25</h4>
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<h4 id="week-24">Week 24: Jun 19 – Jun 25</h4>
 
 
 
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<h4>Week 25: Jun 26 – Jul 2</h4>
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<h4 id="week-25">Week 25: Jun 26 – Jul 2</h4>
 
 
 
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<h4>Week 26: Jul 3 – Jul 9</h4>
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<h4 id="week-26">Week 26: Jul 3 – Jul 9</h4>
 
 
 
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<h4>Week 27: Jul 10 – Jul 16</h4>
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<h4>Week 28: Jul 17 – Jul 23</h4>
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<h4 id="week-28">Week 28: Jul 17 – Jul 23</h4>
 
 
 
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<h4>Week 29: Jul 24 – Jul 30</h4>
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<h4 id="week-29">Week 29: Jul 24 – Jul 30</h4>
 
 
 
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<h4>Week 30: Jul 31 – Aug 6</h4>
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<h4>Week 31: Aug 7 – Aug 13</h4>
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<h4>Week 32: Aug 14 – Aug 20</h4>
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<h4>Week 33: Aug 21 – Aug 27</h4>
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<h4 id="week-33">Week 33: Aug 21 – Aug 27</h4>
 
 
 
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<h4>Week 34: Aug 28 – Sep 3</h4>
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<h4>Week 35: Sep 4 – Sep 10</h4>
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<h4>Week 36: Sep 11 – Sep 17</h4>
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<h4>Week 37: Sep 18 – Sep 24</h4>
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<h4>Week 38: Sep 25 – Oct 1</h4>
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<h4>Week 39: Oct 2 – Oct 8</h4>
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<h4>Week 40: Oct 9 – Oct 15</h4>
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<h4>Week 41: Oct 16 – Oct 22</h4>
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<h4>Week 42: Oct 23 – Oct 29</h4>
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Revision as of 19:51, 19 October 2016



CryptoGE®M
CryptoGE®M
Team
Team
Members Supervisors Collaborations Achievements Contact
Project
Project
Tour Description Design Results Demonstrate Applications Future Notebook
Biology
Biology
Experiments Parts Safety Lab journal
Computing
Computing
Modelling Software Encoding Decoding
Human Practice
Human Practices
Human Practices Gold Silver
Acknowledgements
Support
Sponsors Attributions

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
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