Team:Groningen/Notebook



CryptoGE®M
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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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