Team:Leeds/Notebook

From 2013.igem.org

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* ''Collected our poster for YSB 1.0''
* ''Collected our poster for YSB 1.0''
* ''Practiced presentation for YSB 1.0''
* ''Practiced presentation for YSB 1.0''
-
* ''Transformed components for [[Team:Leeds/Project#Biosystem 2|Biosystem 2]]''
+
* ''Transformed components for [[Team:Leeds/Project#Si4 Binding Peptide|Biosystem 2]]''
* ''Met with Rose Bavage and Louise Crabtree to discuss outreach events''
* ''Met with Rose Bavage and Louise Crabtree to discuss outreach events''
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<br>
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* ''Updated wiki, minor tweaks''
* ''Updated wiki, minor tweaks''
* ''Recorded more audio tracks for tutorial videos''
* ''Recorded more audio tracks for tutorial videos''
-
* ''Bade farewell to [[Team:Leeds/Team#Luke Bawazeer|Luke]], who's off to get married!''
+
* ''Bade farewell to [[Team:Leeds/Team#Luke Bawazer|Luke]], who's off to get married!''
* ''Compiled a '''highly exhaustive''' literature review for the [[Team:Leeds/Project#The Cpx Pathway|Cpx Pathway]]''
* ''Compiled a '''highly exhaustive''' literature review for the [[Team:Leeds/Project#The Cpx Pathway|Cpx Pathway]]''
* ''Debated whether PCR equipment is working properly or if there's something else causing problems?''
* ''Debated whether PCR equipment is working properly or if there's something else causing problems?''
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* ''The team has been working on a summer school workshop for 6th-formers in the middle of August''  
* ''The team has been working on a summer school workshop for 6th-formers in the middle of August''  
* ''Still waiting on our assembly primers''
* ''Still waiting on our assembly primers''
-
* ''Also it's Yorkshire day! Up the Yorkists! Down the Lacastrians!''
+
* ''Also it's Yorkshire day! Up the Yorkists! Down the Lancastrians!''
* ''[[Team:Leeds/Team#Paul Turner|Paul]] butchered some wiki code and html to get [http://commons.wikimedia.org/wiki/Commons:Video#Uploading_a_video video embeds] working, with the videos [https://2013.igem.org/Requirements/Wiki hosted on the iGEM servers!] He has then passed the code on to [[Team:Manchester|Manchester]] and [[Team:Newcastle|Newcastle]] to use for their modelling tutorial videos.''
* ''[[Team:Leeds/Team#Paul Turner|Paul]] butchered some wiki code and html to get [http://commons.wikimedia.org/wiki/Commons:Video#Uploading_a_video video embeds] working, with the videos [https://2013.igem.org/Requirements/Wiki hosted on the iGEM servers!] He has then passed the code on to [[Team:Manchester|Manchester]] and [[Team:Newcastle|Newcastle]] to use for their modelling tutorial videos.''
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<br>
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* ''Undertook a PCR cleanup of Biosystem 2 products''
* ''Undertook a PCR cleanup of Biosystem 2 products''
* ''Gels ran to check the PCR cleanup was successful''
* ''Gels ran to check the PCR cleanup was successful''
-
* ''Assembly PCR of [[Team:Leeds/Project#Biosystem 1|Biosystem 1]] and [[Team:Leeds/Project#Biosystem 2|2]] - Attempt 1!''
+
* ''Assembly PCR of [[Team:Leeds/Project#Phase I|Biosystem 1]] and [[Team:Leeds/Project#Si4 Binding Peptide|2]] - Attempt 1!''
<br>
<br>
<div style="color:darkgreen;font-size:14pt">'''6th August'''</div>
<div style="color:darkgreen;font-size:14pt">'''6th August'''</div>
* ''Day 2 of hiking for Paul, raising money for the [http://www.justgiving.com/Paul-Turner20 Crohn's and Ulcerative Collitis Unit in the Leeds Teaching Hospitals Trust]''
* ''Day 2 of hiking for Paul, raising money for the [http://www.justgiving.com/Paul-Turner20 Crohn's and Ulcerative Collitis Unit in the Leeds Teaching Hospitals Trust]''
* ''We ran a gel of yesterdays PCR products''
* ''We ran a gel of yesterdays PCR products''
-
* ''Assembly PCR of [[Team:Leeds/Project#Biosystem 1|Biosystem 1]] and [[Team:Leeds/Project#Biosystem 2|2]] - Attempt 2!''
+
* ''Assembly PCR of [[Team:Leeds/Project#Phase I|Biosystem 1]] and [[Team:Leeds/Project#Si4 Binding Peptide|2]] - Attempt 2!''
* ''Plasmid prep of GFP producing bacteria and transformation into expression cells for use as controls in experiements''
* ''Plasmid prep of GFP producing bacteria and transformation into expression cells for use as controls in experiements''
<br>
<br>
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* ''[[Team:Leeds/Modeling|Modelling]] discussion with [[Team:Manchester|Manchester]] and [[Team:Newcastle|Newcastle]] regarding modelling tutorial videos - Leeds will be producing one on Virtual Cell and integration of BNGL with VCell''
* ''[[Team:Leeds/Modeling|Modelling]] discussion with [[Team:Manchester|Manchester]] and [[Team:Newcastle|Newcastle]] regarding modelling tutorial videos - Leeds will be producing one on Virtual Cell and integration of BNGL with VCell''
* ''Lab digests''
* ''Lab digests''
-
* ''Construction of [[Team:Leeds/Project#Biosystem 1|Biosystem 1]]''
+
* ''Construction of [[Team:Leeds/Project#Phase I|Biosystem 1]]''
* ''Constructed growth curves for our bacteria that contained our biosystem''
* ''Constructed growth curves for our bacteria that contained our biosystem''
* ''A draft copy of ethics assessment form was produced''
* ''A draft copy of ethics assessment form was produced''
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* ''Wiki formatting cleaned up, favicon enabled, compatibility issue with Chrome and Safari fixed''
* ''Wiki formatting cleaned up, favicon enabled, compatibility issue with Chrome and Safari fixed''
* ''New graph uploaded to [[Team:Leeds/Results|Results]] section''
* ''New graph uploaded to [[Team:Leeds/Results|Results]] section''
-
* ''Construction of [[Team:Leeds/Project#Biosystem 1|Biosystem 1]] finished off, ready for characterisation studies''
+
* ''Construction of [[Team:Leeds/Project#Phase I|Biosystem 1]] finished off, ready for characterisation studies''
* ''Awaiting Fluoro-AFM time for characterisation protocols''
* ''Awaiting Fluoro-AFM time for characterisation protocols''
* ''Started using GraphPad to draw our graphs from labs''
* ''Started using GraphPad to draw our graphs from labs''
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* ''We treated our beads to make them hydrophobic for our experiments''
* ''We treated our beads to make them hydrophobic for our experiments''
* ''Made lots of buffers and reagents for our Nickel column experiment''
* ''Made lots of buffers and reagents for our Nickel column experiment''
-
* ''Additional transformations of [[Team:Leeds/Project#Biosystem 2|Biosystem 2]] and our ordered DNA were undertaken''
+
* ''Additional transformations of [[Team:Leeds/Project#Si4 Binding Peptide|Biosystem 2]] and our ordered DNA were undertaken''
-
* ''[[Team:Leeds/Project#Biosystem 1|Biosystem 1]] was digested and run on a gel to check it was the correct length''
+
* ''[[Team:Leeds/Project#Phase I|Biosystem 1]] was digested and run on a gel to check it was the correct length''
<br>
<br>
<div style="color:darkgreen;font-size:14pt">'''15th August'''</div>
<div style="color:darkgreen;font-size:14pt">'''15th August'''</div>
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<br>
<br>
<div style="color:darkgreen;font-size:14pt">'''16th August'''</div>
<div style="color:darkgreen;font-size:14pt">'''16th August'''</div>
-
* ''Preliminary Fluoro-AFM to help with characterisation of [[Team:Leeds/Project#Biosystem 1|Biosystem 1]]''
+
* ''Preliminary Fluoro-AFM to help with characterisation of [[Team:Leeds/Project#Phase I|Biosystem 1]]''
* ''Meeting with [[Team:Leeds/Team#Michael McPherson|Mike]] to discuss progress, current aims, learning outcomes and looking towards building on this next year''
* ''Meeting with [[Team:Leeds/Team#Michael McPherson|Mike]] to discuss progress, current aims, learning outcomes and looking towards building on this next year''
* ''Ran an SDS-PAGE gel to find out whether our isolation of the INP protein was successful or not''
* ''Ran an SDS-PAGE gel to find out whether our isolation of the INP protein was successful or not''
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<br>
<br>
<div style="color:darkgreen;font-size:14pt">'''22nd August'''</div>
<div style="color:darkgreen;font-size:14pt">'''22nd August'''</div>
-
* ''Carried on with [[Team:Leeds/Project#Biosystem 2|Biosystem 2]] characterisation''
+
* ''Carried on with [[Team:Leeds/Project#Silica Binding Peptide|Biosystem 2]] characterisation''
<br>
<br>
<div style="color:darkgreen;font-size:14pt">'''23rd August'''</div>
<div style="color:darkgreen;font-size:14pt">'''23rd August'''</div>
-
* ''Had a meeting with [[Team:Leeds/Team#Luke Bawazeer|Luke]], [[Team:Leeds/Team#James Ross|James]] and [[Team:Leeds/Team#Michael McPherson|Mike]] about how the project is going''
+
* ''Had a meeting with [[Team:Leeds/Team#Luke Bawazer|Luke]], [[Team:Leeds/Team#James Ross|James]] and [[Team:Leeds/Team#Michael McPherson|Mike]] about how the project is going''
* ''Began characterising [[Team:Leeds/Project|Biosystems]] 2 and 3''
* ''Began characterising [[Team:Leeds/Project|Biosystems]] 2 and 3''
<br>
<br>

Revision as of 12:20, 2 October 2013

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Back to iGEM Main Page
The Log
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Here's our log, you can read about what we've been doing in the lab and the office. (We're working hard, promise)

June 2013

Week 1

24th June
  • We’ve moved into our office, deep in the basement of the research labs in the Miall building.
  • Our time has been taken up getting acquainted with our office ( and our coffee machine!) and roughing out the fine details of our protocol.
  • We’ve pulled together a combination of the teams' various projects to create our final idea, we’re now looking at making a detector platform for physically binding substrates to activate a reporter. (Scintillating no?)
  • Our team has been busy thinking of inventive assay design to characterise our biobricks; frantically trying to code our wiki and taking our team photos (important work)


25th June
  • Jeni, one of our first year biochemists has been working on her primer design, getting everything ready to start in the labs next week. We’ve been compiling our part list and getting our order ready; a buffer and bacteria shopping spree.


26th June
  • We’re trying to plan out our outreach programs, so watch this space. We’re going to be doing instructional videos on RFC-10 and Golden Brick assembly; as well as some more basic introduction to Synthetic Biology for younger students, alongside running some SynBio workshops for summer students that’ll be here at Leeds.


27th June
  • Today we've been working on our presentation; getting it ready for the YSB conference by running it past some of our lecturers; scary stuff
  • We've also been getting comfortable in the lab space, making up stacks of LB broth and preparing for some serious bacterial colonisation


28th June
  • It's been a busy week here at Leeds iGEM HQ. We've got a Biochemist and a Physicist (a rather handsome pair) frantically working on coding the wiki and creating images for the presentations and posters, it's gonna be beautiful (we hope)
  • We've had a team of biochemists (all 3 of them) hard at work designing primers and getting ready to steamroll into the lab next week.



July 2013

Week 2

1st July
  • With our primers in the post, we've been mass producing growth media and agar plates. We've resuspended and transformed a selection of the biobricks we plan on using, including YFP, GFP, INP, and some terminators.
  • The wiki team have been locked in the basement and they're not allowed out till it looks beautiful.


2nd July
  • Today we've been writing out scripts for our tutorial videos, they'll be a series aimed at younger students with an introduction to Synthetic Biology, and a series aimed at Synthetic Biologists on things like Goldengate and Gibson assembly.
  • Then we locked our token nanotechnologist into a lab with a couple of thousand pounds worth of microfluidics chips and we're hoping for the best (and a minimal number of perforations)


3rd July
  • Been a busy day; plasmid preps, glycerol stocks and further transformations of quorum sensing biobricks (pLux and LuxR), promoters and cyan fluorescent proteins.
  • We then had a skype conference with Cyrille Pauthenier, the advisor for the Evry iGEM team.
  • Went into great detail on Goldengate and Goldenbrick assembly methods and their pros and cons.
  • We ended our day doing soundtests for our educational videos; watch for the remix.


4th July
  • Another day of plasmid preps and innoculations in the lab of our newly transformed BioBricks.
  • Meanwhile in the office we have been working on our poster for the Young Synthetic Biologist confrence in London next week.


5th July
  • Today we have done further plasmid preps getting ready for our assembly!
  • In the office we've been working on our poster and presentation for the upcoming Young Synthetic Biologist confrence in London
  • There has also been organisation of trips into schools making a presentation for 6th form students on Synthetic Biology
  • Finally we have been double checking primers and DNA sequences for Gibson assembly



Week 3

8th July
  • Our first BioBrick assembly has been done!(A green Flourescent protein). It will be tested to see if it has worked tomorrow
  • Presented our ideas so far to two more academic staff.
  • We have been doing the finishing touches to our poster for the Young Synthetic Biologist confrence in London this weekend
  • Jonah has been working very hard on our first Youtube tutorial video


9th July
  • Rewrote parts of the presentation
  • Created a new survey on Synthetic Biology to send out to the public
  • Started editing the video
  • Reviewed the wiki design


10th July
  • Sent the poster for YSB-London to the printers
  • Recorded the next audio track for a new video
  • Corrected typos on the wiki, our presentation and the poster
  • Uploaded our first [http://www.youtube.com/watch?v=Hz7pPXJvhVE Youtube Video]
  • Sent out fresh surveys via Artynet


11th July
  • Collected our poster for YSB 1.0
  • Practiced presentation for YSB 1.0
  • Transformed components for Biosystem 2
  • Met with Rose Bavage and Louise Crabtree to discuss outreach events


12th July
  • Caught a very early train down to London for YSB 1.0
  • Met the other UK iGEM teams at YSB 1.0
  • Prepped to present tomorrow at YSB 1.0
  • Collected soil sample tubes from Norwich for Hadrian's Wall
  • Discussed collaboration with nearly every team at YSB 1.0



Week 4

15th July
  • Had a great time at YSB 1.0
  • Jumped back into script writing for Tutorial Videos
  • Ordered primers for Si4 binding domain


16th July
  • Edited and uploaded our 2nd [http://www.youtube.com/watch?v=GJC6kxtji9E Youtube] video
  • Transformed an INP/YFP fusion
  • Innoculated prior transformations to grow overnight
  • Created a workshop plan for Friday, with visiting 6th form students


17th July
  • Meeting with our new sponsors, BioLine
  • Added repeating background image of DNA to wiki


18th July
  • Finalised protocols for the labs
  • Had a meeting with Paul Beale and Fiona Meldrum from the Chemistry department about our project
  • Plasmid preps and more innoculations!
  • Met with some school teachers to discuss a workshop we will be doing with year 13's in September


19th July
  • Done some PCR (Translation from Yorkshire to English: Did some PCR)
  • Recorded more audio for our Youtube videos
  • Had our weekly Friday meeting
  • Presentation and Ethics Workshop with STEM subject 6th Formers - went very well, lots of good feedback!



Week 5

22nd July
  • Fixed broken wiki-code and js for galleries
  • Ran PCR to amplify INP, GFP and D2-Term
  • D2-Term didn't work, re-programmed PCR to run overnight at different gradient, hopefully optimised for the primer melt-temperature


23rd July
  • Re-ran PCR of everything from before
  • Updated wiki, minor tweaks
  • Recorded more audio tracks for tutorial videos
  • Bade farewell to Luke, who's off to get married!
  • Compiled a highly exhaustive literature review for the Cpx Pathway
  • Debated whether PCR equipment is working properly or if there's something else causing problems?
  • Wrote Sabrina's bio!


24th July
  • Wished Jeni a happy birthday!
  • Plasmid Prepped
  • Drafted simplified model for characterising Cpx Pathway


25th July
  • Recorded more Audio tracks for videos
  • Edited together more videos, uploaded onto [http://www.youtube.com/watch?v=pBzLZIVTkes Youtube]
  • Ran more PCR - it is being rather finicky!


26th July
  • Uploaded revised versions of two [http://www.youtube.com/watch?v=KwpLMyV3YTA videos] for [http://www.youtube.com/watch?v=T3vFTUXfxvk Youtube]
  • Meeting with Sarah and Mike, got advice on gels and updated them on our progress - to quote Mike, "I'm really impressed!"
  • Paul revised more of the simplified Cpx Pathway model, hopefully have basic version coded in BNGL by Monday
  • Plotted out workshop ideas for Summer School Students
  • More vids and audio recorded!



Week 6

29th July
  • Hard-coded alpha-version 0.3 of Cpx Pathway model
  • Ran yet more gels
  • Had a project update meeting with S.D.Evans


30th July
  • Paul has been continuing to develop our model for the Cpx pathway.
  • In the labs more gels have been run to make sure our PCR products are what they should be.
  • Characterisation protocols are being finalised


31st July
  • Constructed a control growth curve of our bacteria with and without chloramphenicol.
  • Analytical digests of plasmids



August 2013

Week 6

1st August
  • A gel has been run for the previous days digest
  • We have transformed a plasmid that will produce GFP for some preliminary fluorescence measurements
  • The team has been working on a summer school workshop for 6th-formers in the middle of August
  • Still waiting on our assembly primers
  • Also it's Yorkshire day! Up the Yorkists! Down the Lancastrians!
  • Paul butchered some wiki code and html to get [http://commons.wikimedia.org/wiki/Commons:Video#Uploading_a_video video embeds] working, with the videos hosted on the iGEM servers! He has then passed the code on to Manchester and Newcastle to use for their modelling tutorial videos.


2nd August
  • Made a new page on our wiki for our results to be displayed on
  • More wiki coding, cleanup etc
  • Emails, office work, meetings and modelling



Week 7

5th August
  • Paul starts hiking along Hadrian's Wall for charity!
  • We made an array of buffers to go along with our characterization experiments
  • Undertook a PCR cleanup of Biosystem 2 products
  • Gels ran to check the PCR cleanup was successful
  • Assembly PCR of Biosystem 1 and 2 - Attempt 1!


6th August
  • Day 2 of hiking for Paul, raising money for the [http://www.justgiving.com/Paul-Turner20 Crohn's and Ulcerative Collitis Unit in the Leeds Teaching Hospitals Trust]
  • We ran a gel of yesterdays PCR products
  • Assembly PCR of Biosystem 1 and 2 - Attempt 2!
  • Plasmid prep of GFP producing bacteria and transformation into expression cells for use as controls in experiements


7th August
  • Day 3 of hiking for Paul. He should be very tired by now.
  • Our ordered DNA arrived! Whoop!!
  • Further PCR and PCR cleanups were undertaken
  • Ran even more gels!


8th August
  • Day 4 of hiking for Paul. Nearly done!
  • Transformation of our ordered DNA into our cells
  • Made more agar plates containing different antibiotics
  • Lots of Digestion and ligation occured
  • We undertook a control characterization experiment to see the effect of pH and detergent concentration on the fluorescence of GFP producing bacteria


9th August
  • Final Day for Paul hiking along Hadrian's Wall.
  • Ran gels to confirm digestions and ligations
  • Further digestions and ligations were performed



Week 8

12th August
  • Paul returned! He had a walking stick and everything (Life Lesson: Hiking 20 miles a day with a 30kg pack is not good for the feet)
  • Modelling discussion with Manchester and Newcastle regarding modelling tutorial videos - Leeds will be producing one on Virtual Cell and integration of BNGL with VCell
  • Lab digests
  • Construction of Biosystem 1
  • Constructed growth curves for our bacteria that contained our biosystem
  • A draft copy of ethics assessment form was produced


13th August
  • Wiki formatting cleaned up, favicon enabled, compatibility issue with Chrome and Safari fixed
  • New graph uploaded to Results section
  • Construction of Biosystem 1 finished off, ready for characterisation studies
  • Awaiting Fluoro-AFM time for characterisation protocols
  • Started using GraphPad to draw our graphs from labs


14th August
  • We treated our beads to make them hydrophobic for our experiments
  • Made lots of buffers and reagents for our Nickel column experiment
  • Additional transformations of Biosystem 2 and our ordered DNA were undertaken
  • Biosystem 1 was digested and run on a gel to check it was the correct length


15th August
  • All tutorial videos are now available on the Outreach page, provided your browser is HTML 5 capable and conforms to the open format standard required for all MediaWiki platforms
  • Minor wiki tweaks (it would be nice if browsers were standardised...)
  • Ran a Nickel affinity column in an attempt to isolate our INP-Si4 protein


16th August
  • Preliminary Fluoro-AFM to help with characterisation of Biosystem 1
  • Meeting with Mike to discuss progress, current aims, learning outcomes and looking towards building on this next year
  • Ran an SDS-PAGE gel to find out whether our isolation of the INP protein was successful or not



Week 9

19th August
  • Added direct links to full image page for graphs in Lab Results
  • Set up some more PCR tubes to run to make more of BS2


20th August
  • Updated bios on the wiki
  • Minor layout redesign to accommodate our newest sponsor, [http://www.bangslabs.com/ Bangs Labs!]
  • Wiki tweaks
  • Transformed our ligated BS3 into our bacteria, hoping it will be 5th time lucky?!
  • Had a nice chat to Mike to discuss where to go next with the lab work


21st August
  • Made a start on the characterisation protocol for BS1, 60 tubes needing to be prepared - a lot of pipette action!
  • Ran a Colony PCR!
  • Digested and ligated BS1 into the submission plasmid, ready to be send off to iGEM headquarters


22nd August


23rd August



Week 10

26th August
  • University closed for August Bank Holiday


27th August
  • University closed for August Bank Holiday


28th August
  • Tried to fix HTML5 video tag bugs with Safari... no success yet


29th August
  • Got video tag working with IE9+, but cannot upload the mpeg4 video format required to allow viewing. Videos still can be seen at our [http://www.youtube.com/user/igemleeds Youtube] page
  • Added video thumbnails to videos embedded on the Outreach page
  • Prepped microscope slides for AFM


30th August
  • AFM scope slides coated and stored in walk-in fridge for the weekend
  • Adjusted layout template for some new features on the wiki... coming soon!



September 2013

Week 11

2nd September
  • Began finding work-arounds to use javascript within MediaWiki framework
  • Ran AFM of previously prepped slides. Culture does not seem to have taken very well. Refined slide preparation procedure
  • Prepped fresh slides with grid pattern etc, then cleaned carefully to ensure optical perfection
  • Potential work-around for javascript implemented, still some issues with certain script files


3rd September
  • Fresh nights sleep led to new inspiration to fix javascript issues!
  • All javascript files now uploaded as templates with instructions on use, within the iGEM wiki. Tested for bugs relating to this, all appear to work correctly
  • All of wiki should now meet iGEM 2013 requirements, including all web2.0 elements. Just need to get video embeds working for IE9+ and Safari
  • AFM slides cultured, and stored in walk in ready for Thursday


4th September
  • x


5th September
  • x


6th September
  • x



Week 12

9th September
  • x


10th September
  • Presented at [http://www.cafe-sci.org.uk/ Cafe Scientifique] at 8pm - hopefully it was a success


11th September
  • Met with Andy of [http://www.thesuperposition.org/about/ Superposition] and [http://www.thesuperposition.org/ ASMbly Leeds], to discuss setting up a Bio-hackspace and to feature as main guests at ASMbly this year


12th September
  • Spent today trying to finish off in the labs preparing our DNA for sequencing and submission.


13th September
  • Dan and Jeni went into a local school to discuss synthetic biology and do some demonstrations with sixth form students.


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Geneious, our fine sponsors and suppliers of software Bioline, our fine sponsors and suppliers of equipment Qiagen, our fine sponsors and suppliers of PCR kits
Bangs Laboratories, our fine sponsors and suppliers of silica beads
Leeds Homepage
Retrieved from "http://2013.igem.org/Team:Leeds/Notebook"