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Template:Team:Sheffield/Content:LabProtocols
From 2014.igem.org
Dry Lab Journal
At the start of our project, we undertook a week of boot camp – yes, it was as intense as it sounds! With all team members coming from a range of backgrounds with different abilities, we thought that this would be a good idea to allow everyone to be on the same page with the same basic level of understanding in each component of the project.
Training Week
Monday 16th June
- Laboratory Orientation and Safety Training
- Laboratory Techniques 1
- Pipetting, LB Broth, LB agar and Overnight Cultures
- Project Expectations Discussion
- Medal criteria, weekly meetings to discuss objectives and results, personal logs of what and how things have been done
Tuesday 17th June
- Introduction of Policy and Practices
- Discussion of Social Implications of Synthetic Biology
- Genome 101
- Laboratory Techniques 2
- Plasmid DNA extraction, PCR and Chemical Transformation
Wednesday 18th June
- Introduction to Modelling
- BioBricks and the Registry
- Methodology in Social Science and Data Collection
Thursday 19th June
- Oxford Meet Up
- Wiki and Team Identity Discussion
Friday 20th June
- Project Presentation to the Chemical and Biological Engineering Department at the University of Sheffield
- Weekly Report and Feedback
This week was very useful as it allowed us to become familiar with all aspects of the project. As well as this, it was a great icebreaker that helped our team of students, advisors and supervisors to get to know each other better!
Week 1
Monday 23rd June
- Collated contact details of potential sponsors
- Drafter sponsorship request letters for money, equipment and expertise
Tuesday 24th June
- Continued working towards producing a sponsorship package
- Reading published papers relating to synthetic biology and iGEM regarding awareness and impressions
- Set up two meetings: marketing and industry expertise
Wednesday 25th June
- Mathematica – 4 of our student team members went on a course to learn Mathematica for the modelling aspect of the project
- Further reading of policy and practices papers
- Worked on team identity in preparation for the marketing meeting
- Sponsorship package completed – this can be found here
- Translated written protocols into the lab notation
Thursday 26th June
- Started planning our Meet Up and contacted teams for potential collaboration
- Continued work on the lab notation
- Discussed potential research questions to carry out a study within the University
- Meeting with industry expert within the University of Sheffield; this provided us with new contacts and a better understanding of the UK sewage system and how it functions. It was also very useful as we began to consider the applications of our project and what we may need to consider. Mathematica
Friday 27th June
- Used XML and PYTHON to try to produce a computer language for the lab notation
- Mathematica
- Weekly meeting and report
Week 2
Monday 30th June
- Weekly meeting to set objectives
- Worked on the interview questions to be used for the University of Sheffield case study
- Further research on potential sponsors
- Mathematica
Tuesday 1st July
- Meeting with advisors to discuss suitability of research question and interviews
- Began to consider the ethics needed to go alongside this
- Mathematica
Wednesday 2nd July
- Finalised research questions and sent off ethics approval
- Began learning HTML and other mark up languages for the Wiki
Thursday 3rd July
- Team identity discussion on potential project names and logo
- Researched assays
- Wrote COSHH forms
- Sent out sponsorship packages
- ERASynBio research and application draft
Friday 4th July
- Sent out invitations for the meet up
- Organised speakers and planned the remainder of the meet up
- Continued research on assays and writing COSHH forms
Week 3
Monday 7th July
- Weekly meeting to set objectives
- Write up policy and practices project outline
- Emailed Sheffield 2010 iGEM Team regarding their lab notation work
- Collated more contacts for sponsors
- Contacted modelling expert within the University to set up a meeting
- Wiki development meeting
Tuesday 8th July
- Project implementation discussion and potential designs drawn on CAD
- Assay research
- Researched GMO approval requirements for the safety form
Wednesday 9th July
- Wiki development
- Sponsorship requests
Thursday 10th July
- Sponsorship requests
- Arranged catering for the meet up
- Wiki development
- Discussed the improvement of the lab notation
- Assay database idea discussed
Friday 11th July
- Weekly meeting and report
- Reading research papers regarding FOGs and whey they are caused
- Lab notation development
- Collected assays for the database
- ERASynBio application sent
Week 4
Monday 14th July
- Weekly meeting to set objectives
- Finalised logo design
- Made contact with experts at Northumbrian Water and Anglian Water
- Wiki development meeting
Tuesday 15th July
- Modelling meeting – use of Mathematica to analyse the FadR characterisation, use of CFD to model fluid flow and also control system analysis
- Meeting with industry expert from the University regarding product development
- Produced poster and presentation for the meet up on Friday
- Debugged temporary wiki
Wednesday 16th July
- Discussed second research question further; concluded it would focus on responsibility
- Jamboree meeting
Thursday 17th July
- Set up interviews with Sheffield City Council
- Sent reminder to all teams attending Friday’s meet up
- Finalised meet up details
Friday 18th July
- Meet up
Week 5
Monday 21st July
- Weekly meeting to set objectives
- Discussed interview questions for the responsibility question
- Modelling meeting – biological modelling may be limited; product design may be better to focus on
- FadR characterisation meeting – decided to continue characterising this but not use it in the final construct of our product
- CAD drawings of current designs
- Interview with University lecturer from Molecular Biology and Biotechnology
Tuesday 22nd July
- Researched current enzyme dosing systems to help develop product further
- Interview with a food outlet regarding responsibility
- Started transcribing lab book protocols into HTML code
- Researched the law and legislation regarding fat disposal by the public
Wednesday 23rd July
- Meeting with expert from Anglian Water
- Set up interviews within the University for the faculty wide study
- Skype meeting with Manchester iGEM Team for potential collaboration; found that projects were quite different
Thursday 24th July
- Used SolidWorks for new product designs
- Contacts schools regarding outreach
- Spoke to Oxford iGEM Team regarding collaboration
Friday 25th July
- Weekly meeting and report
- Decided to pursue the Manufacturing track
Week 6
Monday 28th July
- Weekly meeting to set objectives
- Reading FOG papers
- Began writing up parts of the project we have completed so far
- Collaborative links established with Valencia iGEM Team
Tuesday 29th July
- Interview with expert from Northumbrian Water
- Organised lab notation testing sessions and carried these out
- Collaborative links with Oxford iGEM Team
- Interview with University lecturer in Landscape
Wednesday 30th July
- Analysed feedback from lab notation testing and made suggested improvements
- Interviews with University lecturers from the Medical School and Geography
- Began SocioBrick development and discussion
Thursday 31st July
- Contacted Paris Bettencourt iGEM Team to be featured in their newsletter
Friday 2nd August
- Weekly meeting and report
- Interviews with University lecturers from Civil Engineering and Biomedical Science
- SocioBrick development
Week 7
Monday 4th August
- Weekly meeting to set objectives
- Finished improved lab protocols
- Skype meetings with Oxford iGEM and Paris Bettencourt iGEM Teams
- Interview with a food outlet for the responsibility study
Tuesday 5th August
- Started writing up SocioBrick descriptions
- Wiki development
- Product design
Wednesday 6th August
- Interview with University lecturer from Automatic Control and Systems Engineering
- Wiki development
- Product design
Thursday 7th August
- Interviews with University lecturers from Music and Biblical Studies
- Product design
- Analysis of interviews conducted over the past few weeks
Friday 8th August
- Weekly meeting and report
- Skype meeting with Oxford iGEM Team
- Added to the wiki write ups
Week 8
Monday 11th August
- Weekly meeting to set objectives
- Interview analysis
Tuesday 12th August
- Write up of the interviews conducted within the University
- Product development
- SocioBrick development
Wednesday 13th August
- Interview with a representative from the Labour party
- Wiki development
- Product development
Thursday 14th August
- SocioBrick development
- Product development
Friday 15th August
- Weekly meeting and report
- Wrote project abstract for the iGEM official team page
Week 9
Monday 18th August
- Weekly meeting to set objectives
- Researched more analysis SocioBricks as these were lacking
Tuesday 19th August
- Product design
- Interview analysis for responsibility report
- Wiki development
Wednesday 20th August
- Wiki team meeting to set up deadlines for the next few weeks
- Designs for the wiki layout made
- Writing up responsibility report
Thursday 21st August
- Writing up responsibility report
- Interviewed more food outlets and analysed the results
- Contacted more water companies
- Set up a trip to Veolia for late September
Friday 22nd August
- Weekly meeting and report
- Collaborative link with Valencia_UPV iGEM Team – agreed to test our lab notation
- Interview with a Labour councillor
Week 10
Monday 25th August
- Bank Holiday
Tuesday 26th August
- Planned outreach events for schools
- Made poster for YSB/UCL meet up
- Sent improved lab notation to Edinburgh iGEM Team for collaboration
- Writing up responsibility report
Wednesday 27th August
- Made presentation for YSB/UCL meet up
- Product development
- Safety form
Thursday 28th August
- Treatment plant visit and interviews with the workers there
- Product development
Friday 29th August
- Weekly meeting and report – everyone given specific deadlines to meet over the next month
- Finalised poster and presentation for YSB/UCL meet up
- Wiki development
- Uploaded project title and abstract to the official iGEM team page
- Uploaded project title and abstract to the official iGEM team page
