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Newcastle University/26 June 2008
From 2008.igem.org
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Minutes
Minute Taker = Nina Nielson
Action Plan for next week
Group
• Meeting with Jan-Willem Veening at 12pm on 28/06 in Medical School to discuss positive control BioBrick (Morgan, Mark and Nina will meet at 11.45 outside Claremont Tower).
• Day by day lab journal to be written on external wiki rather than internal wiki from now on. The students must also edit their lab journals so far so that some of the relevant progress can also be put on the external wiki.
• Write a report about “iGem Experience” for next potential students.
Megan • List all the parts for the two component systems we shall be using and gather some generic parts.
• Do user story on Java for the interface between the EA and parts repository
• 15 minute presentation to go over ComC two component system in detail. Include all the parts and how the promoters work.
Nina
• Do user story on Java for the interface between the EA and constraints repository.
• Continue on with structure of database. Use Access as it is easier to link up to Java. Make an up to date ERD and write SQL queries.
Mark
• 15 minute presentation of how he designed and wrote up his cellML model for the Lac Operon and how he plugged it in to Java and his EA.
• Get JSim working with CellML
• Email Mike and James for help using CellML
Time: 14:30 – 17:00
Attended by:
Neil Wipat - Supervisor
Matthew Pocock - Supervisor
Morgan Taschuk – Project 5
Jan-Willem Veening – advisor
Leendert Hamoen - advisor
Mark Wappett – Project 3
Nina Nielsen – Project 2
Absent:
Jennifer Hallinan
Megan Aylward
Meeting Content
Agenda 1: Positive Control BioBrick
Nina explains that JW has recommended incorporating a wt Bacillus subtilis strain SpaRK two component system into Bacillus subtilis 168 amyE locus. The SpaRK genes of the wt B.subtilis are autoregulated by the modified peptide subtilin. If GFPs were attached to the promoter of this system and the system was induced by subtilin, the GFP would fluoresce. This BioBrick would indicate a proof of principle.
Matt suggests that the output levels could be controlled by using different promoters and/or FPs. This may give values for the strength of the promoters and the FPs. This information may help when defining the constraints and would be very useful for the EA. Simulations could be run until “graph” reaches the appropriate slope/magnitude.
Nina mentions that the paper by JW does compare and contrast promoters in this way.
http://aem.asm.org/cgi/reprint/71/12/8818
Agenda 2: Making composite models
Mark is struggling to make composite models.
Morgan mentions she also is having problems with CellML.
Matt suggests that it might be wise to create part models and constraints models in SPML rather than CellML. SPML doesn’t natively support importing but we can do it programmatically. We will need to ask Neil.
Agenda 3: Interface
Mark says it’s nearly ready to rock and roll. User stories need to be added however.
Nina queries over her “giveMeInteractionTypeName” call. This does not actually belong in interface since it is only for between the constraints repository and the workbench. The workbench will not be part of the interface.
WE ALL MAKE OUR WAY TO THE PLAY HOUSE TO MEET NEIL AND JAN.
Agenda 4: Funding
Neil mentions that Rhea (our biologist) is due to start working in the lab on the 1st of July in Collins Lab and that we have received funding from numerous organizations. After hearing about our idea for the positive control BioBrick, it is decided that she will start work on this when she arrives. We shall have to design the first sequence of the positive control before then.
Neil also mentions that the flights to Boston have been booked by Jen. Hotels have yet to be booked. At the moment they are looking quite pricey. We may look into either staying at a youth hostel or renting an apartment.
Neil also mentions that one of the organizations that have given us funding (Neepaf - not sure how to spell this company) are willing to do some proteomics on our theme afterwards.
In terms of the cellML issues we are having, Neil recommends we email Mike and James to ask for help.
Agenda 5: Positive control BioBrick (again)
Neil suggests putting in the agr model in the BioBrick as well as the wt B. subtilis.
Matt mentions the idea of getting relative calibrations of the FPs by using an array of promoters to find out their strengths. This would also be a cheap easy way of getting pretty pictures in our presentation.
JAN AND LEENDERT ARRIVE
Neil asks if any one knows of any other students (not PHD level) who could help with the iGem team.
Jan mentions a German student that is coming to the lab that may be able to. However she is coming at the end of August and this may be too late??
Topic returns back to positive control BioBrick. Jan, Morgan, Mark and Nina will produce the sequence on Saturday. They can even just type it out in text editor.
The first sequence for the positive control BB deadline is set at 3/07/08
Matt asks Jan if it is possible to calibrate the FPs (mentioned above).
Jan states that this is possible with western blotting.
Leendert queries the price of synthesis currently and Neil mentions it is possible to do it for $0.66 per base. Neil is currently attempting to make the university buy a synthesizer.
We are only going to be synthesizing about 2Kb though so it shouldn’t be too bad.
Agenda 5: Edinburgh trip
One of the prerequisites for award eligibility is to help another team taking part in Igem. Since we are part of the Edinburgh Network, we have been invited to visit them on the 15th-16th July. We therefore plan to attempt to help them to fulfil the requirements.
Neil asked if Jan and Leendert would be interested in joining us in Edinburgh. Nina will forward them the email and information.
Leendert mentions that he is very interested in what we are attempting to do and wondered if the team would give the same/or similar presentation, after the presentation in Boston, to the Medical School in Newcastle.
Depending on where the students are, this should be possible.
Agenda 6: Logos
Morgan accessed the Jpeg of the logos on her laptop and we all discuss which ones we prefer.
Neil suggests that a copy of the logos (numbered) should be sent to everyone so that we can vote for our favourite one.
AOB
• Nina is away next week.
• Morgan goes to Canada on Tuesday
