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CAROL
Modelling Meeting
Today, we went over to ICT to discuss about how the two types of modelling can be put together as a whole. We discussed what both projects are capable of doing and the weaknesses in both models. The main task that matlab based modelling can help us achieve is to understand the signalling pathway in more depth. By characterizing the system via testing different parts of the circuit, we can understand more about the AI-2 system. If our results from the lab do not match the model, then either we are missing something in our model or there might be a step that we did not consider in the biological model. However, membrane computing gives us a better picture of the overall picture. It has the power to look at populations of cells as well as focus on one cell. I think the appropriate way to sell both modelling systems is to sell MC as a simulation tool and using the matlab based model, we can understand the signalling cascade within the cell more. There are a list of things we need to research about in the next few days for friday. We have another meeting on Friday for more discussion.
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CHINMOYEE
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EMILY
Wiki and Overnight Cultures
Today I talked with Mandy about some things that are still missing from the Wiki. I looked at some other wiki's to get some ideas for the bottom section of ours that has a gap that needs filling. I also worked on the NEWS section of our Wiki, starting to add stuff about the Fort Mac trip. I also made overnight cultures of my J13002-LuxOD47E-B0015 T2-C3 construct so that I can make glycerol stocks of this tomorrow. Fahd and I also met briefly about Ethics to outline what needs to get accomplished over the next couple of days.
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FAHD
Media Coverage and Marketing
Today I started my day by contacting and researching on the following companies:
1)Albian Sands Inc.
2)Life Technologies
3)ALPAC
4)Critical Outcome Technologies
I also joined the Energy Futures Network, which is an online forum for discussing future innovations in the Oil & Gas industry and debating current issues relating to the energy sector.
For media, I setup a radio interview with our community radio network called CJSW 90.9. I also emailed our University of Calgary iGEM July newsletter to CTV News and NUTV.
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IMAN
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JAMIE
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JEREMY
Isolating plasmid of PQ-OU in pCS26 and start of Response Circuit
Plasmid was isolated from eight overnight cultures of PQ-B-R-OU-B in pCS26 using the QIAprep Spin MiniPrep Kit (QIAGEN). Plasmid purity and concentration were measured using the NanoDrop Spectrophotometer.
The response circuit began today with the start of construction of aiiA with a terminator and eventually ribosome binding site. This construct will eventually be placed behind the Pqrr4 promoter and c1 lambda inverter.
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KATIE
Determining the Proper Orientation of Objects
For the majority of today, I spent time:
- Working on getting the nucleotides for the DNA replication animation to line up correctly without using a function to set position using the current location of corresponding nucleotides since this will change when the display is moved to the bottom of the spiral for levels. This involved dividing each nucleotide by the same amount of space apart on each strand of DNA. However, the orientation of the nucleotides become off the further the DNA polymerase moves down the leading strand so I may have to have the polymerase listen fo the position of each corresponding nucleotide so it can get the position right.
- Primase now rezzes the primers required for the lagging strand in replication and I will make it add a single primer to the beginning of the leading strand tomorrow
- Changing positions of the equipment certain things were sent to in the second virtual lab
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KEVIN
Attemptted at making Pqrr4+I13500 competent
An attempt was made to make Pqrr4+I13500 cells competent again in order to transform in the mutant circuits; however, due to my short term memory, I had put them in an LB media with chloramphenicol, which the cells don't have resistence to. Failure, Failure, and another failure.
Overnight culture of Pqrr4+I13500 cells
Because of today's failure at making those cells competent, I have to grow another overnight culture and give it another try from scratch.
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MANDY
Usability of the Wiki
Did some modifications to the wiki, continuing from Monday:
- The site map has a complete guide to the navigational tools which are buttons that outline contributions by each sub-team.
- A comment widget has been added to the front page to limit the stretch on the other boxes (by our growing list of sponsors) and to allow some communication with our visitors.
Biobricker User Interface Design
I began designing the buttons and indicators that will appear on the biobricker userface for the second component of the island. So far, I have:
- promoters
- terminators
- coding sequences for various proteins
- proteins
- co-factors
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PRIMA
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STEFAN
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VICKI
Meeting with the modelling team
The modelling crew met today to discuss how we could integrate our work into a cohesive section in a presentation. Our main focal points were (a) why model; (b) what questions can be answered by each modelling approach; (c) what does each modelling approach NOT answer; and (d) can we resolve the gaps in one modelling approach by bringing in the other? This will help frame our descriptions of our approaches and help us convince others that what we're doing is worth it.
On the MatLab side, we have found that SimBiology does not provide the simulation power that can be achieved by membrane computing. For instance, the platform does not offer a convenient way of modelling more than one cell, making it very difficult to introduce a space/location component into our model. We are having trouble resolving what questions can be anwered with the SimBiology simulation model that cannot be answered by using membrane computing. Accordingly, we are focussing more heavily on characterisation. As we will be biobricking ~5 different promoter-LuxPQ components, each one of those circuits can be contributed to the registry in characterised form, so that future users will be able to use our characterisation data to compare parts. It is sensible to approach this with MatLab because the membrane computing model cannot answer many of these aspects - for example, what is the best temperature to culture and maintain our cells for optimal performance? Or how does the broth in which our cells are cultured affect the dynamic performance? By collecting that data and fitting it to equations, future users of our registry contributions will have a quantitative way to compare parts and select the best one for their purposes.
Our next meeting will be at noon on Friday. By then, this is what I hope to achieve:
- play with SimBiology at the GUI and command line levels to see if we can build in a multicellular approach
- check out the optimisation toolbox and see if there would be a nice way to implement some form of evolutionary optimisation in MatLab. This will be useful in helping us optimise reaction constants for the simulation model. Work with Afshin on this - if it can't be done on Matlab, we might be able to implement something in mathematica using the same data.
- work with the Fort Mac crew to prepare a cohesive, relevant presentation on our experience on the oilsands tour and how synthetic biology can tie into that. Note that iGEM also focusses on ethics and social responsibility, which will be a critical consideration in forging any future alliances, regardless of the industry with which our potential partners are affiliated.
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