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| - | Descriptive Title of What You're Doing
| + | Gillespie's Alogorithm and Interface |
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| - | WIKI CODING HERE
| + | This week Afshin is gone to Mathematica conference in US. Afshin is supposed to work on the new signalling system model (AI-2 signaling system) and I am reading some papers about Gillespie’s algorithm. Gillespie’s algorithm brings randomness for our model and makes our membranes dynamic. This algorithm has been tested many times and it is proven that Gillespie’s algorithm is a suitable function that could be used to model biological systems. Since this algorithm was set to work with a single compartment, we had to manipulate it in order to use it for multicompartment systems. Afshin has done a fantastic job and implemented that in Mathematica and now I am learning how this algorithm works as it is a key for learning the entire model. On the other hand, there are so many functions involved in our simulation that I tried to learn about during this week, so I could be more involved in the new model which is intended to simulate AI-2 signalling system. |
| | + | I also worked on a user friendly interface that would be used for our model. In this interface the users type in the information needed to run the simulation and the get the results in an organized way. They are able to run the system with different numbers of cells and they can choose what kind of results (graphs, charts, patterns, and visualization) they want to observe at the end of their simulation. |
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CAROL
Descriptive Title of What You’re Doing
WIKI CODING HERE
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CHINMOYEE
Preparation for the University Fair.
Colouring the posters, building your own bacterium , packing presents... FUN
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EMILY
Preparation for Campus Fair
Today we spent the majority of the day preparing for the Campus Fair, one of our Outreach initiatives. We created posters, prepared 'Bacteria' craft kits and purchased and wrapped-up prizes for our tube counting game and pipetting colour competition. We finalized the detaails for all of our activities and made up a schedule for the day for shifts/ events.
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FAHD
Marketing and Outreach for June 5th 2009
Today, I continued filling out funding applications for some O&G development companies. Some of these companies include Petro Canada, EnCana and Talisman Eneregy. I almost got them completed and once they are done, I will run them through other marketing teammates
I spent most of my day working on the campus fair agenda such as organizing my volunteers, getting the rain plans ready, deciding shifts for the volunteers, deciding on the prizes etc. However the planning would not have been successful without my team members
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IMAN
Gillespie's Alogorithm and Interface
This week Afshin is gone to Mathematica conference in US. Afshin is supposed to work on the new signalling system model (AI-2 signaling system) and I am reading some papers about Gillespie’s algorithm. Gillespie’s algorithm brings randomness for our model and makes our membranes dynamic. This algorithm has been tested many times and it is proven that Gillespie’s algorithm is a suitable function that could be used to model biological systems. Since this algorithm was set to work with a single compartment, we had to manipulate it in order to use it for multicompartment systems. Afshin has done a fantastic job and implemented that in Mathematica and now I am learning how this algorithm works as it is a key for learning the entire model. On the other hand, there are so many functions involved in our simulation that I tried to learn about during this week, so I could be more involved in the new model which is intended to simulate AI-2 signalling system.
I also worked on a user friendly interface that would be used for our model. In this interface the users type in the information needed to run the simulation and the get the results in an organized way. They are able to run the system with different numbers of cells and they can choose what kind of results (graphs, charts, patterns, and visualization) they want to observe at the end of their simulation.
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JAMIE
Descriptive Title of What You're Doing
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JEREMY
Descriptive Title of What You're Doing
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KATIE
Continuation of June 4th
I am continuing to change the PCR machine script so that it uses dialog boxes instead of the chat window and I have named the objects that are rezzed from the PCR machine. Since it is possible to give items directly to an avatar’s inventory I believe I will do this instead of rezzing the object later on, which at this time is a random object selected from my own inventory and means nothing.
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KEVIN
Competent cells, and Preparation for University of Calgary Campus Fair on June 6th
Competent cells
Competent TOP10 cells are regularly required in our labs because they are used to transform most of our plasmids. In order to make TOP10 cells competent, we need to go through several cycles of heat and cold shocking them, and exposing them to CaCl 2. This pokes holes in their membrane, which allows plasmids to move through. These competent cells were then verified via transformation of pBluescript, which are very small and easy for cells to uptake.
Figure 1. Verification of competent cells via transformation of pBluescript
Preparation of the campus fair
Prepared for the campus fair by making bacteria with art and drawing posters.
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MANDY
Descriptive Title of What You're Doing
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PATRICK
Descriptive Title of What You're Doing
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PRIMA
Campus Fair Arrangment
We visit Michael's to buy crafts and decorations for the iGEM Campus Fair. We organized craft activities, pipetting competitions and raffle draws for kids of different age groups. We designed craft bacterias, made displays and outlined the activity plans for the day. We made up schedules, shifts for volunteers and planned for the big day!
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STEFAN
The Synthetic Kingdom
The area I will be working on within our island is called the Synthetic Kingdom. It will include some interactive applications of synthetic biology and will show people what is possible. Most of all, it will make learning fun and get people interested in synthetic biology and iGEM!. I've been making bacteria all week that will roam around the underwater portion of the island. The scripts inside will allow them to move freely and a highly advanced swarming script was put in some bacteria (not made by me but modified to suit what I am working on).
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VICKI
Outreach focus: preparation for campus fair
All other activities were suspended so that we could finish preparing our display for the campus fair. With this activity, we are trying to appeal to what we hope will be our next generation of synthetic biologists and genetic engineers. Our focus will be on entertaining and inciting interest in the children, while also garnering enthusiasm among the parents.
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