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Team:Calgary/19 June 2009
From 2009.igem.org
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* To ensure that the site is successfully mutated, the mutated plasmid (after mini-prep from overnight cultures) was digested with XbaI. | * To ensure that the site is successfully mutated, the mutated plasmid (after mini-prep from overnight cultures) was digested with XbaI. | ||
* 0.6% agarose gel showed that there is only one 6KB band, which suggests that the site is successfully mutated. Since there is no positive control, will repeat this procedure after the weekend to ensure that site is mutated before sequencing. | * 0.6% agarose gel showed that there is only one 6KB band, which suggests that the site is successfully mutated. Since there is no positive control, will repeat this procedure after the weekend to ensure that site is mutated before sequencing. | ||
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Looked at papers : | Looked at papers : | ||
| - | + | *Deterministic characterization of stochastic genetic circuits | |
| - | + | *Mathematical Modeling of Genetic Regulatory Networks | |
| - | + | *Protein-protein interactions and cellular regulation | |
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| - | Today we had our team | + | Today we had our team presentations. I presented on behalf of the Human Practices aspect of our project. |
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The new model for AI-2 signalling system is written by Afshin in the period of Mathematica conference. The way this notebook works is different than the old model for AHL signalling system. When a simulation is executed in this model, the results are written in a text file and then the text file is read by other functions to demonstrate the results. In this way, less memory is used and the simulation is quit faster. However, the text file could be very huge if the simulation runs for thousands steps and as a result it might be really time consuming to extract the results out of it. I have worked on this file this week. Now, a summary of the simulation is written in the file and the simulation runs faster and smoother. The reason that we care a lot about the speed of the model is, we eventually would like to run the system with hundreds cells for thousands steps and in order to do so, we need the simulation to work very efficient. I also worked on extracting graphs out of the simulation. We will have two types of graphs. First type will demonstrate the change of concentration for each element in all the cells, and second type shows the change of concentration of each element in each cell. First type could be used to observe “emergent properties” whereas second type is ideal to see the trend of each cell by itself. I also had two meetings this week. One with iGEM people on Friday and the second one with Lindsay project on Thursday. | The new model for AI-2 signalling system is written by Afshin in the period of Mathematica conference. The way this notebook works is different than the old model for AHL signalling system. When a simulation is executed in this model, the results are written in a text file and then the text file is read by other functions to demonstrate the results. In this way, less memory is used and the simulation is quit faster. However, the text file could be very huge if the simulation runs for thousands steps and as a result it might be really time consuming to extract the results out of it. I have worked on this file this week. Now, a summary of the simulation is written in the file and the simulation runs faster and smoother. The reason that we care a lot about the speed of the model is, we eventually would like to run the system with hundreds cells for thousands steps and in order to do so, we need the simulation to work very efficient. I also worked on extracting graphs out of the simulation. We will have two types of graphs. First type will demonstrate the change of concentration for each element in all the cells, and second type shows the change of concentration of each element in each cell. First type could be used to observe “emergent properties” whereas second type is ideal to see the trend of each cell by itself. I also had two meetings this week. One with iGEM people on Friday and the second one with Lindsay project on Thursday. | ||
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[[Image:2009.06.19.luxPQ_RD_Redo(E+P_X+S_ N).png|700px]] | [[Image:2009.06.19.luxPQ_RD_Redo(E+P_X+S_ N).png|700px]] | ||
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Weekly update. | Weekly update. | ||
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I barely understood how the simple system worked, so trying to make use of the advanced xyzzy text display system was out of the question. But I've learned a lot since early summer, and the limit of 13-14 characters per name for objects is becoming a limitation (how many letters in 'Repressilator'? 13, phew! How about 'TetR Repressable Promoter'?) So, I'll put this on the wishlist for later. | I barely understood how the simple system worked, so trying to make use of the advanced xyzzy text display system was out of the question. But I've learned a lot since early summer, and the limit of 13-14 characters per name for objects is becoming a limitation (how many letters in 'Repressilator'? 13, phew! How about 'TetR Repressable Promoter'?) So, I'll put this on the wishlist for later. | ||
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[[Image:Calgary Sculpty_001.png|700px]] | [[Image:Calgary Sculpty_001.png|700px]] | ||
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Revision as of 06:19, 20 October 2009
UNIVERSITY OF CALGARY
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