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| - | June 19, 2009
| + | JUNE 19, 2009 |
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| | <div class="heading"> | | <div class="heading"> |
| - | Descriptive Title of What You’re Doing
| + | Enzyme Digestion with XbaI |
| | </div> | | </div> |
| | <br> | | <br> |
| | <div class="desc"> | | <div class="desc"> |
| | </html> | | </html> |
| - | WIKI CODING HERE
| + | * 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. |
| | + | |
| | <html> | | <html> |
| | </div> | | </div> |
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| | </html> | | </html> |
| | Looked at papers : | | Looked at papers : |
| - | <br>Deterministic characterization of stochastic genetic circuits
| + | *Deterministic characterization of stochastic genetic circuits |
| - | <br>Mathematical Modeling of Genetic Regulatory Networks
| + | *Mathematical Modeling of Genetic Regulatory Networks |
| - | <br>Protein-protein interactions and cellular regulation
| + | *Protein-protein interactions and cellular regulation |
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| | <br> | | <br> |
| | <div class="heading"> | | <div class="heading"> |
| - | Descriptive Title of What You're Doing
| + | Bake Sale Preparations |
| | </div> | | </div> |
| | <br> | | <br> |
| | <div class="desc"> | | <div class="desc"> |
| | </html> | | </html> |
| - | WIKI CODING HERE
| + | Today I spent some time cleaning up the classroom and preparing iGEM bake sale posters for our bake sale next week. We also made smaller posters and hung them up around the health science center. |
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| - | Today we had our team presentaions. I presented on behalf of the Human Practices aspect of our project. | + | Today we had our team presentations. I presented on behalf of the Human Practices aspect of our project. |
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| | <br> | | <br> |
| | <div class="heading"> | | <div class="heading"> |
| - | Descriptive Title of What You're Doing
| + | Moving Toward an Efficient Simulation |
| | </div> | | </div> |
| | <br> | | <br> |
| | <div class="desc"> | | <div class="desc"> |
| | </html> | | </html> |
| - | WIKI CODING HERE
| + | 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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| | <div class="heading"> | | <div class="heading"> |
| - | Descriptive Title of What You're Doing
| + | Continued Construction of Signalling Circuit |
| | </div> | | </div> |
| | <br> | | <br> |
| | <div class="desc"> | | <div class="desc"> |
| | </html> | | </html> |
| - | WIKI CODING HERE
| + | luxOU (XbaI) C2 and luxOU (EcoRI) C1 were selected for continued construction. The overall goal of building the construct of BBa_B0015-BBa_R0040-luxOU-BBa_B0015 was segmented into building (1) BBa_B0015-BBa_R0040 and (2) luxOU-BBa_B0015. BBa_B0015-BBa_R0040 was constructed in psB1AK3 and luxOU-BBa_B0015 was constructed in psB1AC3. |
| | + | |
| | + | (1) BBa_B0015-BBa_R0040 |
| | + | Digest BBa_B0015 with ''Spe''I and ''Pst''I and BBa_R0040 with ''Xba''I and ''Pst''I (Invitrogen, CA). Phosphatase treatment, ligation and transformation into TOP10 cells. |
| | + | |
| | + | (2) luxOU-BBa_B0015 |
| | + | Digest luxOU with ''Spe''I and ''Pst''I and BBa_B0015 with ''Xba''I and ''Pst''I (Invitrogen, CA). Phosphatase treatment, ligation and transformation into TOP10 cells. |
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| | <br> | | <br> |
| | <div class="heading"> | | <div class="heading"> |
| - | Descriptive Title of What You're Doing
| + | Restriction Digest Redo to verify presence of LuxPQ in psB1AK3 |
| | </div> | | </div> |
| | <br> | | <br> |
| | <div class="desc"> | | <div class="desc"> |
| | </html> | | </html> |
| - | WIKI CODING HERE
| + | Purpose: verify the presence of LuxPQ in psB1AK3. The pure DNA was cut with the following combinations of enzymes: EcoRI and PstI, XbaI and SpeI, NotI. The following gel depicts the RD products as they have been run on a 0.8% agarose gel – uncut plasmid was run this time. We expect to see two bands: one at 3.2kb (vector – psB1AK3) and one at 3.8kb (luxPQ). We also expect to see all the same sizes for each of the cuts (if all the restriction sites are there). It becomes clear that we do not see what is expected, and we must thus look into other verification techniques to see if LuxPQ is in the BBK vector (specifically PCR). |
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| - | <html>
| + | [[Image:2009.06.19.luxPQ_RD_Redo(E+P_X+S_ N).png|700px]] |
| - | </div>
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| - | </td>
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| - | </tr>
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| - | | + | |
| - | <tr>
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| - | <td height="10px" bgcolor="#222222">
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| - | </td>
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| - | </tr>
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| - | | + | |
| - | <tr>
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| - | <td>
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| - | <a name="Katie"></a>
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| - | <br>
| + | |
| - | <div class="heading">
| + | |
| - | KATIE
| + | |
| - | </div>
| + | |
| - | <br>
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| - | <div class="heading">
| + | |
| - | Descriptive Title of What You're Doing
| + | |
| - | </div>
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| - | <br>
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| - | <div class="desc">
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| - | </html>
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| - | WIKI CODING HERE
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| - | <a name="Mandy"></a> | + | <a name="Patrick"></a> |
| | <br> | | <br> |
| | <div class="heading"> | | <div class="heading"> |
| - | MANDY
| + | PATRICK |
| | </div> | | </div> |
| | <br> | | <br> |
| | <div class="heading"> | | <div class="heading"> |
| - | Descriptive Title of What You're Doing
| + | HUD: Heads Up Display |
| | </div> | | </div> |
| | <br> | | <br> |
| | <div class="desc"> | | <div class="desc"> |
| - | </html> | + | </html>Retrospective Notebook: This entry was not written on this day, but derived later from working notes I made that day. |
| - | WIKI CODING HERE
| + | |
| | | | |
| - | <html>
| + | Began working on the biobrick simulator HUD. This would be a little display screen that sits in one corner of your second life window, and is where a huge part of the biobrick simulator 'lives'. It gives access to levels, parts, biobrick device building tools, unbind commands, help files, all sorts of guidance. |
| - | </div>
| + | |
| - | </td>
| + | |
| - | </tr>
| + | |
| | | | |
| - | <tr>
| + | I knew that I would need to display all sorts of textual information on this display, so I began looking at a whiteboard object that someone else in the team had found. This whiteboard (called xyzzy-text, and available for free) could take a message sent to it by a user, and translate that into a series of textures on its surface encoding the letters of the message. This is *extremely* cool. |
| - | <td height="10px" bgcolor="#222222">
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| - | </td>
| + | |
| - | </tr>
| + | |
| | | | |
| - | <tr>
| + | It actually works using only a single texture (image file), containing all the letters of the alphabet, and symbols for punctuation besides. Then, based on the input sentence, it calculates which part of that image has the symbol we want to display, and transfers those coordinates to SL's rendering system. The script actually controls a number of display tiles, arrayed in rows columns, giving each the coordinates for one character in the sentence we wanted to display. |
| - | <td>
| + | |
| - | <a name="Patrick"></a>
| + | I wound up not using very much of the xyzzy-text code, since I knew I would have to edit it a lot to implement the features the biobrick simulator HUD needs, all while not using most of the features it already had. It made more sense to start from a the minimum of what I would require; I did keep a few critical pieces of the whiteboard though: texture with all the characters on it, and the function to calculate the coordinates in that texture from a string of letters. These two parts were crucial for displaying text in the HUD, and it would have taken me a very very long time to develop anything as good. |
| - | <br>
| + | |
| - | <div class="heading">
| + | Xyzzy-text actually has a more advanced text display function that would have been nice to use, but that I wasn't able to understand whatsoever. The system I borrowed displays a single letter per tile, so on the biobricker's 8x15 display I can have up to 120 letters or symbols. But xyzzy-text actually has a second more advanced text display system, that displays *two* characters per tile, basically doubling the resolution. This makes much better use of your screen's real estate, and the HUD could definitely use a few more letters here and there! But the cost of this system is greater complexity: each tile can only display a single texture at a time (or a small part of one, as the simple xyzzy-text system uses). So, we can't simply take the part of the texture for letter A and glue it to the part for letter Z. To display two characters per tile, we need to generate textures with every single possible two character permutation! And then, we need to write code to break the input sentence into pairs of letters, compute which texture and at what location inside that texture has the two letter pair we're looking for, and send those coordinates to the tile object for display. |
| - | PATRICK
| + | |
| - | </div>
| + | 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. |
| - | <br>
| + | |
| - | <div class="heading">
| + | |
| - | Descriptive Title of What You're Doing
| + | |
| - | </div>
| + | |
| - | <br>
| + | |
| - | <div class="desc">
| + | |
| - | </html>
| + | |
| - | WIKI CODING HERE
| + | |
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| | [[Image:Calgary Sculpty_001.png|700px]] | | [[Image:Calgary Sculpty_001.png|700px]] |
| | </center> | | </center> |
| - |
| |
| | | | |
| | <html> | | <html> |
|
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CAROL
Enzyme Digestion 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.
|
|
|
CHINMOYEE
Research into Deterministic modelling
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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EMILY
Bake Sale Preparations
Today I spent some time cleaning up the classroom and preparing iGEM bake sale posters for our bake sale next week. We also made smaller posters and hung them up around the health science center.
|
|
|
FAHD
Team Presentation today
Today we had our team presentations. I presented on behalf of the Human Practices aspect of our project.
|
|
|
IMAN
Moving Toward an Efficient Simulation
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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JAMIE
Continued Construction of Signalling Circuit
luxOU (XbaI) C2 and luxOU (EcoRI) C1 were selected for continued construction. The overall goal of building the construct of BBa_B0015-BBa_R0040-luxOU-BBa_B0015 was segmented into building (1) BBa_B0015-BBa_R0040 and (2) luxOU-BBa_B0015. BBa_B0015-BBa_R0040 was constructed in psB1AK3 and luxOU-BBa_B0015 was constructed in psB1AC3.
(1) BBa_B0015-BBa_R0040
Digest BBa_B0015 with SpeI and PstI and BBa_R0040 with XbaI and PstI (Invitrogen, CA). Phosphatase treatment, ligation and transformation into TOP10 cells.
(2) luxOU-BBa_B0015
Digest luxOU with SpeI and PstI and BBa_B0015 with XbaI and PstI (Invitrogen, CA). Phosphatase treatment, ligation and transformation into TOP10 cells.
|
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JEREMY
Restriction Digest Redo to verify presence of LuxPQ in psB1AK3
Purpose: verify the presence of LuxPQ in psB1AK3. The pure DNA was cut with the following combinations of enzymes: EcoRI and PstI, XbaI and SpeI, NotI. The following gel depicts the RD products as they have been run on a 0.8% agarose gel – uncut plasmid was run this time. We expect to see two bands: one at 3.2kb (vector – psB1AK3) and one at 3.8kb (luxPQ). We also expect to see all the same sizes for each of the cuts (if all the restriction sites are there). It becomes clear that we do not see what is expected, and we must thus look into other verification techniques to see if LuxPQ is in the BBK vector (specifically PCR).
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KEVIN
Weekly meeting of teams
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PATRICK
HUD: Heads Up Display
Retrospective Notebook: This entry was not written on this day, but derived later from working notes I made that day.
Began working on the biobrick simulator HUD. This would be a little display screen that sits in one corner of your second life window, and is where a huge part of the biobrick simulator 'lives'. It gives access to levels, parts, biobrick device building tools, unbind commands, help files, all sorts of guidance.
I knew that I would need to display all sorts of textual information on this display, so I began looking at a whiteboard object that someone else in the team had found. This whiteboard (called xyzzy-text, and available for free) could take a message sent to it by a user, and translate that into a series of textures on its surface encoding the letters of the message. This is *extremely* cool.
It actually works using only a single texture (image file), containing all the letters of the alphabet, and symbols for punctuation besides. Then, based on the input sentence, it calculates which part of that image has the symbol we want to display, and transfers those coordinates to SL's rendering system. The script actually controls a number of display tiles, arrayed in rows columns, giving each the coordinates for one character in the sentence we wanted to display.
I wound up not using very much of the xyzzy-text code, since I knew I would have to edit it a lot to implement the features the biobrick simulator HUD needs, all while not using most of the features it already had. It made more sense to start from a the minimum of what I would require; I did keep a few critical pieces of the whiteboard though: texture with all the characters on it, and the function to calculate the coordinates in that texture from a string of letters. These two parts were crucial for displaying text in the HUD, and it would have taken me a very very long time to develop anything as good.
Xyzzy-text actually has a more advanced text display function that would have been nice to use, but that I wasn't able to understand whatsoever. The system I borrowed displays a single letter per tile, so on the biobricker's 8x15 display I can have up to 120 letters or symbols. But xyzzy-text actually has a second more advanced text display system, that displays *two* characters per tile, basically doubling the resolution. This makes much better use of your screen's real estate, and the HUD could definitely use a few more letters here and there! But the cost of this system is greater complexity: each tile can only display a single texture at a time (or a small part of one, as the simple xyzzy-text system uses). So, we can't simply take the part of the texture for letter A and glue it to the part for letter Z. To display two characters per tile, we need to generate textures with every single possible two character permutation! And then, we need to write code to break the input sentence into pairs of letters, compute which texture and at what location inside that texture has the two letter pair we're looking for, and send those coordinates to the tile object for display.
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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PRIMA
Bake Sale posters
Today, the artistic members of the team began designing eye-catching posters for the bake sale on Monday. While the artists were busy drawing, the rest of the team divided up their shifts for the sale, colored posters and helped to clean up the class room. We made two giant posters and put up posters all around the building and the Health Science campus.
We also emailed the BHSc coordinator to send out an email to all the BHSc students to advertise our bake sale.
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STEFAN
Stations!
so I've developed some cool things over the past few days. These are:
- A collision script to be used when bacteria collides with oil (mist maker turned black) which is the foundation of the oil cleanup game
- Command script which allows actions to be carried out through chat (type colicin in chat and it will make the bacteria stop and turn red)
- A bacteria that makes vitamins pop out of it when you click
I have also been messing around with some 3D modeling programs so I can make some irregular shapes to import into Second Life. These are called sculpties and will be useful for making rod shaped bacteria.
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VICKI
Convocation ceremonies
...and as such, I did not work on the project today.
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