Team:Calgary/12 June 2009

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* Spun the cells down from overnight cultures and froze cells overnight for the weekend.  
* Spun the cells down from overnight cultures and froze cells overnight for the weekend.  
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Presented Ander's Modeling examples of the Three Gene Repressilator .
Presented Ander's Modeling examples of the Three Gene Repressilator .
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Looked at the Optimization Toolbox.
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*Had a team meeting where each subproject presented their recent work.  Lab group talked about verification of genes of interest in TOPO vectors, BBK ampliciation PCR and cloning into Biobrick vectors (psB1AC3 and psB1AK3).
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*Had a team meeting where each subproject presented their recent work.  Lab group talked about verification of genes of interest in TOPO vectors, BBK amplification PCR and cloning into Biobrick vectors (psB1AC3 and psB1AK3).
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Today we had our team meeting and I presented on behalf of the Human Practises aspect of our project
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Today we had our team meeting and I presented on behalf of the Human Practices aspect of our project
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As Afshin was away for this week, I worked on various functions involved in the model namely “trippleNumbers”, “calProbibility”, “applyRule”, “updateEnv”, and “simulate”. The first two functions get the information from each membrane and send the information to Gillespie’s algorithm. Then this algorithm chooses a rule which is most likely to occur. The chosen rule applies to the system using “applyRule” function. Then we need to update the system, and inform the other membranes about the rule applied to the system. It is the responsibility of “updateEnv”. I had two meetings this week as well, one with iGEM members and the other one with Lindsay members. I worked on the kidney model for Lindsay project, which I am not going to explain about it here.  
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As Afshin was away for this week, I worked on various functions involved in the model namely “trippleNumbers”, “calProbibility”, “applyRule”, “updateEnv”, and “simulate”. The first two functions get the information from each membrane and send the information to Gillespie’s algorithm. Then this algorithm chooses a rule which is most likely to occur. The chosen rule applies to the system using “applyRule” function. Then we need to update the system, and inform the other membranes about the rule applied to the system. It is the responsibility of “updateEnv”. I had two meetings this week as well, one with iGEM members and the other one with Lindsay members. I worked on the kidney model for Lindsay project, which I am not going to explain about it here.
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JAMIE
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WIKI CODING HERE
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[[Image:2009.06.12.LuxPQ_Gradient_PCR.png|700px]]
[[Image:2009.06.12.LuxPQ_Gradient_PCR.png|700px]]
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No lab experiments were performed
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No lab experiments were performed.
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Second Life Brainstorming
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WIKI CODING HERE
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While continuing my writing of notecards for gel prep, gel electrophoresis, and LB plate prep, we had a mini-SL team meeting in order to list the components we wanted to teach and thus what we wanted to build so we could check things off the list in order to ensure that we completed as much of it as possible by the end of the summer.
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This is the restriction digest component of the construction protocol, which we describe on our protocol page. We attempted the construction with 2 different sets of enzymes: 6 tubes with cuts at XbaI and PstI , and 6 tubes with cuts at EcoRI and PstI. Both were prepared in REact 2 buffer. Once prepared, the tubes were left in the water bath at 37 degrees C for 6.5 hours; heatshocked at 65 degrees C on a heating block to deactivate the restriction enzymes in the tube; and placed in the -20 degrees C freezer.
This is the restriction digest component of the construction protocol, which we describe on our protocol page. We attempted the construction with 2 different sets of enzymes: 6 tubes with cuts at XbaI and PstI , and 6 tubes with cuts at EcoRI and PstI. Both were prepared in REact 2 buffer. Once prepared, the tubes were left in the water bath at 37 degrees C for 6.5 hours; heatshocked at 65 degrees C on a heating block to deactivate the restriction enzymes in the tube; and placed in the -20 degrees C freezer.
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Latest revision as of 02:18, 20 October 2009

University of Calgary

UNIVERSITY OF CALGARY



THIS MONTH

June
MTWTFSS
[http://2009.igem.org/Team:Calgary/1_June_2009 1] [http://2009.igem.org/Team:Calgary/2_June_2009 2] [http://2009.igem.org/Team:Calgary/3_June_2009 3] [http://2009.igem.org/Team:Calgary/4_June_2009 4] [http://2009.igem.org/Team:Calgary/5_June_2009 5] [http://2009.igem.org/Team:Calgary/6_June_2009 6] [http://2009.igem.org/Team:Calgary/7_June_2009 7]
[http://2009.igem.org/Team:Calgary/8_June_2009 8] [http://2009.igem.org/Team:Calgary/9_June_2009 9] [http://2009.igem.org/Team:Calgary/10_June_2009 10] [http://2009.igem.org/Team:Calgary/11_June_2009 11] [http://2009.igem.org/Team:Calgary/12_June_2009 12] [http://2009.igem.org/Team:Calgary/13_June_2009 13] [http://2009.igem.org/Team:Calgary/14_June_2009 14]
[http://2009.igem.org/Team:Calgary/15_June_2009 15] [http://2009.igem.org/Team:Calgary/16_June_2009 16] [http://2009.igem.org/Team:Calgary/17_June_2009 17] [http://2009.igem.org/Team:Calgary/18_June_2009 18] [http://2009.igem.org/Team:Calgary/19_June_2009 19] [http://2009.igem.org/Team:Calgary/20_June_2009 20] [http://2009.igem.org/Team:Calgary/21_June_2009 21]
[http://2009.igem.org/Team:Calgary/22_June_2009 22] [http://2009.igem.org/Team:Calgary/23_June_2009 23] [http://2009.igem.org/Team:Calgary/24_June_2009 24] [http://2009.igem.org/Team:Calgary/25_June_2009 25] [http://2009.igem.org/Team:Calgary/26_June_2009 26] [http://2009.igem.org/Team:Calgary/27_June_2009 27] [http://2009.igem.org/Team:Calgary/28_June_2009 28]
[http://2009.igem.org/Team:Calgary/29_June_2009 29] [http://2009.igem.org/Team:Calgary/30_June_2009 30]


NOTEBOOK PAGE INDEX



CALENDAR

May
MTWTFSS
        [http://2009.igem.org/Team:Calgary/1_May_2009 1] [http://2009.igem.org/Team:Calgary/2_May_2009 2] [http://2009.igem.org/Team:Calgary/3_May_2009 3]
[http://2009.igem.org/Team:Calgary/4_May_2009 4] [http://2009.igem.org/Team:Calgary/5_May_2009 5] [http://2009.igem.org/Team:Calgary/6_May_2009 6] [http://2009.igem.org/Team:Calgary/7_May_2009 7] [http://2009.igem.org/Team:Calgary/8_May_2009 8] [http://2009.igem.org/Team:Calgary/9_May_2009 9] [http://2009.igem.org/Team:Calgary/10_May_2009 10]
[http://2009.igem.org/Team:Calgary/11_May_2009 11] [http://2009.igem.org/Team:Calgary/12_May_2009 12] [http://2009.igem.org/Team:Calgary/13_May_2009 13] [http://2009.igem.org/Team:Calgary/14_May_2009 14] [http://2009.igem.org/Team:Calgary/15_May_2009 15] [http://2009.igem.org/Team:Calgary/16_May_2009 16] [http://2009.igem.org/Team:Calgary/17_May_2009 17]
[http://2009.igem.org/Team:Calgary/18_May_2009 18] [http://2009.igem.org/Team:Calgary/19_May_2009 19] [http://2009.igem.org/Team:Calgary/20_May_2009 20] [http://2009.igem.org/Team:Calgary/21_May_2009 21] [http://2009.igem.org/Team:Calgary/22_May_2009 22] [http://2009.igem.org/Team:Calgary/23_May_2009 23] [http://2009.igem.org/Team:Calgary/24_May_2009 24]
[http://2009.igem.org/Team:Calgary/25_May_2009 25] [http://2009.igem.org/Team:Calgary/26_May_2009 26] [http://2009.igem.org/Team:Calgary/27_May_2009 27] [http://2009.igem.org/Team:Calgary/28_May_2009 28] [http://2009.igem.org/Team:Calgary/29_May_2009 29] [http://2009.igem.org/Team:Calgary/30_May_2009 30] [http://2009.igem.org/Team:Calgary/31_May_2009 31]


June
MTWTFSS
[http://2009.igem.org/Team:Calgary/1_June_2009 1] [http://2009.igem.org/Team:Calgary/2_June_2009 2] [http://2009.igem.org/Team:Calgary/3_June_2009 3] [http://2009.igem.org/Team:Calgary/4_June_2009 4] [http://2009.igem.org/Team:Calgary/5_June_2009 5] [http://2009.igem.org/Team:Calgary/6_June_2009 6] [http://2009.igem.org/Team:Calgary/7_June_2009 7]
[http://2009.igem.org/Team:Calgary/8_June_2009 8] [http://2009.igem.org/Team:Calgary/9_June_2009 9] [http://2009.igem.org/Team:Calgary/10_June_2009 10] [http://2009.igem.org/Team:Calgary/11_June_2009 11] [http://2009.igem.org/Team:Calgary/12_June_2009 12] [http://2009.igem.org/Team:Calgary/13_June_2009 13] [http://2009.igem.org/Team:Calgary/14_June_2009 14]
[http://2009.igem.org/Team:Calgary/15_June_2009 15] [http://2009.igem.org/Team:Calgary/16_June_2009 16] [http://2009.igem.org/Team:Calgary/17_June_2009 17] [http://2009.igem.org/Team:Calgary/18_June_2009 18] [http://2009.igem.org/Team:Calgary/19_June_2009 19] [http://2009.igem.org/Team:Calgary/20_June_2009 20] [http://2009.igem.org/Team:Calgary/21_June_2009 21]
[http://2009.igem.org/Team:Calgary/22_June_2009 22] [http://2009.igem.org/Team:Calgary/23_June_2009 23] [http://2009.igem.org/Team:Calgary/24_June_2009 24] [http://2009.igem.org/Team:Calgary/25_June_2009 25] [http://2009.igem.org/Team:Calgary/26_June_2009 26] [http://2009.igem.org/Team:Calgary/27_June_2009 27] [http://2009.igem.org/Team:Calgary/28_June_2009 28]
[http://2009.igem.org/Team:Calgary/29_June_2009 29] [http://2009.igem.org/Team:Calgary/30_June_2009 30]


July
MTWTFSS
    [http://2009.igem.org/Team:Calgary/1_July_2009 1] [http://2009.igem.org/Team:Calgary/2_July_2009 2] [http://2009.igem.org/Team:Calgary/3_July_2009 3] [http://2009.igem.org/Team:Calgary/4_July_2009 4] [http://2009.igem.org/Team:Calgary/5_July_2009 5]
[http://2009.igem.org/Team:Calgary/6_July_2009 6] [http://2009.igem.org/Team:Calgary/7_July_2009 7] [http://2009.igem.org/Team:Calgary/8_July_2009 8] [http://2009.igem.org/Team:Calgary/9_July_2009 9] [http://2009.igem.org/Team:Calgary/10_July_2009 10] [http://2009.igem.org/Team:Calgary/11_July_2009 11] [http://2009.igem.org/Team:Calgary/12_July_2009 12]
[http://2009.igem.org/Team:Calgary/13_July_2009 13] [http://2009.igem.org/Team:Calgary/14_July_2009 14] [http://2009.igem.org/Team:Calgary/15_July_2009 15] [http://2009.igem.org/Team:Calgary/16_July_2009 16] [http://2009.igem.org/Team:Calgary/17_July_2009 17] [http://2009.igem.org/Team:Calgary/18_July_2009 18] [http://2009.igem.org/Team:Calgary/19_July_2009 19]
[http://2009.igem.org/Team:Calgary/20_July_2009 20] [http://2009.igem.org/Team:Calgary/21_July_2009 21] [http://2009.igem.org/Team:Calgary/22_July_2009 22] [http://2009.igem.org/Team:Calgary/23_July_2009 23] [http://2009.igem.org/Team:Calgary/24_July_2009 24] [http://2009.igem.org/Team:Calgary/25_July_2009 25] [http://2009.igem.org/Team:Calgary/26_July_2009 26]
[http://2009.igem.org/Team:Calgary/27_July_2009 27] [http://2009.igem.org/Team:Calgary/28_July_2009 28] [http://2009.igem.org/Team:Calgary/29_July_2009 29] [http://2009.igem.org/Team:Calgary/30_July_2009 30] [http://2009.igem.org/Team:Calgary/31_July_2009 31]


August
MTWTFSS
          [http://2009.igem.org/Team:Calgary/1_August_2009 1] [http://2009.igem.org/Team:Calgary/2_August_2009 2]
[http://2009.igem.org/Team:Calgary/3_August_2009 3] [http://2009.igem.org/Team:Calgary/4_August_2009 4] [http://2009.igem.org/Team:Calgary/5_August_2009 5] [http://2009.igem.org/Team:Calgary/6_August_2009 6] [http://2009.igem.org/Team:Calgary/7_August_2009 7] [http://2009.igem.org/Team:Calgary/8_August_2009 8] [http://2009.igem.org/Team:Calgary/9_August_2009 9]
[http://2009.igem.org/Team:Calgary/10_August_2009 10] [http://2009.igem.org/Team:Calgary/11_August_2009 11] [http://2009.igem.org/Team:Calgary/12_August_2009 12] [http://2009.igem.org/Team:Calgary/13_August_2009 13] [http://2009.igem.org/Team:Calgary/14_August_2009 14] [http://2009.igem.org/Team:Calgary/15_August_2009 15] [http://2009.igem.org/Team:Calgary/16_August_2009 16]
[http://2009.igem.org/Team:Calgary/17_August_2009 17] [http://2009.igem.org/Team:Calgary/18_August_2009 18] [http://2009.igem.org/Team:Calgary/19_August_2009 19] [http://2009.igem.org/Team:Calgary/20_August_2009 20] [http://2009.igem.org/Team:Calgary/21_August_2009 21] [http://2009.igem.org/Team:Calgary/22_August_2009 22] [http://2009.igem.org/Team:Calgary/23_August_2009 23]
[http://2009.igem.org/Team:Calgary/24_August_2009 24] [http://2009.igem.org/Team:Calgary/25_August_2009 25] [http://2009.igem.org/Team:Calgary/26_August_2009 26] [http://2009.igem.org/Team:Calgary/27_August_2009 27] [http://2009.igem.org/Team:Calgary/28_August_2009 28] [http://2009.igem.org/Team:Calgary/29_August_2009 29] [http://2009.igem.org/Team:Calgary/30_August_2009 30]
[http://2009.igem.org/Team:Calgary/31_August_2009 31]


September
MTWTFSS
  [http://2009.igem.org/Team:Calgary/1_September_2009 1] [http://2009.igem.org/Team:Calgary/2_September_2009 2] [http://2009.igem.org/Team:Calgary/3_September_2009 3] [http://2009.igem.org/Team:Calgary/4_September_2009 4] [http://2009.igem.org/Team:Calgary/5_September_2009 5] [http://2009.igem.org/Team:Calgary/6_September_2009 6]
[http://2009.igem.org/Team:Calgary/7_September_2009 7] [http://2009.igem.org/Team:Calgary/8_September_2009 8] [http://2009.igem.org/Team:Calgary/9_September_2009 9] [http://2009.igem.org/Team:Calgary/10_September_2009 10] [http://2009.igem.org/Team:Calgary/11_September_2009 11] [http://2009.igem.org/Team:Calgary/12_September_2009 12] [http://2009.igem.org/Team:Calgary/13_September_2009 13]
[http://2009.igem.org/Team:Calgary/14_September_2009 14] [http://2009.igem.org/Team:Calgary/15_September_2009 15] [http://2009.igem.org/Team:Calgary/16_September_2009 16] [http://2009.igem.org/Team:Calgary/17_September_2009 17] [http://2009.igem.org/Team:Calgary/18_September_2009 18] [http://2009.igem.org/Team:Calgary/19_September_2009 19] [http://2009.igem.org/Team:Calgary/20_September_2009 20]
[http://2009.igem.org/Team:Calgary/21_September_2009 21] [http://2009.igem.org/Team:Calgary/22_September_2009 22] [http://2009.igem.org/Team:Calgary/23_September_2009 23] [http://2009.igem.org/Team:Calgary/24_September_2009 24] [http://2009.igem.org/Team:Calgary/25_September_2009 25] [http://2009.igem.org/Team:Calgary/26_September_2009 26] [http://2009.igem.org/Team:Calgary/27_September_2009 27]
[http://2009.igem.org/Team:Calgary/28_September_2009 28] [http://2009.igem.org/Team:Calgary/29_September_2009 29] [http://2009.igem.org/Team:Calgary/30_September_2009 30]


October
MTWTFSS
      [http://2009.igem.org/Team:Calgary/1_October_2009 1] [http://2009.igem.org/Team:Calgary/2_October_2009 2] [http://2009.igem.org/Team:Calgary/3_October_2009 3] [http://2009.igem.org/Team:Calgary/4_October_2009 4]
[http://2009.igem.org/Team:Calgary/5_October_2009 5] [http://2009.igem.org/Team:Calgary/6_October_2009 6] [http://2009.igem.org/Team:Calgary/7_October_2009 7] [http://2009.igem.org/Team:Calgary/8_October_2009 8] [http://2009.igem.org/Team:Calgary/9_October_2009 9] [http://2009.igem.org/Team:Calgary/10_October_2009 10] [http://2009.igem.org/Team:Calgary/11_October_2009 11]
[http://2009.igem.org/Team:Calgary/12_October_2009 12] [http://2009.igem.org/Team:Calgary/13_October_2009 13] [http://2009.igem.org/Team:Calgary/14_October_2009 14] [http://2009.igem.org/Team:Calgary/15_October_2009 15] [http://2009.igem.org/Team:Calgary/16_October_2009 16] [http://2009.igem.org/Team:Calgary/17_October_2009 17] [http://2009.igem.org/Team:Calgary/18_October_2009 18]
[http://2009.igem.org/wiki/index.php?title=Team:Calgary/19_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 19] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/20_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 20] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/21_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 21] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/22_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 22] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/23_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 23] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/24_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 24] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/25_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 25]
[http://2009.igem.org/wiki/index.php?title=Team:Calgary/26_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 26] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/27_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 27] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/28_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 28] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/29_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 29] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/30_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 30] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/31_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 31]



JUNE 12, 2009


CAROL

Second Attempt to Plasmid Isolation

  • Spun the cells down from overnight cultures and froze cells overnight for the weekend.


CHINMOYEE

Three Gene Repressilator Presentation

Presented Ander's Modeling examples of the Three Gene Repressilator .

Looked at the Optimization Toolbox.


EMILY

Friday Team Meeting

  • Had a team meeting where each subproject presented their recent work. Lab group talked about verification of genes of interest in TOPO vectors, BBK amplification PCR and cloning into Biobrick vectors (psB1AC3 and psB1AK3).


FAHD

Team Meeting for July 12th 2009

Today we had our team meeting and I presented on behalf of the Human Practices aspect of our project


IMAN

Writing and Learning Functions

As Afshin was away for this week, I worked on various functions involved in the model namely “trippleNumbers”, “calProbibility”, “applyRule”, “updateEnv”, and “simulate”. The first two functions get the information from each membrane and send the information to Gillespie’s algorithm. Then this algorithm chooses a rule which is most likely to occur. The chosen rule applies to the system using “applyRule” function. Then we need to update the system, and inform the other membranes about the rule applied to the system. It is the responsibility of “updateEnv”. I had two meetings this week as well, one with iGEM members and the other one with Lindsay members. I worked on the kidney model for Lindsay project, which I am not going to explain about it here.


JEREMY

Gel of BBK Amplification of LuxPQ

A 0.8% agarose gel was made and the gradient PCR products (see June 11) were ran at 90V. The gel below shows the results, with wells 1-12 having luxPQ template and well 13 being the negative control (water). We can see that all PCR products are of the correct size (~3.8kb = luxPQ).

2009.06.12.LuxPQ Gradient PCR.png


KEVIN

Team meeting

No lab experiments were performed.


MANDY

Second Life Brainstorming

While continuing my writing of notecards for gel prep, gel electrophoresis, and LB plate prep, we had a mini-SL team meeting in order to list the components we wanted to teach and thus what we wanted to build so we could check things off the list in order to ensure that we completed as much of it as possible by the end of the summer.


PATRICK

Stay Put

Retrospective Notebook: This entry was not written on this day, but derived later from working notes I made that day.

Began working on a newer 'stay put' script for the objects, this one changing their physics status when the object is clicked. With physics off, an object hangs frozen in space, and can intersect with other objects without difficulty. With physics on, an object can be dragged around with the mouse, and be made to collide with other objects (but cannot occupy the same space as another!) By default, objects would be nonphysical, and only set to physical when the user needs to move them around. The end result is that all of the objects are *much* less twitchy and glitchy, as the physics engine often makes physical objects pop around.

Began planning out just what material we would need to present within the sim, to get users up to speed for using the biobricks.


PRIMA

Shadowed Vicky with her Restriction digest

We had a team meeting where each iGEM subdivision presented their work for the week.

I shadoewd Vicky wither her Restriction Digest today. Although I did not quite understand her part completely, I tried my best to follow through the procedures and to understand why she was doing what she was doing.

Procedure for RD:

oth the vector and the insert need to have their own separate tube, at least in the beginning. This is important because it allows for clean addition new parts to a the circut

In the Insert Tube...

-600ng of DNA (To figure out the volume, the calculation is 600 / concentration of plasmid. This gives you volume in μL). -Water, so that the volume of DNA and water in the tube is 35 μL -4 μL of React 1 Buffer -0.5 μL of EcoR1 -0.5 μL of Spe1

In the vector Tube...

-250ng of DNA (To figure out the volume, the calculation is 250 / concentration of plasmid. This gives you volume in μL). -Water, so that the volume of DNA and water in the tube is 35 μL -4 μL of React 2 Buffer -0.5 μL of EcoR1 -0.5 μL of Xba1

Put both tubes into the 37°C water bath for one hour. After, place them into the 65°C heating block for 10 minutes. This destroys any enzymes in the tube (which is ok, because by now they’ve done all they need to). Take the insert out, and put it in a -20°C freezer.


STEFAN

More things added into the Synthetic Kingdom

Added a bunch of new bacteria and replicated them...the place is now teeming with life. Started brainstorming some interactive applications of synthetic biology I could showcase.


VICKI

Purification of gradient PCR product

Purpose: to purify the LuxOD47A BBk that was produced yesterday in the gradient PCR

Protocol: Please refer to the protocol page. Concentrations were measured after the product was purified.


Restriction digest of LuxOD47A BBk (insert) and psB1AC3 (vector)

Purpose: The LuxOD47A BBk DNA from yesterday’s gradient PCR is in linear form. This will prepare the ends so that it can be inserted into a BioBrick vector.

Protocol:

This is the restriction digest component of the construction protocol, which we describe on our protocol page. We attempted the construction with 2 different sets of enzymes: 6 tubes with cuts at XbaI and PstI , and 6 tubes with cuts at EcoRI and PstI. Both were prepared in REact 2 buffer. Once prepared, the tubes were left in the water bath at 37 degrees C for 6.5 hours; heatshocked at 65 degrees C on a heating block to deactivate the restriction enzymes in the tube; and placed in the -20 degrees C freezer.