UIUC-Illinois-Software/7 August 2010

From 2010.igem.org

(Difference between revisions)
(→August 1 – August 7)
 
(One intermediate revision not shown)
Line 2: Line 2:
=Weekly Lab Notebook=
=Weekly Lab Notebook=
===August 1 – August 7===
===August 1 – August 7===
 +
 +
'''Colin''' -
 +
 +
'''Jeremy''' - This week was consumed mostly with move-in and various fundraisers, including the Dip'n Dots sale. I devoted what coding time I had to the list of short tasks that builds up.
 +
 +
'''Anna''' - Continued on the COBRA script, looked more deeply into the COBRA functions as well. I will need to install everything on the server. How should I change the bound values? What sorts of boundaries should I set for the FVA, also how can I easily find reaction rates. 
 +
"Certain safety precautions must be taken in order to ensure that an organism does not grow rapidly or multiply out of control and upset the order of balance in an environment. A safeguard to prevent this scenario could be to analyze the balance of adenosine tri-phosphate(ATP) produced. ATP is the energy within a cell and a majority of what it relies on to flourish. If the energy production is too high, the organism may be too dominant in its environment. If energy production is too low, it may be too difficult to keep the organism alive. By limiting ATP produced we lessen the chances of a cell growing vigorously and being a potential danger to the environment. The actual means to prevent this is by creating a script that will analyze ATP metabolism of an organism and then engineer it so that it works under minimal ATP constraints thereby being restrained from growing out of control. Ideally, ATP consumption and production should be adjusted so that the cell can fulfill its purpose and then die off shortly after. " COBRA can do this!!

Latest revision as of 03:40, 28 October 2010

presenting the 2010 UIUC Software Team!

      • The notebook is organized into weeks. Click on the Saturday of each week to view that week's notebook entry
May
MTWTFSS
          [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/1_May_2010&action=edit 1] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/2_May_2010&action=edit 2]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/3_May_2010&action=edit 3] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/4_May_2010&action=edit 4] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/5_May_2010&action=edit 5] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/6_May_2010&action=edit 6] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/7_May_2010&action=edit 7] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/8_May_2010&action=edit 8] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/9_May_2010&action=edit 9]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/10_May_2010&action=edit 10] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/11_May_2010&action=edit 11] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/12_May_2010&action=edit 12] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/13_May_2010&action=edit 13] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/14_May_2010&action=edit 14] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/15_May_2010&action=edit 15] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/16_May_2010&action=edit 16]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/17_May_2010&action=edit 17] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/18_May_2010&action=edit 18] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/19_May_2010&action=edit 19] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/20_May_2010&action=edit 20] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/21_May_2010&action=edit 21] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/22_May_2010&action=edit 22] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/23_May_2010&action=edit 23]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/24_May_2010&action=edit 24] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/25_May_2010&action=edit 25] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/26_May_2010&action=edit 26] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/27_May_2010&action=edit 27] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/28_May_2010&action=edit 28] [http://2010.igem.org/UIUC-Illinois-Software/29_May_2010 29] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/30_May_2010&action=edit 30]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/31_May_2010&action=edit 31]
June
MTWTFSS
  [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/1_June_2010&action=edit 1] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/2_June_2010&action=edit 2] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/3_June_2010&action=edit 3] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/4_June_2010&action=edit 4] [http://2010.igem.org/UIUC-Illinois-Software/5_June_2010 5] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/6_June_2010&action=edit 6]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/7_June_2010&action=edit 7] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/8_June_2010&action=edit 8] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/9_June_2010&action=edit 9] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/10_June_2010&action=edit 10] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/11_June_2010&action=edit 11] [http://2010.igem.org/UIUC-Illinois-Software/12_June_2010 12] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/13_June_2010&action=edit 13]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/14_June_2010&action=edit 14] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/15_June_2010&action=edit 15] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/16_June_2010&action=edit 16] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/17_June_2010&action=edit 17] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/18_June_2010&action=edit 18] [http://2010.igem.org/UIUC-Illinois-Software/19_June_2010 19] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/20_June_2010&action=edit 20]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/21_June_2010&action=edit 21] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/22_June_2010&action=edit 22] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/23_June_2010&action=edit 23] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/24_June_2010&action=edit 24] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/25_June_2010&action=edit 25] [http://2010.igem.org/UIUC-Illinois-Software/26_June_2010 26] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/27_June_2010&action=edit 27]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/28_June_2010&action=edit 28] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/29_June_2010&action=edit 29] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/30_June_2010&action=edit 30]
July
MTWTFSS
      [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/1_July_2010&action=edit 1] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/2_July_2010&action=edit 2] [http://2010.igem.org/UIUC-Illinois-Software/3_July_2010 3] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/4_July_2010&action=edit 4]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/5_July_2010&action=edit 5] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/6_July_2010&action=edit 6] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/7_July_2010&action=edit 7] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/8_July_2010&action=edit 8] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/9_July_2010&action=edit 9] [http://2010.igem.org/UIUC-Illinois-Software/10_July_2010 10] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/11_July_2010&action=edit 11]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/12_July_2010&action=edit 12] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/13_July_2010&action=edit 13] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/14_July_2010&action=edit 14] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/15_July_2010&action=edit 15] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/16_July_2010&action=edit 16] [http://2010.igem.org/UIUC-Illinois-Software/17_July_2010 17] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/18_July_2010&action=edit 18]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/19_July_2010&action=edit 19] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/20_July_2010&action=edit 20] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/21_July_2010&action=edit 21] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/22_July_2010&action=edit 22] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/23_July_2010&action=edit 23] [http://2010.igem.org/UIUC-Illinois-Software/24_July_2010 24] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/25_July_2010&action=edit 25]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/26_July_2010&action=edit 26] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/27_July_2010&action=edit 27] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/28_July_2010&action=edit 28] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/29_July_2010&action=edit 29] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/30_July_2010&action=edit 30] [http://2010.igem.org/UIUC-Illinois-Software/31_July_2010 31]
August
MTWTFSS
            [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/1_August_2010&action=edit 1]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/2_August_2010&action=edit 2] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/3_August_2010&action=edit 3] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/4_August_2010&action=edit 4] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/5_August_2010&action=edit 5] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/6_August_2010&action=edit 6] [http://2010.igem.org/UIUC-Illinois-Software/7_August_2010 7] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/8_August_2010&action=edit 8]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/9_August_2010&action=edit 9] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/10_August_2010&action=edit 10] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/11_August_2010&action=edit 11] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/12_August_2010&action=edit 12] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/13_August_2010&action=edit 13] [http://2010.igem.org/UIUC-Illinois-Software/14_August_2010 14] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/15_August_2010&action=edit 15]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/16_August_2010&action=edit 16] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/17_August_2010&action=edit 17] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/18_August_2010&action=edit 18] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/19_August_2010&action=edit 19] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/20_August_2010&action=edit 20] [http://2010.igem.org/UIUC-Illinois-Software/21_August_2010 21] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/22_August_2010&action=edit 22]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/23_August_2010&action=edit 23] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/24_August_2010&action=edit 24] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/25_August_2010&action=edit 25] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/26_August_2010&action=edit 26] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/27_August_2010&action=edit 27] [http://2010.igem.org/UIUC-Illinois-Software/28_August_2010 28] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/29_August_2010&action=edit 29]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/30_August_2010&action=edit 30] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/31_August_2010&action=edit 31]
September
MTWTFSS
    [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/1_September_2010&action=edit 1] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/2_September_2010&action=edit 2] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/3_September_2010&action=edit 3] [http://2010.igem.org/UIUC-Illinois-Software/4_September_2010 4] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/5_September_2010&action=edit 5]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/6_September_2010&action=edit 6] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/7_September_2010&action=edit 7] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/8_September_2010&action=edit 8] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/9_September_2010&action=edit 9] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/10_September_2010&action=edit 10] [http://2010.igem.org/UIUC-Illinois-Software/11_September_2010 11] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/12_September_2010&action=edit 12]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/13_September_2010&action=edit 13] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/14_September_2010&action=edit 14] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/15_September_2010&action=edit 15] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/16_September_2010&action=edit 16] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/17_September_2010&action=edit 17] [http://2010.igem.org/UIUC-Illinois-Software/18_September_2010 18] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/19_September_2010&action=edit 19]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/20_September_2010&action=edit 20] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/21_September_2010&action=edit 21] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/22_September_2010&action=edit 22] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/23_September_2010&action=edit 23] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/24_September_2010&action=edit 24] [http://2010.igem.org/UIUC-Illinois-Software/25_September_2010 25] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/26_September_2010&action=edit 26]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/27_September_2010&action=edit 27] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/28_September_2010&action=edit 28] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/29_September_2010&action=edit 29] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/30_September_2010&action=edit 30]
October
MTWTFSS
        [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/1_October_2010&action=edit 1] [http://2010.igem.org/UIUC-Illinois-Software/2_October_2010 2] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/3_October_2010&action=edit 3]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/4_October_2010&action=edit 4] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/5_October_2010&action=edit 5] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/6_October_2010&action=edit 6] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/7_October_2010&action=edit 7] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/8_October_2010&action=edit 8] [http://2010.igem.org/UIUC-Illinois-Software/9_October_2010 9] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/10_October_2010&action=edit 10]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/11_October_2010&action=edit 11] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/12_October_2010&action=edit 12] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/13_October_2010&action=edit 13] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/14_October_2010&action=edit 14] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/15_October_2010&action=edit 15] [http://2010.igem.org/UIUC-Illinois-Software/16_October_2010 16] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/17_October_2010&action=edit 17]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/18_October_2010&action=edit 18] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/19_October_2010&action=edit 19] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/20_October_2010&action=edit 20] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/21_October_2010&action=edit 21] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/22_October_2010&action=edit 22] [http://2010.igem.org/UIUC-Illinois-Software/23_October_2010 23] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/24_October_2010&action=edit 24]
[http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/25_October_2010&action=edit 25] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/26_October_2010&action=edit 26] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/27_October_2010&action=edit 27] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/28_October_2010&action=edit 28] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/29_October_2010&action=edit 29] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/30_October_2010&action=edit 30] [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/31_October_2010&action=edit 31]

Weekly Lab Notebook

August 1 – August 7

Colin -

Jeremy - This week was consumed mostly with move-in and various fundraisers, including the Dip'n Dots sale. I devoted what coding time I had to the list of short tasks that builds up.

Anna - Continued on the COBRA script, looked more deeply into the COBRA functions as well. I will need to install everything on the server. How should I change the bound values? What sorts of boundaries should I set for the FVA, also how can I easily find reaction rates. "Certain safety precautions must be taken in order to ensure that an organism does not grow rapidly or multiply out of control and upset the order of balance in an environment. A safeguard to prevent this scenario could be to analyze the balance of adenosine tri-phosphate(ATP) produced. ATP is the energy within a cell and a majority of what it relies on to flourish. If the energy production is too high, the organism may be too dominant in its environment. If energy production is too low, it may be too difficult to keep the organism alive. By limiting ATP produced we lessen the chances of a cell growing vigorously and being a potential danger to the environment. The actual means to prevent this is by creating a script that will analyze ATP metabolism of an organism and then engineer it so that it works under minimal ATP constraints thereby being restrained from growing out of control. Ideally, ATP consumption and production should be adjusted so that the cell can fulfill its purpose and then die off shortly after. " COBRA can do this!!

Retrieved from "http://2010.igem.org/UIUC-Illinois-Software/7_August_2010"