IllinoisTools/1 August 2009

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== 7/26-8/1 ==
== 7/26-8/1 ==
'''Donny'''
'''Donny'''
 +
I attempted to use RPAIR data as another potential weight (with the help of Kanishka's research). One helpful thing was to read about other similar applications to determine their weighting scheme. I rearranged our class models to incorporate stoichiometry with Palak and modified the database accordingly.
'''Riyad'''
'''Riyad'''
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'''Palak'''
'''Palak'''
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This week I spent time getting stoichiometry information about the into our database. We decided to incorporate a stoichiometric matrix as part of our
+
This week I spent time getting stoichiometry information about the into our database. We decided to incorporate a stoichiometric matrix as part of our program output. I also rearranged some of our models so in order to incorporate the stoichiometric information properly. 
 +
 
 +
'''Kanishka'''
 +
 
 +
I read articles to find a weighing system and found how to incorporate weights with different point values.  I also spent time thinking about ideas for the webpage.
 +
 
 +
'''Nate'''
 +
 
 +
In the beginning of the week, I worked on examining certain reactions that required multiple enzymes to facilitate them.  One reaction had as many as 66 different types of enzymes needed!!  This is a little ambiguous point about KEGG and/or the naming of enzymes.  It is hard to discern if the types of enzymes listed for a reaction are either all needed (they are all subunits), or some of them are interchangeable (the organism makes two different enzymes that facilitate the same reaction).  After reporting my findings to Donny, I set work on writing code that would ideally export the data obtained with IMPtools in a xgmml file format.  Xgmml is a coding language that specifies a graph of nodes and edges.  This type of code is recognized by Cytoscape, a program that we had looked at in the beginning of the summer.  We have recently decided to use cytoscape for graphically representing the outputs of IMPtools. I was very successful with my program, as it makes a nice, easy to see graph of any reaction pathway.  I sent this code to Donny, so that he may work it into our website.  This has been a super fun summer!

Latest revision as of 18:36, 21 October 2009

Notebookanimationillinoistools.gif

      • Note: Our notebook is organized in a weekly fashion. Click on the Saturday of every week to view the notes from the previous week.


May
MTWTFSS
        [http://2009.igem.org/IllinoisTools/1_May_2009 1] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/2_May_2009&action=edit 2] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/3_May_2009&action=edit 3]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/4_May_2009&action=edit 4] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/5_May_2009&action=edit 5] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/6_May_2009&action=edit 6] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/7_May_2009&action=edit 7] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/8_May_2009&action=edit 8] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/9_May_2009&action=edit 9] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/10_May_2009&action=edit 10]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/11_May_2009&action=edit 11] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/12_May_2009&action=edit 12] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/13_May_2009&action=edit 13] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/14_May_2009&action=edit 14] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/15_May_2009&action=edit 15] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/16_May_2009&action=edit 16] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/17_May_2009&action=edit 17]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/18_May_2009&action=edit 18] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/19_May_2009&action=edit 19] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/20_May_2009&action=edit 20] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/21_May_2009&action=edit 21] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/22_May_2009&action=edit 22] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/23_May_2009&action=edit 23] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/24_May_2009&action=edit 24]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/25_May_2009&action=edit 25] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/26_May_2009&action=edit 26] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/27_May_2009&action=edit 27] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/28_May_2009&action=edit 28] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/29_May_2009&action=edit 29] [http://2009.igem.org/IllinoisTools/30_May_2009 30] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/31_May_2009&action=edit 31]
June
MTWTFSS
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/1_June_2009&action=edit 1] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/2_June_2009&action=edit 2] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/3_June_2009&action=edit 3] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/4_June_2009&action=edit 4] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/5_June_2009&action=edit 5] [http://2009.igem.org/IllinoisTools/6_June_2009 6] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/7_June_2009&action=edit 7]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/8_June_2009&action=edit 8] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/9_June_2009&action=edit 9] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/10_June_2009&action=edit 10] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/11_June_2009&action=edit 11] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/12_June_2009&action=edit 12] [http://2009.igem.org/IllinoisTools/13_June_2009 13] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/14_June_2009&action=edit 14]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/15_June_2009&action=edit 15] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/16_June_2009&action=edit 16] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/17_June_2009&action=edit 17] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/18_June_2009&action=edit 18] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/19_June_2009&action=edit 19] [http://2009.igem.org/IllinoisTools/20_June_2009 20] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/21_June_2009&action=edit 21]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/22_June_2009&action=edit 22] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/23_June_2009&action=edit 23] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/24_June_2009&action=edit 24] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/25_June_2009&action=edit 25] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/26_June_2009&action=edit 26] [http://2009.igem.org/IllinoisTools/27_June_2009 27] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/28_June_2009&action=edit 28]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/29_June_2009&action=edit 29] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/30_June_2009&action=edit 30]
July
MTWTFSS
    [http://2009.igem.org/wiki/index.php?title=IllinoisTools/1_July_2009&action=edit 1] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/2_July_2009&action=edit 2] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/3_July_2009&action=edit 3] [http://2009.igem.org/IllinoisTools/4_July_2009 4] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/5_July_2009&action=edit 5]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/6_July_2009&action=edit 6] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/7_July_2009&action=edit 7] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/8_July_2009&action=edit 8] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/9_July_2009&action=edit 9] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/10_July_2009&action=edit 10] [http://2009.igem.org/IllinoisTools/11_July_2009 11] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/12_July_2009&action=edit 12]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/13_July_2009&action=edit 13] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/14_July_2009&action=edit 14] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/15_July_2009&action=edit 15] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/16_July_2009&action=edit 16] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/17_July_2009&action=edit 17] [http://2009.igem.org/IllinoisTools/18_July_2009 18] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/19_July_2009&action=edit 19]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/20_July_2009&action=edit 20] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/21_July_2009&action=edit 21] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/22_July_2009&action=edit 22] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/23_July_2009&action=edit 23] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/24_July_2009&action=edit 24] [http://2009.igem.org/IllinoisTools/25_July_2009 25] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/26_July_2009&action=edit 26]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/27_July_2009&action=edit 27] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/28_July_2009&action=edit 28] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/29_July_2009&action=edit 29] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/30_July_2009&action=edit 30] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/31_July_2009&action=edit 31]
August
MTWTFSS
          [http://2009.igem.org/IllinoisTools/1_August_2009 1] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/2_August_2009&action=edit 2]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/3_August_2009&action=edit 3] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/4_August_2009&action=edit 4] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/5_August_2009&action=edit 5] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/6_August_2009&action=edit 6] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/7_August_2009&action=edit 7] [http://2009.igem.org/IllinoisTools/8_August_2009 8] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/9_August_2009&action=edit 9]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/10_August_2009&action=edit 10] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/11_August_2009&action=edit 11] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/12_August_2009&action=edit 12] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/13_August_2009&action=edit 13] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/14_August_2009&action=edit 14] [http://2009.igem.org/IllinoisTools/15_August_2009 15] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/16_August_2009&action=edit 16]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/17_August_2009&action=edit 17] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/18_August_2009&action=edit 18] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/19_August_2009&action=edit 19] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/20_August_2009&action=edit 20] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/21_August_2009&action=edit 21] [http://2009.igem.org/IllinoisTools/22_August_2009 22] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/23_August_2009&action=edit 23]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/24_August_2009&action=edit 24] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/25_August_2009&action=edit 25] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/26_August_2009&action=edit 26] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/27_August_2009&action=edit 27] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/28_August_2009&action=edit 28] [http://2009.igem.org/IllinoisTools/29_August_2009 29] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/30_August_2009&action=edit 30]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/31_August_2009&action=edit 31]
September
MTWTFSS
  [http://2009.igem.org/wiki/index.php?title=IllinoisTools/1_September_2009&action=edit 1] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/2_September_2009&action=edit 2] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/3_September_2009&action=edit 3] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/4_September_2009&action=edit 4] [http://2009.igem.org/IllinoisTools/5_September_2009 5] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/6_September_2009&action=edit 6]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/7_September_2009&action=edit 7] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/8_September_2009&action=edit 8] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/9_September_2009&action=edit 9] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/10_September_2009&action=edit 10] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/11_September_2009&action=edit 11] [http://2009.igem.org/IllinoisTools/12_September_2009 12] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/13_September_2009&action=edit 13]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/14_September_2009&action=edit 14] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/15_September_2009&action=edit 15] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/16_September_2009&action=edit 16] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/17_September_2009&action=edit 17] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/18_September_2009&action=edit 18] [http://2009.igem.org/IllinoisTools/19_September_2009 19] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/20_September_2009&action=edit 20]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/21_September_2009&action=edit 21] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/22_September_2009&action=edit 22] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/23_September_2009&action=edit 23] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/24_September_2009&action=edit 24] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/25_September_2009&action=edit 25] [http://2009.igem.org/IllinoisTools/26_September_2009 26] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/27_September_2009&action=edit 27]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/28_September_2009&action=edit 28] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/29_September_2009&action=edit 29] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/30_September_2009&action=edit 30]
October
MTWTFSS
      [http://2009.igem.org/wiki/index.php?title=IllinoisTools/1_October_2009&action=edit 1] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/2_October_2009&action=edit 2] [http://2009.igem.org/IllinoisTools/3_October_2009 3] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/4_October_2009&action=edit 4]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/5_October_2009&action=edit 5] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/6_October_2009&action=edit 6] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/7_October_2009&action=edit 7] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/8_October_2009&action=edit 8] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/9_October_2009&action=edit 9] [http://2009.igem.org/IllinoisTools/10_October_2009 10] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/11_October_2009&action=edit 11]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/12_October_2009&action=edit 12] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/13_October_2009&action=edit 13] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/14_October_2009&action=edit 14] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/15_October_2009&action=edit 15] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/16_October_2009&action=edit 16] [http://2009.igem.org/IllinoisTools/17_October_2009 17] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/18_October_2009&action=edit 18]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/19_October_2009&action=edit 19] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/20_October_2009&action=edit 20] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/21_October_2009&action=edit 21] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/22_October_2009&action=edit 22] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/23_October_2009&action=edit 23] [http://2009.igem.org/IllinoisTools/24_October_2009 24] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/25_October_2009&action=edit 25]
[http://2009.igem.org/wiki/index.php?title=IllinoisTools/26_October_2009&action=edit 26] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/27_October_2009&action=edit 27] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/28_October_2009&action=edit 28] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/29_October_2009&action=edit 29] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/30_October_2009&action=edit 30] [http://2009.igem.org/wiki/index.php?title=IllinoisTools/31_October_2009&action=edit 31]

7/26-8/1

Donny

I attempted to use RPAIR data as another potential weight (with the help of Kanishka's research). One helpful thing was to read about other similar applications to determine their weighting scheme. I rearranged our class models to incorporate stoichiometry with Palak and modified the database accordingly.

Riyad

Wrote a program to identify possible trivial compounds by seeing how many compounds go into and come out of a given compound and then going through the top 100 compounds and deciding which seemed trivial or not.

Palak

This week I spent time getting stoichiometry information about the into our database. We decided to incorporate a stoichiometric matrix as part of our program output. I also rearranged some of our models so in order to incorporate the stoichiometric information properly.

Kanishka

I read articles to find a weighing system and found how to incorporate weights with different point values. I also spent time thinking about ideas for the webpage.

Nate

In the beginning of the week, I worked on examining certain reactions that required multiple enzymes to facilitate them. One reaction had as many as 66 different types of enzymes needed!! This is a little ambiguous point about KEGG and/or the naming of enzymes. It is hard to discern if the types of enzymes listed for a reaction are either all needed (they are all subunits), or some of them are interchangeable (the organism makes two different enzymes that facilitate the same reaction). After reporting my findings to Donny, I set work on writing code that would ideally export the data obtained with IMPtools in a xgmml file format. Xgmml is a coding language that specifies a graph of nodes and edges. This type of code is recognized by Cytoscape, a program that we had looked at in the beginning of the summer. We have recently decided to use cytoscape for graphically representing the outputs of IMPtools. I was very successful with my program, as it makes a nice, easy to see graph of any reaction pathway. I sent this code to Donny, so that he may work it into our website. This has been a super fun summer!