IllinoisTools/27 June 2009

From 2009.igem.org

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(6/21-6/27)
 
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'''Kanishka'''
'''Kanishka'''
 +
worked on Biobricks
worked on Biobricks
 +
 +
'''Riyad'''
 +
 +
worked on BioBricks as well with Kanishka
'''Palak'''
'''Palak'''
-
This week I worked through the Django tutorials and learned how to make databases using Django and SQLite. I began creating models for the categories of databases that we would need. We went through many of the KEGG files to determine the way that we are going to organize our databases.
+
This week I worked through the Django tutorials and learned how to make databases using Django and SQLite. I began creating models for the categories of databases that we would need. We went through many of the KEGG files to determine the way that we are going to organize our databases. We used the KEGG API to write scripts to create some of the databases and the FTP server to create the rest.  
'''Nate'''
'''Nate'''
This week was not as exciting as last week.  I at first started looking over the FTP files on the KEGG database, and tried to better understand how they organize their data.  One thing that is really confusing about KEGG is the topic of cofactors.  They have an odd way of organizing this data.  In the FTP file for enzyme data, there is a section specific for listing relevant cofactors for the enzyme.  However, there are some enzymes that list cofactors in the comment section of each enzyme as well.  This makes things somewhat more frustrating when trying to organize cofactor data.  I also brainstormed some on how I could organize information that is relevant to us in a way that we could use it.  I didn't come up with any good way in the end.  We ended meeting with the professors again this week.  After the meeting, I decided to look more into graphical ways to represent our outputs of program once it is completed.  I mostly investigated Networkx, but I also investigated other libraries that python can work with to see how else I can make a graph using python.  I learned some new things, but I am not sure if they will be useful to us in the future.
This week was not as exciting as last week.  I at first started looking over the FTP files on the KEGG database, and tried to better understand how they organize their data.  One thing that is really confusing about KEGG is the topic of cofactors.  They have an odd way of organizing this data.  In the FTP file for enzyme data, there is a section specific for listing relevant cofactors for the enzyme.  However, there are some enzymes that list cofactors in the comment section of each enzyme as well.  This makes things somewhat more frustrating when trying to organize cofactor data.  I also brainstormed some on how I could organize information that is relevant to us in a way that we could use it.  I didn't come up with any good way in the end.  We ended meeting with the professors again this week.  After the meeting, I decided to look more into graphical ways to represent our outputs of program once it is completed.  I mostly investigated Networkx, but I also investigated other libraries that python can work with to see how else I can make a graph using python.  I learned some new things, but I am not sure if they will be useful to us in the future.

Latest revision as of 15:43, 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]

6/21-6/27

Donny

During this week I put a lot of focus into writing code to update our database. Eventually, we will be able to re-use some of this code in an automated process that keeps our network up to date with the Kegg database.

Kanishka

worked on Biobricks

Riyad

worked on BioBricks as well with Kanishka

Palak

This week I worked through the Django tutorials and learned how to make databases using Django and SQLite. I began creating models for the categories of databases that we would need. We went through many of the KEGG files to determine the way that we are going to organize our databases. We used the KEGG API to write scripts to create some of the databases and the FTP server to create the rest.

Nate

This week was not as exciting as last week. I at first started looking over the FTP files on the KEGG database, and tried to better understand how they organize their data. One thing that is really confusing about KEGG is the topic of cofactors. They have an odd way of organizing this data. In the FTP file for enzyme data, there is a section specific for listing relevant cofactors for the enzyme. However, there are some enzymes that list cofactors in the comment section of each enzyme as well. This makes things somewhat more frustrating when trying to organize cofactor data. I also brainstormed some on how I could organize information that is relevant to us in a way that we could use it. I didn't come up with any good way in the end. We ended meeting with the professors again this week. After the meeting, I decided to look more into graphical ways to represent our outputs of program once it is completed. I mostly investigated Networkx, but I also investigated other libraries that python can work with to see how else I can make a graph using python. I learned some new things, but I am not sure if they will be useful to us in the future.