From 2010.igem.org
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| | =Weekly Lab Notebook= | | =Weekly Lab Notebook= |
| | ===May 30 – June 5=== | | ===May 30 – June 5=== |
| | + | '''Colin''' - This week, I have been more than a bit under the weather, and thus, have not been able to get as much done as I hoped. However, this week we determined the name for our project. The name is BioMORTAR, which stands for Metabolic Optimization Research Tool And Registry. After deciding between several names, this one was picked because it relates to the focus of our project: the automated design of a plasmid using BioBricks to construct it. Another break through with the project is the fact that we might have the chance, in the fall, to present our project at the Chemical and Biological Defense Conference. Since the application to the CBD S&T, requires an abstract to be submitted, I have been working, this week, on getting the abstract to be good enough to present to the Department of Defense. |
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| | + | Finally, we have decided this week that we will be needing a server dedicated to our program, just in case of high traffic and because we do not like having to bother Dr. Bhalerao by putting our stuff on his server. |
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| | + | '''Jeremy''' - I spent this week upgrading my integration of RPAIR. The database had to be manually downloaded, manually converted, and manually integrated into the main mysql database. I wrote some functions to automate these processes. While not strictly necessary, I was still feeling my way around django. |
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| | + | '''Bobak''' - Team tutorials in python and django |
| | + | Connecting IMPtools pathway results to strain designer |
| | + | Updating reaction database from KEGG, migrating to mysql |
| | + | Working with Jeremy on rpair for reaction coordination |
| | + | |
| | + | '''Anna''' - Continued to learn about Django this week. Django is able to take each application and gives a |
| | + | view file. This view file is where all the functions are carried out and each function references a unique |
| | + | page request within the website. We also learned more more about how IMPTools functions. To find |
| | + | a reaction pathway, IMPTools uses Dijkstra’s algorithm by making compounds nodes and edges the |
| | + | reactions between them. It takes the input and out and sets it as a start and end and looks at both |
| | + | points in a bidirectional path and eventually the paths overlap which gives you the best first search. |
| | + | Within each step you find neighbors until you reach the overlap. This graph-implementation yields a |
| | + | giant dictionary that maps from compounds to reactions. This exact algorithm is titled ‘Pickle’ within the |
| | + | code. We discussed sharing the codes more, this will require getting access to Dr. Bhalerao’s SVN server |
| | + | so that we can place the code in one web repository. The IMPTools server is a development that can |
| | + | host Django, but it needs Apache. The code ‘SSH’ will allow us to access the server. Some goals for next |
| | + | week will be to parse the KEGG database using Python. We looked at the abstract some more and also |
| | + | discussed the Department of Defense competition. May newsletter came out! |
Latest revision as of 03:01, 28 October 2010
- The notebook is organized into weeks. Click on the Saturday of each week to view that week's notebook entry
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| [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]
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| [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]
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| [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]
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| [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]
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| [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]
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/31_May_2010&action=edit 31]
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| June
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| [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]
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| [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]
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| [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]
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| [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]
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| [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]
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| July
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| [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]
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| [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]
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| [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]
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| [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]
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| [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]
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| August
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| [http://2010.igem.org/wiki/index.php?title=UIUC-Illinois-Software/1_August_2010&action=edit 1]
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| [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]
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| [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]
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| [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]
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| [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]
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| [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]
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| [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]
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| [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]
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| [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]
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| [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]
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| [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]
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| [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]
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| [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]
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| [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]
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| [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]
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Weekly Lab Notebook
May 30 – June 5
Colin - This week, I have been more than a bit under the weather, and thus, have not been able to get as much done as I hoped. However, this week we determined the name for our project. The name is BioMORTAR, which stands for Metabolic Optimization Research Tool And Registry. After deciding between several names, this one was picked because it relates to the focus of our project: the automated design of a plasmid using BioBricks to construct it. Another break through with the project is the fact that we might have the chance, in the fall, to present our project at the Chemical and Biological Defense Conference. Since the application to the CBD S&T, requires an abstract to be submitted, I have been working, this week, on getting the abstract to be good enough to present to the Department of Defense.
Finally, we have decided this week that we will be needing a server dedicated to our program, just in case of high traffic and because we do not like having to bother Dr. Bhalerao by putting our stuff on his server.
Jeremy - I spent this week upgrading my integration of RPAIR. The database had to be manually downloaded, manually converted, and manually integrated into the main mysql database. I wrote some functions to automate these processes. While not strictly necessary, I was still feeling my way around django.
Bobak - Team tutorials in python and django
Connecting IMPtools pathway results to strain designer
Updating reaction database from KEGG, migrating to mysql
Working with Jeremy on rpair for reaction coordination
Anna - Continued to learn about Django this week. Django is able to take each application and gives a
view file. This view file is where all the functions are carried out and each function references a unique
page request within the website. We also learned more more about how IMPTools functions. To find
a reaction pathway, IMPTools uses Dijkstra’s algorithm by making compounds nodes and edges the
reactions between them. It takes the input and out and sets it as a start and end and looks at both
points in a bidirectional path and eventually the paths overlap which gives you the best first search.
Within each step you find neighbors until you reach the overlap. This graph-implementation yields a
giant dictionary that maps from compounds to reactions. This exact algorithm is titled ‘Pickle’ within the
code. We discussed sharing the codes more, this will require getting access to Dr. Bhalerao’s SVN server
so that we can place the code in one web repository. The IMPTools server is a development that can
host Django, but it needs Apache. The code ‘SSH’ will allow us to access the server. Some goals for next
week will be to parse the KEGG database using Python. We looked at the abstract some more and also
discussed the Department of Defense competition. May newsletter came out!
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