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Team:Illinois-Tools/Notebook/Week2
From 2009.igem.org
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We got Cobra working so I spent the majority of the week getting used to how Python and Cobra worked. | We got Cobra working so I spent the majority of the week getting used to how Python and Cobra worked. | ||
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| + | '''Palak''' | ||
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| + | I began working with the various functions in COBRA. I spent a lot of time understanding the output of COBRA and determining what aspects are necessary in creating an optimal pathway. I also looked at the inputs required for various COBRA functions and looked into ways that we can pass information from the KEGG database into COBRA. Additionally, I spend some time looking at the COBRA source code to see what we could modify to fit the needs of our program. | ||
Revision as of 21:54, 10 June 2009
Donny
This week, I learned the basics of the python programming language. I spend most of my time working with the Kegg API to access data via the SOAP protocol. I was able to utilize this new information to create a module that converts the common name to a usable kegg_id and also to convert the kegg_id back to a name. One concern I have is that even these simple functions are somewhat slow. Perhaps we will find ways to speed these processes up in the weeks to come. I looked into the possibility of Google App Engine. The one shortcoming (although it is pretty cool) was that there were some restrictions as to which libraries can be used. I foresee this as a problem and am looking into other options.
Riyad
We got Cobra working so I spent the majority of the week getting used to how Python and Cobra worked.
Palak
I began working with the various functions in COBRA. I spent a lot of time understanding the output of COBRA and determining what aspects are necessary in creating an optimal pathway. I also looked at the inputs required for various COBRA functions and looked into ways that we can pass information from the KEGG database into COBRA. Additionally, I spend some time looking at the COBRA source code to see what we could modify to fit the needs of our program.
