Team:Illinois-Tools/Notebook/Week4

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'''Donny'''
'''Donny'''
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I have compiled a dictionary of over 200 chemicals determined by the EPA to be toxic linked to their respective Kegg IDs. I followed the tutorials for creating a webpage with django and have decided that this will be a good fit for our project. The dictionary of chemicals was made into an HTML drop down menu. In the upcoming weeks, I will make the html form linked to our SQL database so that it can be automatically updated as the EPA list is updated. I am working on making a simple layout for the page where the user can select a toxin from a list as well as select a desired product- the page will respond to these selections and indicate that it recognizes the choices made. Although this is an unimpressive feat, it will lay some foundation for our pages IO. I am also currently investigating how to improve the pathfinding algorithm that Palek found on the net. It is nowhere near efficient enough for our purposes. Ideally, this algorithm will be able to quickly scan the huge network of reactions and show every possible series of reactions that can go from input compound to output compound. Unfortunately, this is only the beginning because we will have to then determine our method of choosing which path will be the most realistic and also optimal in the sense of production.  
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I have compiled a dictionary of over 200 chemicals determined by the EPA to be toxic linked to their respective Kegg IDs. I followed the tutorials for creating a webpage with django and have decided that this will be a good fit for our project. The dictionary of chemicals was made into an HTML drop down menu. In the upcoming weeks, I will make the html form linked to our SQL database so that it can be automatically updated as the EPA list is updated. I am working on making a simple layout for the page where the user can select a toxin from a list as well as select a desired product- the page will respond to these selections and indicate that it recognizes the choices made. Although this is an unimpressive feat, it will lay some foundation for our pages IO. I am also currently investigating how to improve the pathfinding algorithm that Palak found on the net. It is nowhere near efficient enough for our purposes. Ideally, this algorithm will be able to quickly scan the huge network of reactions and show every possible series of reactions that can go from input compound to output compound. Unfortunately, this is only the beginning because we will have to then determine our method of choosing which path will be the most realistic and also optimal in the sense of production.  
In other news, I'm still not on the Illinois iGEM mailing list so I don't find out about things like team beer pong tournaments and birthday celebrations. (I assume I'm not missing much- but if I don't get invited to summer thanksgiving I'll be pretty upset).
In other news, I'm still not on the Illinois iGEM mailing list so I don't find out about things like team beer pong tournaments and birthday celebrations. (I assume I'm not missing much- but if I don't get invited to summer thanksgiving I'll be pretty upset).
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""Ankit""
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So after receiving Donny's intimidating email, I finally feel like I should write in the lab notebook. I am still without my laptop, which makes it harder to work on code. But for the last week I have been working on getting COBRA sources codes uploaded to our program. I found a program called OMPC. Apparently, OMPC allows running MATLAB®'s m-files using Python interpreter. OMPC reads m-files and translates them into Python compatible code.
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Note having a laptop, I have been unable to check if this program works. Hopefully my laptop comes in tomorrow, so I can check this out because it will save us a lot of time by note having to convert about 30-40 COBRA source codes written in MATLAB to Phyton.
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Moreover, I am still concerned with our project. It seems as we are just doing what the Maranas group has already done with the OptStrain (OptStrain: a computational framework for redesign of microbial production systems. {Maranas 2004}). It seems like they have already done what we have done but their code is in GAMMS and isn't an open source program. Hopefully when our program is done, we will have some awesome cool features.
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P.S. on a unrelated notes and knowing that none technicians that are currently repairing my laptop are reading this, I just like to say that I WANT MY LAPTOP NOW!

Revision as of 16:26, 22 June 2009

back to notebook

<<previous week next week>>


6/14-6/20

Donny

I have compiled a dictionary of over 200 chemicals determined by the EPA to be toxic linked to their respective Kegg IDs. I followed the tutorials for creating a webpage with django and have decided that this will be a good fit for our project. The dictionary of chemicals was made into an HTML drop down menu. In the upcoming weeks, I will make the html form linked to our SQL database so that it can be automatically updated as the EPA list is updated. I am working on making a simple layout for the page where the user can select a toxin from a list as well as select a desired product- the page will respond to these selections and indicate that it recognizes the choices made. Although this is an unimpressive feat, it will lay some foundation for our pages IO. I am also currently investigating how to improve the pathfinding algorithm that Palak found on the net. It is nowhere near efficient enough for our purposes. Ideally, this algorithm will be able to quickly scan the huge network of reactions and show every possible series of reactions that can go from input compound to output compound. Unfortunately, this is only the beginning because we will have to then determine our method of choosing which path will be the most realistic and also optimal in the sense of production.

In other news, I'm still not on the Illinois iGEM mailing list so I don't find out about things like team beer pong tournaments and birthday celebrations. (I assume I'm not missing much- but if I don't get invited to summer thanksgiving I'll be pretty upset).


""Ankit""

So after receiving Donny's intimidating email, I finally feel like I should write in the lab notebook. I am still without my laptop, which makes it harder to work on code. But for the last week I have been working on getting COBRA sources codes uploaded to our program. I found a program called OMPC. Apparently, OMPC allows running MATLAB®'s m-files using Python interpreter. OMPC reads m-files and translates them into Python compatible code.

Note having a laptop, I have been unable to check if this program works. Hopefully my laptop comes in tomorrow, so I can check this out because it will save us a lot of time by note having to convert about 30-40 COBRA source codes written in MATLAB to Phyton.

Moreover, I am still concerned with our project. It seems as we are just doing what the Maranas group has already done with the OptStrain (OptStrain: a computational framework for redesign of microbial production systems. {Maranas 2004}). It seems like they have already done what we have done but their code is in GAMMS and isn't an open source program. Hopefully when our program is done, we will have some awesome cool features.


P.S. on a unrelated notes and knowing that none technicians that are currently repairing my laptop are reading this, I just like to say that I WANT MY LAPTOP NOW!

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