Posts Tagged Modeling

Protein visualization (Rachel / Thomas)

Solved crystal structure of BRCA1 BRCT (made in Jmol):

Electrostatic map of BRCA1 BRCT (made in Pymol):

Sequence of BRCA1 BRCT showing features such as beta strands and alpha helices:

The structure has a diameter of ~27 A.  ~55 A in length.

There are a variety of secondary structures including beta turns, beta strands and alpha helices.

BRCA1 is composed of 215 residues.

Conserf run (MSA):

Dark purple regions are conserved.  Notice ligands binding in that region.

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Thomas Lane (Bioquest day 1)

The bulk of the first day regarded becoming aquatinted with tools thought to be commonly (or should) be used by scientists.  Such as: a way to organize resources (Mendeley), a way to quickly share indexed information (Diigo, although more like a glorified bookmarking system) and the basics of readers (such as Google Reader).  The most useful tool out of this set was Mendeley, the other two are really more of a personal preference of how one organizes information, perhaps unnecessarily adding layers of complexity.

The second portion of the Bioquest presentation regarding mathematical modeling was by far more applicable.  Gapminder is a useful tool that is very easy to jump into and start using (the applications are apparent).  The actual step by step process of modeling cancer in a specific case was insightful.  For experimentalists this offers a sort of step toward how computationalists approach questions/hypotheses, which seems like the major aim of this workshop.

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Gapminder & Excel

Yesterday afternoon the workshop for Gapminder was very interesting. I personally enjoy looking at how things influence each other. Having so much data from so many countries is for lack of better word “awesome”. I would like to use gapminder to look at other correlations between different demographics.

Also, I was under the impression that I knew how to use excel. I learned yesterday that I still need to journey through the program because there is a lot more applications and uses for the program than I thought.

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Mathematical Modeling of Cancer Tumor

The mathematical modeling of the cancer tumors was amazing. It baffles me how we can use math to approximate when the tumor began and when it could have been detected. I feel we are not too far away from predicting when tumors will begin.

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Wonderful way to end the day

Using excel, we worked with modeling progression of cancerous tumors to get comfortable with representing biological data as mathematical equations. After spending our time understanding administrative matters and learning how to use new tools available online, its great to end the day with something I love–math.

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Day 1

Gapminder and Mendeley were interesting to learn about and potentially useful, and the math and excel refreshers were a good way to get my brain back in gear for the semester.   I’m not so sure about the other online tools though.  I don’t really see myself ever using them, and I also have privacy concerns about the social aspects.

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Mathematical Modeling

The mathematical modeling portion of the workshop made it clear how long it was since I last took real math. That being said, I definitely found Gapminder to be a very cool website and potentially a great way to model data in the future. Numb3r5 count was interesting as well. Although I don’t know how often I will use it, having various groups of data to test a model could come in handy. Overall, the second half of the day felt like a nice chance to get myself re-acquainted with math and all the wonderful things math can do.

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