Power of the Craft: Amélie Lamont Spotlight (Research Update #1)

I believe it would be unfair of me to have a favorite subject of study in my research project. All the individuals and organizations that I have decided to study bring unique styles of interactions to the forefront of my research, often in ways that challenge me to rethink what exactly I’m looking at. No one online community is quite like another, and this project seeks to highlight this simple fact among those figures who belong to marginalized communities – those whose voices “in real life” are more often than not suppressed or ignored.

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Week 6: Interpreting the distance matrix and trying to detect biased insertion/retention of TEs

Last week, I fixed the bug in the code and regenerated the density plots of TEs. I also regrouped the transposons by family and ran a program called emma on each of the families. From that, I got an alignment file, and a tree file. Then I used PHYLIP to turn the tree file to a visualized tree. This week, I spent some time trying to figure out a way to make inference from the phylogenetic trees. However, after talking with Dr. Puzey, we decided to use distance matrix instead of the trees. It was hard to extract accurate information from a tree graph, especially when they were composed by samples of data. Thus, I ran distmat on the output alignment files from emma for each TE family. And I ran transform_matrix.py to get csv files of the reformatted distance matrix. In this way, I made the matrix into a data frame. I then imported the data frames to Jupyter Notebook and made the distance histograms of each transposon family. Note that the distance ranged from 0 to 100, but it actually was the number of substitutions per 100 bases. This meant that I had to divide it by 100 for the num of substitution per base. It would be a percentage showing how divergent a certain TE was compared to others.

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Living Shoreline- Week 3

Hey again y’all!

 

Week 3 was a little less exciting than my escapades last time- but still incredibly valuable as an experience!

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Research Week Five

I spent this past week doing a lot of manual entry of information, namely 2010 poverty data that my advisor found. One way that we were looking to control the research findings on maternal mortality was by collecting information on the number of people below the federal poverty line within each state during a median year in the timeline (i.e. 2010), or the unemployment rate. It was preferable to my advisor if I was to find the poverty data, however, I was not able to find the information that on any of the public access databases that was up to par. So once my advisor found this pdf with the information we needed from the census bureau, it was my job to manually transfer the data to an excel spreadsheet since the hyperlink within it did not take me to an active online site.

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Living Shoreline- Week 2

Hey all!

 

I’m a bit backlogged in my postings since we’ve been so busy, but I’ll be all caught up in a few days! In a general update, looks like I’ll be staying a bit longer than my expected 7 weeks, as research is going so well that I don’t really want to leave.

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