Dr. Holly Bik gave a presentation last week on the
difficulties of visualization of data in the biology field. Dr. Bik explained her personal research on
the marine species called “Nematodes” (which are also in our drinking water
too!). She estimated that there are
around 4000 marine species actually sequenced and described. There is an estimated 1-100 million different
species of Nematodes and per 1 m2 of the sea floor the abundance of
a Nematodes can range anywhere from 100,000 to 84 million. Due to the vast
amount of Nematode species there are Dr. Bik explained to us the difficulties
of visualizing all the data. There are
many different approaches used currently, the most common separating the
nematodes into “OTUs”, operational taxonomic units. The OUT is a classification that separates
species based upon rRNA. Dr. Bik told us
that it is difficult using this classification system because there could can
as many as 10,000 copies of rRNA and therefore it is hard to make inferences. Dr. Bik continued on explaining that a way to
combat this is to make “cutoffs” based on species similarity in OUT
“clouds”. These clouds and cutoffs
create a way to better cluster species into different branches on a tree.
Dr.
Bik introduced us to a new sort of “pipeline” for metagenomic data analysis
called “phylosift”. She says that it is
an innovative new way to help sort through species data and organize them in a
more effective way. Dr. Bik claims that
the current system for visualizing and organizing data is inefficient and
difficult to understand, which led to the creation of phylosift. It was very
interesting to hear her different ideas and ways she would like to better
improve the bioinformatics field. I also really enjoyed the lecture because I didn’t
know there was such a problem; I honestly thought that the way current things
were going were okay. I sincerely hope
that in the next few years the field of bioinformatics is heavily emphasized,
because it is crucial that we can visualize and interpret data we collect from experiments
in an effective manor.
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