My name is Saran Ousseini. I am 22 years old, and I just graduated from Southern New Hampshire University, with a degree of Bachelor of Science in Biology. During my time at Southern New Hampshire University, I was fortunate to partake in a coding class called Bio-informatic. This class introduced me to R-Studio and though me the basics of coding. I was able to explore more about the new wave of science with the mix of biology and informatics/coding. This class uses technology like computers and databases, it also uses math, and statistics to analyze, collect, organize, and store large amounts of biological information. Through this class, I was able to observe biological data works that could have taken weeks to achieve and be done in less than a minute. Some of the projects I was able to work on are:
My first project is called Penguin Analysis. This is the project that introduced me to the basics of bioinformatics We used the Palmer Penguin data set to learn how R studio works. We ran an analysis and ran different codes. We used a small subset of 44 penguins. This analysis can be found Here
My second project focused on practicing technical analysis skills, such as documenting and communicating analysis, conducting exploratory analysis, generating hypotheses, and connecting exploratory analysis to hypotheses. In this project, I made a new notebook and wrote an abstract and an introduction, annotated exploratory analysis with a narrative, continued exploratory analysis, generated hypotheses, and used Git to push changes to a GitHub repository. All of this was done by using the data from a dataset called “Bird Bath”, and running different codes in order to make charts,graphs, and find connections within all of the data acquired, This analysis can be found Here
My third project was a group project, it consisted of an Introduction, Part I, Part II, III, IV, and V. In this project, we started with the introduction. In the introduction, we had 10 challenges. Through these 10 challenges, we were able to create a list of nucleotides, we used functions such as sample() which helped create randome genomes from the characters in the nucleotide list. We also use the function paste() as well as collapse = “” to collapse the random genome into one string of nucleotides. In the introduction we learned how to use the function set.seed() which helps set a seed of a random number generator, this made our result reproducible. We were also introduced to for loop to repeat a set of simple instructions. Next, we started Part I. Part I had 5 challenges, during these challenges, we learned to write reusable code using functions. In addition, we developed skills in working with genomes, such as identifying patterns of a specific length and counting their occurrences within a genome. These two tasks were important in identifying the Replication Origin. Following Part 1, we talked about Part 2, which consisted of 2 challenges. These challenges gave us the capability to scan a genome and identify frequent “near” k-mers, as well as their reverse-complements, which can be defined as genetic substrings that serve as signals for DNA polymerase replication. Lastly, we tackled Part III. This part was a combination of all the other codes we worked on, and functions we created, to finally be able to create the function clump_finding(). This analysis can be found HERE
Throughout my different works and projects, I was able to have more understanding of coding. I have acquired skills and new knowledge that I believe could be once helpful to others. In addition to learning bioinformatics, I was also lucky to partake in an undergrad research study. The study focused on chytrid fungus in New Hampshire. The research consisted of four steps. For the first step, we collected a bunch of frogs from different collecting sites, swab them, preserve the swab DNA in an alcohol solution, and put it in a refrigerator. The second step consisted of DNA Extraction: In this step, DNA was extracted by using a Qiagen DNeasy Blood and Tissue Kit. The third step was the Polymerase Chain Reaction also known as PCR. The last step Gel Electrophoresis, this step occurred two weeks after the sample was stored in a freezer. After numerous testing and collection, we decided to present our research at the Southern New Hampshire Undergrad Research Day, as well as writing a proposal. The proposal written and our presentation can be found Here
Thanks for reading my webpage. I hope you enjoyed my work and found it interesting