Jenny reflects on research in Mangul Lab
I have been in the lab since a junior year at UCLA, and I started out learning about the error correction benchmarking project. I began by learning about the general structure of the project and the functions of different scripts from generating results, evaluating them to summarizing them. Then I learned to install all the tools from different platforms, and modifying or writing the wrappers to run them. During the summer, with Jaque’s help, I generated the summary data of the tools needed for the project and helped organized the results and uploaded the files onto GitHub.
What I learned in the lab:
I started out wanting to learn more about the application of software and coding in bioinformatics research. And through this experience, I am exposed to the concepts of benchmarking, how genetic data is processed and evaluated during research, and have a better grasp of the field of bioinformatics and the types of research done here.
I learned to submit and run jobs through hoffman2 (Jenny Wu).
Technically, I learned to used UNIX and write bash script much more competently, to navigate HOFFMAN2, and to understand and run python scripts independently and generate results. Hoffman is a HPC cluster that we used to run big datasets online through the server. I was able to use it well by the end of the project through learning the commands from Serghei and my colleagues. I became better at using google or StackOverflow to find solutions to debug a piece of code or solve installation problems, which I rarely did before for projects in computer science classes, but now realized how useful it is in real-life settings. I learned how to contribute to, upload, and download from GitHub.
I also became better at collaborating with others in a lab and asking questions. Sei and Jaque both taught me a lot technically and about organizing big datasets through excel or on Hoffman to improve efficiency. I had the chance to learn about the projects of other students in the lab and how to present research results. From Serghei I learned more about how to lead and coordinate research projects of several people, give everyone clear instructions, and move the project forward.
With the knowledge I acquired during project, I eventually contributed as the fourth author on the paper published on Genome Biology. https://www.biorxiv.org/content/10.1101/642843v2.full.
Finally, I became better at time management, balancing school work with research projects.
The experience in the lab has been a really valuable experience during my college year. Serghei was really supportive and cared about my learning from the very beginning. He patiently taught me details about the project and introduced me to skills that he thinks would benefit my career. I also learned a lot about how the research team works and how to communicate with others clearly from him and other members on the project.
I’m now going to Northwestern for their data analytic program after getting accepted to all the programs that I applied. I’m very interested in becoming a data scientist in computational social science research in media studies or public health and help to solve problems in policy making.
Interested in developing and applying bioinformatics methods for big data? Join our lab!
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