PRIME 2011, Osaka University, Osaka, Japan
Every year the PRIME internship program sends undergraduates to different locations in Asia to work on a research project. Over the summer I went to Osaka University to develop a workflow for modeling proteins using computer clusters. The PRIME internship gave me an outstanding opportunity to develop independent, critical-thinking skills in a real-world research environment. I applied scientific concepts that I learned in my class, such as protein structure, to develop a computational workflow for predicting protein folding. While I received feedback from my mentors weekly, my fellow PRIME scholar and I independently completed the project together. This semi-independent research project allowed both of us to make errors, investigate solutions, and implement these corrections to create a fully functional workflow at the end of the internship. This form of trial-and-error learning forced me to think about where I went wrong and how to correct these mistakes. On a cross-cultural level, I enhanced my communication skills by interacting with Osaka University faculty and students daily. Because most of the students at the university spoke limited English, I had trouble communicating with them in the first week of the program. However, I soon adapted to limited communication by learning some Japanese and by being more patient in my conversations. By trying to explain the meanings of my sentences in many different ways, I ultimately became a much clearer communicator both in Japanese and in English. In addition, I learned about Japanese culture by going to many cultural sites and participating in festivals. I now desire to learn more about other cultures by studying or performing research abroad.
In summer 2011, as part of the PRIME program, I performed computational biological research at Osaka University in Japan. This unique experience taught me many skills that I could not have learned in a classroom or in a domestic research experience. For example, I learned how to perform independent research and collaborate with other researchers. During my internship, I also learned how to communicate better and develop connections with eminent faculty at an international university. Furthermore, I learned much more about the Japanese culture and am now eager to learn more about other cultures. PRIME teaches much more than just research; it teaches numerous intangible skills that many other programs do not focus on.
During my nine weeks at Osaka University, my partner and I developed a workflow to model proteins on the PRAGMA supercomputer grid. MODELLER, a homology protein folding program**, was originally designed for a single computer cluster and requires large amounts of computation and time. By implementing MODELLER on the supercomputer grid, parallel processing greatly increases the speed of this process.
I did not learn much in my biochemistry classes on how computers model protein folding; instead, I had to find independently the information I needed to complete the project. While I learned some scripting and background information on MODELLER a few months before I arrived in Japan, I still did not possess enough information about protein modeling. Because the mentors in Japan mainly focused on computer science and I could not contact my mentor in San Diego constantly, I had to research relevant articles myself. After reading several articles, I learned much more about protein folding and MODELLER. While I started out reading technical papers very slowly, I now can read scientific papers much faster. Additionally, I learned how to use research tools to independently answer the questions that I had.
I collaborated with a partner during this program. My partner and I often discussed aspects of our research project. These productive discussions ensured that we both knew the information. For example, if we disagreed about certain data, we would cite papers to back up our arguments. Furthermore, we often read different articles and combined our knowledge to improve the protein modeling workflow. With a handful of exceptions, many university classes only focus on individual learning. However, most research groups and companies work in teams to split up work. This project would not have been so successful had we not worked in parallel and contributed equally.
While at Osaka University, I would attempt to talk with the students and faculty, but I did not realize the huge communication barriers I had to overcome, forcing me to develop better communication skills. I realized that few students spoke fluent English only after I arrived in Japan. Similarly, I only knew rudimentary Japanese. In order to talk with each other, we would have to use a mix of English and Japanese. Through this experience, I learned to listen actively to the other person's sentences and speak clearer. In active listening, I made sure to ask clarification questions to avoid ambiguity in the meaning, and I would often try to think of alternate meanings of a sentence to make sure I knew what the other person was saying. Having learned this, I now incorporate active listening in all of my conversations now.
By talking, having lunch, going to arcades, and even going on a lab trip with all the international students and professors, I developed strong connections with eminent faculty abroad. These relationships continue with research collaboration of virtual screening and protein modeling. I feel comfortable talking with faculty from international universities and realize the benefits of collaborating with them. For example, Osaka University has built many computer clusters but does not have many applications for them. Bioengineers and biologists on the other hand, do not have access to these computers but have lots of data for computers to analyze. By collaborating, both groups can benefit. Osaka University can ensure their computers work while biologists at San Diego can analyze their data. For example, our project used many of Osaka University's computer clusters to model 20 proteins in a matter of weeks.
In addition to conducting research, I often went on cultural excursions on the weekends to learn more about Japan's culture. Neighboring Osaka was Nara and Kyoto, the old capitals cities of Japan, which had many cultural sites that I could visit. These visits taught me about Japan's rich history. The PRIME program places a huge emphasis on cultural enrichment, making it different from other programs that focus on professional development or research only.
Learning about a different culture is important in today's globalized community. Future scientists and researchers such as me need to learn about these different cultures and respect them. I feel the easiest way to learn about a new culture is to immerse myself for a few months in a foreign country, learning about its history and cultural habits. Only a few research programs like PRIME give me the opportunity to perform research and become a scientific ambassador at the same time. After the PRIME program, I am now ready to learn more about other cultures around the world, possibly through studying abroad.
PRIME is more than just a research program. It contains many other facets that make it unique, such as its emphasis on international collaboration. It has not only taught me valuable independent research skills, but has also let me develop important communication skills. PRIME let me become part of an international collaborative effort. I would like to relive this experience in the future as a scientist collaborating with other researchers around the globe.
*Excerpt from PRIME: Providing Global Education in “Education in Action,” pp. 307-314,
**Webb, B. (2011, September 28). Modeller: Program for Comparative Protein Structure Modeling by Satisfaction of Spatial Restraints. http:/ /salilab.org/modeller/