SoyKB project provides student researchers real world experience
By design, computational projects used in undergraduate computer science courses generally are small-scale, idealized assignments, known as “toy problems,” that teach students how to respond to a hypothetical need. But scalability may remain elusive until students are able to apply the knowledge in a setting that supports large numbers of clients or patrons.
“This is really an important issue for students,” said Professor Dong Xu, department chair in MU’s Computer Science Department. “SoyKB provides a platform for students to work on real world applications with large-scale software engineering, enterprise-level software and the ability to work with and communicate with others in the profession.
“Companies are not in a position to train students, so it is our responsibility. [SoyKB] has produced some very successful students who have experience when they go into industry.”
Two students who got a taste of computational scalability and the other benefits of involvement with SoyKB are Michael Fitzpatrick and Danny Franklin.
Fitzpatrick, now a master’s student at Stanford University, currently is focused on genomics for a project/system known as DeepDive that uses machine-learning techniques for a variety of applications. He came to the MU campus in 2010 as a Discovery Fellow with the MU Honors College, guaranteeing him the opportunity to work with a faculty member on a research project.
“A few weeks into my freshman year, I started working in Dong Xu’s lab,” said Fitzpatrick, who started doing basic programming and worked with a web design tool when he was in the third grade. “A lot of the programming languages they were using were familiar, and I was able to make some immediate contributions.”
Franklin, who has worked as an operating systems software engineer at Microsoft Corp. for two years, began working with the SoyKB team in 2009 during his sophomore year.
“When I started with SoyKB, I didn’t know much about it at all. I’m surprised they even let me work there,” Franklin said. “[Assistant CS Research Professor] Trupti Joshi was very helpful and guided me through it. Then later, when I took [programming] classes, they were a breeze.”
Fitzpatrick said search engine analysis tools must be efficient to process all of the data and then the data must be displayed in a smart way. Visualization tools were one of the things he worked on for the project.
“SoyKB allows you to view a chromosome as well as gene expression because of the visualization tools,” Fitzpatrick said. “One of the reasons bioinformatics is so cool is that there are discoveries still being made and exciting problems to solve.”
Fitzpatrick has committed to work as a software engineer for Google once he earns his master’s but credits his research roots with SoyKB as a pivotal in his career trajectory.
The opportunity to work alongside and collaborate with graduate students and co-author publications in computer science impacted Franklin in a number of ways.
“Even now in my career, when there are projects that I don’t know much about, I remember my experiences with SoyKB, and I just do it,” Franklin said.
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