Intern Life at NextBio

Interns at NextBio learn to set the stage for a unique kind of data exploration

At NextBio, genomic data snakes through the hands of scientific teams and the automated pipelines they design, connecting people intellectually and socially. Each department is responsible for their own piece of the NextBio puzzle as well as helping new team members cultivate their skills.

The data curation team at NextBio mimics the work of a heart, channeling in the public genomic data that’s essential to the NextBio platform. Beatrice Chiu, who graduated from the Molecular and Cell biology program at UC Berkeley, began her journey at NextBio as a Web Product intern, conducting usability tests to optimize the NextBio user interface. She switched over to the curation team earlier this year to help with a large scale GWAS (genome-wide association study) tagging project. As Beatrice explains, “All studies in the NextBio database usually have a minimum of a biodesign tag, like disease vs. normal, response to a drug, etc. and then a more specific phenotype tag, say for a disease. GWAS studies can also get classified using case-control or other association tags.”

“This helps users filter data in so many different ways, rather than just looking for studies on a particular disease or method,” she adds. Beatrice explains that working in both the Curation and Product teams “helps her understand different aspects of the NextBio correlation engine fully.”

Data imported by curation is then analyzed by the Bio-Computing team, where Meenakshi Mali, Computer Science graduate from San Jose State University, interns. Meenakshi first found out about NextBio through a friend, and was “amazed at the impact of NextBio’s work in this field and how the data processing here is revolutionizing the way researchers work.” Specifically, “researchers can use this information to find correlated studies and make hypotheses based on this data,” explains Meenakshi. The bio-computing team creates and uses different algorithms to process curated data and integrate it into different features on the NextBio site. When searching for a specific study, users can view the relative score of different parameters to construct their own research experiments. This technology is part of what inspired Meenakshi to bring her scripting skills to NextBio. Meenakshi points out that “dealing with the basic scripts, that make a product [like NextBio]” is one of her favorite aspects of working here. On a typical day she conducts quality analysis to improve the algorithms used to analyze curated data, making sure that improvements in the statistical analysis are accurate and error-free.

Qing Zhang, Engineering intern and graduate from the University of Wisconsin Milwaukee, also knows a thing or two about coding. She assists in building the search engine that powers NextBio’s databases by designing data mining programs that are as accurate, efficient, and fast as possible. After all, crafting high-precision software is essential to maintain a database that integrates (and indexes) users to index over 20 million PubMed documents. Improving processing time for each document by merely one millisecond can reduce the time it takes to process a document by five hours. The incredible amount of information and genetic data that high-throughput technology has made available to the public keeps the entire NextBio team on their toes.

Nonetheless, all three agree, the continual teamwork and collaboration adds to the rewarding and enriching experience. For Beatrice, her favorite part of working at NextBio is the people: “Working here is truly a group effort,” she says. Qing notes that it is this effort that has produced “a sophisticated system used by several thousands of people.” So what does the future hold for this group of NextBio interns? Qing loves the fast pace and excitement of industry, and wants to continue perfecting the world of data mining. Meenakshi plans to delve deeper into the statistical analysis side of bio-computing, embracing the human calculator. And Beatrice? Well, she would like to be the boss…but all joking aside, she plans to continue her journey in data curation, populating the NextBio database one study at a time.