Community Highlight: Bridget Allen
My name is Bridget Allen (BA) and I am a recent graduate of St. John’s University. This summer I worked with Dakota Blair to add the bamtofastq tool from bedtools, a genome arithmetic toolkit, to KBase. Implementing Bamtofastq into KBase means that bioinformaticians can streamline their data analysis in KBase. Biologists who often use BAM file types, will benefit from having this feature, as they no longer have to learn the bedtools functionality and do the conversion in the commandline. Rather, all of the conversion and analysis will be put together in the Narrative interface. This saves researchers time and make their processes more efficient when they are working with multiple file types.
How has using KBase supported your research or project?
(BA) Working in KBase has given me the opportunity to learn more software development topics and techniques. Doing app development and writing unit tests was something I had never done before, so it taught me about the complexity of backend coding. In the future, applying this knowledge of software engineering will help my career prosper.
What role do you see KBase having in open science principles?
(BA) KBase – accepting microbial, environmental, and plant genome data – has the potential to aid in new discoveries in microbiology, environmental science, and ecology. While scientists across the DOE are doing experimental science, field work, and collecting samples; KBase will enable interpretation of those results and provide access to great findings that can be transformative for our environment. These results can range from discovering new biofuels to saving endangered species.
For my project, in order to understand the goal better, it’s helpful to collaborate with bioinformaticians across the DOE. In order to make KBase as useful as it possibly could be, the KBase team takes suggestions from the user. A common request was to add the conversion functionality for different data types, which is what I’ve worked on. In an ongoing effort to provide this functionality, the effort can be continued and different tools from bedtools can be added to expand this effort.
What is your favorite part about using KBase?
(BA) My favorite part of KBase is the accessibility and flexibility it has. Working with bedtools has shown me all of the cool things we’re able to do with diverse genome sets, and the potential there is for implementing those tools into KBase. Having used other genome software before, such as Galaxy and BLAST, I prefer the KBase interface. It’s user friendly and clear to understand.
Follow Bridget on LinkedIn: www.linkedin.com/in/bridget-allen-01994b223/
Stay tuned for app releases for more on bedtools in KBase!
