Bioinformatics Bites: Repurposing publicly available data

I’m going in a bit of a different direction with this bioinformatics bite segment. Instead of explicitly describing how to use a database or tool, I wanted to tell you all about a little project that I’m working on with a vet student from CSU.

Just because I don’t have a lab or large amounts of research funding doesn’t mean I can’t do science! There’s a wealth of bioinformatic data publicly available online and some user friendly tools that are available. We’re using these freely available resources to ask questions about how the distribution of microbes in the environment correlates with specific landmarks.

Our research question is as follows: Are there differences in microbial populations at sites that are close to zoos in the NYC area compared to the farther away. To address this question, we are using data from the PathoMap project, which swabbed surfaces in transit stops all over New York City. (This project is also being expanded to the top 10 cities worldwide for public transit ridership by a project called MetaSub.) See this publication for more information.

pathomap Pathomap main page

We determined test and control sites by looking up how city planners determine the distance people are willing to walk to a transit stop. We are also using a tool called GeneGis 2 to analyze and visualize these data. See this publication for more information on GenGIS.

gengisGenGIS output from their wiki

Repurposing data forces you to think differently. Our research question was designed in the context of what data and tools were publicly available. This type of research will only get easier as the mindset of creating well-designed community resources expands. Initiatives like Big Data to Knowledge (BD2K) and the Center for Open Science are driving this new trend.

If you’re curious about data repurposing, or how to find datasets and tools, please see the bioinformatics section of our new Research Support Pages or set up a consultation to discuss your questions.

  • Tobin Magle, biomedical sciences research support specialist.

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