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Researching to Help Researchers

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  • Title: Assistant Professor, Emory University
  • Education: PhD, Pennsylvania State University, 2006
  • Recommender: Ross Hardison

James Taylor is one researcher dedicated to making life easier for other researchers. Taylor is addressing what he views as a severe lack of user-friendly interfaces for genomic data management and effective ways to make data analysis reproducible and easily shared. The UCSC Genome Browser is a beautiful thing, for instance, but what is an investigator to do after downloading millions of SNPs and gigabytes' worth of alignments?

To help overwhelmed scientists get organized and make the most out of all the data, Taylor and his colleagues are developing Galaxy, a Web-based genome analysis tool set that allows users to conduct on-the-fly analysis of multiple genome data sets in any format by integrating a range of bioinformatics tools and linking them out to various data warehouses. Galaxy lets users save and share every step of their analysis and workflow with other users, and also allows people to analyze multiple alignments, compare genomic annotations, and profile metagenomic samples, among other tasks.

The bigger picture for Taylor is not just to provide tools and infrastructure with projects like Galaxy, but also to facilitate a cultural change among biologists and computer scientists. "In the future, experimental and computational biology are only going to become more intertwined and even inseparable," Taylor says. "What I hope to see is a culture that absolutely requires rigorous peer review of both aspects, that understands that software used in a published analysis needs to be open, needs to be delivered with the supporting information to allow reviewers to verify derived results, and in general that if it isn't transparent and reproducible, it isn't science."

Taylor says it was his exposure to the disconnect between those developing computational tools and those generating the data early in his career that set him on his present crusade. "During the course of my PhD work, I came to notice how big a gap there is between people who are experimentalists by training and people who are computational by training, and how inefficient that relationship is both in terms of how people developing methods provide those methods to the community and people who want to use those methods and what resources are available to them to actually analyze their own data," he says. Taylor also believes that his work is very timely due to the growth in data generation with next-gen sequencing platforms and density increases in tiling arrays.

Looking ahead

Considering future plans, Taylor says his goal is for disparate research groups to communicate more effectively through an informatics infrastructure. "I think a lot of the data storage and the databases are pretty ad hoc, so five years down the road we are going to face difficulties figuring out how things were done in the past," he says. "What I'd really like to see is the community develop a lot of these communication standards and really have a focus on the question of both reproducibility and openness in research."

Publications of note

Last year in Current Protocols in Bioinformatics, Taylor published a paper entitled "Using Galaxy to perform large-scale interactive data analyses," which presented the Galaxy interface to the bioinformatics user community. The paper shows how Galaxy can be used to help researchers find the top 100 protein-coding exons in the human genome with the most density of SNPs by accessing Galaxy's URL and following a specific protocol. 

And the Nobel goes to …

Taylor says that if he were to win a Nobel, he would like it to be for the discovery of some "new form of heritable information, without which we are completely stumped now, but which makes everything completely obvious."

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