Weekend Workshop Hones Researchers’ Computational Skills

February 26, 2015

Feb. 26 — A new skillset is in demand among scientists: As the size of datasets increases with enhanced data collection technologies, researchers must be proficient not only in their selected field of study, but also in the ability to use computers to analyze, interpret, and visualize increasingly larger datasets.

This means that many researchers, who are usually untrained in computer sciences, must independently acquire these computational skills in order to thrive in their career fields.

A workshop held on the University of Arizona campus last weekend, hosted by the iPlant Collaborative in partnership with its affiliate organization, Software Carpentry, helped to ease that burden. The two-day session offering instruction to researchers, students, and educators on how to run computational analyses as well as store, share, and visualize data.

“The iPlant Software Carpentry Workshop this past weekend was an awesome realization of iPlant’s collaborative nature,” said Uwe Hilgert, Director of Science, Technology, Engineering, and Mathematics Education for the BIO5 Institute and iPlant, who organized the workshop. “Bringing together Software Carpentry, iPlant, BIO5 and the UA, this workshop served a large group of students and staff from a wide variety of backgrounds and a wide array of interests.”

The iPlant Collaborative, a National Science Foundation-funded national project that provides infrastructure support and software services for the life sciences, presented the workshop in partnership with its affiliate organization, Software Carpentry. Software Carpentry aims to instruct scientists in the use of computational tools to further their research.

“Collaboration between Software Carpentry and iPlant is a very synergistic fit,” said Jason Williams, iPlant’s officer in charge of Education, Outreach and Training, and who was recently elected to the 2015 steering committee of the Software Carpentry Foundation. “We are all interested in giving scientists, educators, and students the ability to be more productive. Users who’ve participated in software carpentry training are better positioned to make full use of iPlant platforms and deliver higher impact science.”

“This was a great team effort,” said Nirav Merchant, co-principal investigator of the iPlant Collaborative. “Having users that can scale and manage their data and computation from laptop to cloud and high performance computer with a good grasp over their digital assets is central for iPlant. It was very good to see faculty along with their whole labs with them. They are trying very hard to bring in best practices to improve their labs’ computational efficiency.”

Registration for the workshop filled in 36 hours after it was announced, which reflects the high demand for computational training, said Hilgert. “The fact that demand by far exceeded workshop seats clearly shows that there is a strong need for this kind of training,” he said. “And the need for these skills transcends biologists.”

The workshop audience spanned Arizona’s universities, with attendees from the UA, Arizona State University and Northern Arizona University. Research disciplines represented included biosciences, management information systems, computer sciences, engineering, physics, and statistics.

Attendee Karan Nandwani, who is pursuing his master’s degree in management information systems at the UA Eller College of Management, said the skills taught was a primary reason for his interest in the workshop. “Everything is moving toward collaboration, so these skills for sharing data are in high demand, especially moving into career fields,” he said.

Over the course of the weekend in Tucson, Ariz, researchers, staff and students collectively worked through methods of organizing, storing and sharing data; running scripts and projects; completing analyses using R, a statistical analysis program; visualizing data; and interfacing between using their personal computer desktops, the Internet and cloud-based platforms.

Ann Danowitz, systems administrator for the Arizona Genomics Institute and also in the Sanderson Lab at the UA’sDepartment of Ecology and Evolutionary Biology, said the instruction enhanced her skills even though she already has roughly 20 years’ experience working with computational analysis programs. “Now I can proceed with my own self-learning,” she said.

“In teaching these workshops, I find it’s better to tell a narrative, a story,” said Jonathon Strootman, a software engineer for the iPlant Collaborative and an instructor for the workshop along with UA Plant Sciences postdoctoral researcher Naupaka Zimmerman. “We try to make all lessons cohesive, to carry a theme all the way through as to how everything works together. We want people to walk out of the workshop with the affirmation to start applying their newly-learned skills to their individual areas of study.”

“The workshop was a ‘tour de force’ that enabled users to move their science to the next level,” said Hilgert.

The software carpentry workshop was supported by the Arizona Environmental Grid Infrastructure Service (AEGIS), a statewide Arizona initiative to provision the transition to informatics-intensive research programs, funded by a Regents’ Innovation Award to the UA, ASU and NAU. Additional workshops to follow include software carpentry events at the ASU and NAU campuses, and a data carpentry workshop to be held at the UA in April.

Source: iPlant Collaborative

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