30 Nov, 2021

Creating Open Access Software for COVID Research

A University of Arizona postdoctoral researcher working remotely in India uses CyVerse to share her software for COVID cellular assays with collaborators and scientists worldwide.

"Science happens faster if you have immediate responses."

Ruchika Bhat should know. She's a University of Arizona associate researcher in the Nikoich-Žugich Lab in the Department of Immunobiology and currently works remotely from Bhopal, India. To get her science done, she relies upon computational options to collaborate with colleagues and students worldwide. 

A headshot of Ruchika Bhat.
Ruchika Bhat

Bhat's research spans studying what happens behind the scenes within single biological cells and how these cells are affected by viral diseases such as COVID-19, to immuno-aging research – how the immune system changes with age and what metabolic processes cause humans to age.

To understand changes happening inside cells infected by COVID-19, Bhat uses single-cell RNA sequencing, or scRNA-seq, a technique that detects and analyzes messenger RNA molecules, the building blocks of cells. The scRNA-seq technique is more refined than traditional bulk RNA sequencing, allowing researchers to better understand changes in individual cells.

Since scRNA-seq was first performed in 2009, the technique has grown considerably, Bhat said. "The technique is helping us find out the gene signatures inside cells, and understand the difference between cells from a COVID-19 patient with serious disease and one with mild disease."

Bhat often writes her own computational programs to analyze her scRNA-seq datasets, but she needed a way to share these programs with collaborators.

"Using CyVerse, there is an option to create our own apps and share them with our communities," Bhat explained. "Every app needs some basic infrastructure so that it runs smoothly."

CyVerse provides that infrastructure, as well as personalized assistance publishing an app Bhat created, rstudio-seurat, that analyzes scRNA-seq data. CyVerse Science Analyst Reetu Tuteja helped Bhat streamline her app and publish it in CyVerse's Discovery Environment, making it accessible to other CyVerse users.

"CyVerse is very comprehensive for bioinformaticians," Bhat observed, "from the point where we start uploading our own data to sharing with users anywhere in the world. Each of us has the opportunity to edit the data individually, which I feel is a very important thing that is lacking in other platforms."

Bhat and Tuteja together taught a virtual workshop to students and researchers in Nebraska in May, 2021. Because scRNA-seq is still very new, many biologists and bioinformaticians were eager to learn more about it, Bhat said: "We taught them how we can do it at our fingertips now from anywhere on the globe and integrate the data. The attendees were very interested because these are data that they can access easily and assess bioinformatically, even if they aren't knowledgeable about machine learning."

Bhat later was invited to teach another virtual workshop for students, graduates, and faculty at the University of Serbia in Belgrate, funded by the Science Fund of the Republic of Serbia. She taught about 100 people, including several online attendees. "It was a massive audience of people very interested to know about single cell RNA-seq and how to use it."

"CyVerse has been flawless," she added. "I can write the script and it will work, and my students and collaborators can use the same program at their end to decode the data. And the most important thing, you can just transfer and share the data with your collaborators. It's easy, friendly, shareable, compact, and very comprehensive."

"CyVerse is proud to provide a one-stop shop for all forms of data science," said CyVerse Principal Investigator Eric Lyons. "As the datasets generated by the field of genomics have grown, our infrastructure has grown to match them, enabling health researchers like Ruchika Bhat to collaborate seamlessly and get results almost instantaneously."