Lab gets grant to advance cloud computing in Maine

BAR PORT – The MDI Biological Laboratory has been awarded a grant to promote the shift to cloud computing among students and researchers at the 14 education and research institutions in Maine that are part of the federally funded Maine INBRE (IDeA Network of Biomedical Research Excellence) network, a program to enhance biomedical research and research training in Maine.

The $126,449 grant is a one-year supplement to a five-year $18 million Maine INBRE grant awarded to the lab by the lab. National Institute of General Medical Sciences (NIGMS) in 2019.

The cloud refers to computational infrastructure and services that reside off-site and are owned by commercial providers such as Google. Cloud-based services include networks, servers, storage, and applications, and other data computation and hosting tools and services accessible over the Internet. Such services offer the advantages of being scalable, accessible, cost-effective, flexible and secure.

The cloud lab program will address the cost and time associated with analyzing the complex data sets generated as a result of the advent of the genomic era. The volume and complexity of these data sets puts a strain on researchers and institutions and hinders the analysis and exchange of information between those in geographically dispersed locations.

Under the cloudlab program, Maine INBRE students will learn to use the Google Cloud platform to develop workflows for the analysis of large data sets. The program will also provide research support to Maine INBRE scholars, graduate students and postgraduate students, as well as assistance to Maine INBRE institutions in implementing and managing cloud computing services.

Maine INBRE, which is led by the MDI Biological Laboratory, is one of four entities to support the cloud lab program for NIGMS, an institute of the National Health Institutes (NIH), including the University of Arkansas, Historically Black Colleges and Universities, and Tribal Colleges and Universities.

In Maine, the INBRE network consists of 14 educational and research institutions, including University of Maine, The Jackson Laboratory, and University of New England, as well as Bates, Bowdoin, and Colby Colleges, College of the Atlantic, Southern Maine Community College, the University of Maine Honors College and the Universities of Maine at Farmington, Fort Kent, Machias and Presque Isle.

The cloud lab program will be introduced in Maine INBRE courses for students of these institutions held at the MDI Biological Laboratory.

The cloud lab program is part of NIH STEPS (Science and Technology Research Infrastructure for Discovery, Experimentation, and Sustainability) initiative.

Maine students will be trained in RNA sequencing analysis using a generic workflow analysis module developed by Benjamin L. King, Ph.D., assistant professor of bioinformatics at the University of Maine and co-director of the Maine INBRE Bioinformatics Core. The module will use data on antibiotic resistant non-tuberculosis mycobacteria generated by: Sally D. Molloy, Ph.D., also from the University of Maine.

The training module provides an example of how cloud computing can advance biomedical knowledge. Using the workflow, students can quickly identify genes associated with antibiotic resistance in non-tuberculosis mycobacteria. Such research could lead to the development of treatments that are effective against this type of infection, which can cause serious lung damage and is a growing health problem.

The module allows students to perform analysis with a keystroke that would otherwise have taken days and would only have been possible at institutions with powerful computing capabilities, King said. While the generic module can be adapted to other research, future plans call for teaching students and researchers how to develop analysis workflows adapted to their research needs.

Leave a Comment