SU-ODU Bioinformatics Course Trains Filipino, American Researchers

SU-ODU Bioinformatics Course Trains Filipino, American Researchers

Silliman University, through the Silliman University Angelo King Center for Research and Environmental Management (SUAKCREM), and the Old Dominion University (ODU) in the United States collaborate anew, this time on a bioinformatics course/workshop from June 18 to July 3 at the Mariano and Lina Lao Activity Center on campus.

To run for 12 days, the workshop on ‘omics and bioinformatics gathers a target audience of around 30 students, researchers and scholars from different institutions in the Philippines and the US. It is designed to give participants an introduction to the skills and knowledge needed to develop a project using genomics or transcriptomics.

Topics are clustered into three weeks, progressing in level from beginner, intermediate to advanced, with each week’s discussions being a foundation to the next.  They range from overview of molecular ecology, application of ‘omics in answering biological questions, computer sessions dealing with processing next-generation sequencing data in a mostly command line environment, molecular theory in properly handling data during processing and analysis to advanced analysis with SNP data.

Workshop participants will also gain experience running analyses via high performance computing (HPC) resources through ODU’s Turing Community Cluster. Supported by ODU’s Information Technology Services, the Turing cluster contains more than 190 multi-core compute nodes each containing between 16 and 32 cores and 128Gb of RAM, allowing researchers to use parallel programming applications for quick processing of the large amounts of data generated by the latest genomics methodologies.

Lecturers are professors from the Texas A&M University Corpus Christy (TAMUCC), Rutgers University (RU) and ODU. They are Chris Bird (TAMUCC), Dave Gauthier (ODU), Dan Barshis (ODU), Malin Pinsky (RU), Rene Clark (RU), John Whalen (ODU) and Maddy Kenton (ODU).

The upcoming workshop runs under a bigger five-year (2018-2022) project collaboration between Silliman and ODU known as the Partnerships for International Research and Education (PIRE): Centennial Genetic and Species Transformations in the Epicenter of Marine Biodiversity. It is funded by the US National Science Foundation and is administered under the supervision of ODU professor of biological sciences Dr. Kent E. Carpenter as principal investigator. National Scientist and Silliman Professor Emeritus Dr. Angel C. Alcala heads the team in the Philippines as project leader

It is the second time that Silliman and ODU linked up under the PIRE project. The first time was in 2011 involving the broader Coral Triangle region where, among others, researchers and graduate students at the University’s Institute of Environmental and Marine Sciences (IEMS) were trained in molecular ecology and larval distribution techniques and laboratory methods. Heading the Coral Triangle-PIRE project for the University that time was IEMS Director Dr. Hilconida P. Calumpong.

Participants in the ‘omics and bioinformatics workshop have already been identified. They are undergraduate and graduate students from the US (ODU, TAMUCC and RU) and the Philippines, faculty and researchers from the Silliman’s IEMS, Biology Department and College of Computer Studies, and researchers and scholars from the Mindanao State University-Tawi-Tawi, De La Salle University, University of the Philippines Mindanao, University of the Philippines-Marine Science Institute and the National Fisheries Research and Development Institute of the Bureau of Fisheries and Aquatic Resources.

(Accompanying photo appearing on the homepage is lifted from the US National Science Foundation website.)