UP’s genome center rolled-out a bioinformatics training and internship program last June after accepting a challenge from Undersecretary for R&D Rowena Guevara to train 100 interns in a year.
Now on its 4th run, Dr. Jan Michael Yap and his team recently welcomed a mix of twenty-five (25) students with degrees in a science or engineering field, as well as young professionals in health & medicine who make up the last batch of interns to complete a 6-week bioinformatics training and internship program.
The Internship and Training PrograM in Bioinformatics Utility and Expertise (IMBUE) is a six-week training and internship program to train 100 Filipino scientists from varied educational backgrounds and expertise from the life and computational sciences in the area of bioinformatics. The program was conducted in four (4) batches with 25 interns per batch at the Philippine Genome Center. The first three batches were conducted in 2019: June – July, August – September, and November – December, with the current batch ongoing, starting 20 January 2020 until 28 February 2020. During the first two weeks of the program, interns are given course lectures on relevant topics in biology: molecular biology, population genetics, and next-generation sequencing, followed by topics in computation: statistics, programming and bioinformatics analyses. The remaining four weeks then focus on independent research projects in bioinformatics with topics ranging from the use of machine learning in vaccine design, to the use of ancient chicken DNA to trace human migration patterns in Southeast Asia.
Viewing it as an opportunity to build a critical mass of bioinformaticians, the DOST’s Philippine Council for Industry, Energy, and Emerging Technology Research and Development fueled a PhP8.5M grant to implement the IMBUE training & internship program.
“From the training application alone this project yielded us actionable data in moving forward” says Dr. Yap who leads the project. Yap’s team screened about 400 applications to fill in the 100 slots since the internship debuted last June 2019. This overwhelming response, tough as it seems for the screening team, is among the considerations in scaling up the project. “With the set eligibility to be accepted in the program, the data shows how big the ‘pond’ we need to fill; secondly, it also gave us ideas how to possibly replicate this training and internship program in Visayas and Mindanao, if given the chance” added Yap.
The IMBUE project and interns gain recognition at international education confab
The IMBUE team consisting of Dr. Jan Michael Yap, Dominic Albao, Kenneth Kim, Shebna Rose Fabilloren, Rosjel Jolly Lambungan, and Carlo Lapid presented their work and won at the 2019 Education Conference, jointly organized by the International Union of Biochemistry and Molecular Biology (IUBMB) and Philippine Society for Biochemistry and Molecular Biology (PSBMB) at The Manila Hotel, Manila City, Philippines on November 13-15, 2019. The poster entitled “A Project-Based Internship To Train Filipino Undergraduates and Professionals in Bioinformatics” won second place in the Education Category. Moreover, the team is also set to present their work in the upcoming international conference “New Perspectives in Science Education” in Florence, Italy on March 19-20, 2020.
Meanwhile, a few of the research projects performed during the internship program have also gained recognition in international conferences. 1st batch interns, Marc Jeronne Castro, Rian Fritz Jalandoni and Yumi Briones presented their internship work entitled “A Directed Minimum Connected Dominating Set for Protein-Protein Interaction Networks” at the Workshop on Computation: Theory and Practice held at De La Salle University in partnership with the University of Tokyo last September 26-27, 2019. Brian Joseph Permejo, Maria Charlene Tapia and Aleimar Villabrille, who were also part of the 1st batch of interns, presented their project titled “Modelling and Molecular Dynamics of Integrin Heterodimers Related to Chronic Kidney Disease” while Michelle Narciso and Elcid Aaron Pangilinan, also from 1st batch, presented their work “Workflow Management System for De Novo Genome Assembly through Tool Containerization and the Common Workflow Language” at the 46th PSBMB Annual Convention last November.
Portable & executable learning kit
Building on its training syllabus and methodology, interns’ feedback, and available platforms, the team is also poised to “design and patent” a portable leaning tool kit that will make bioinformatics training more accessible to interested learners, thereby increasing more avenues for learning. This training tool kit is akin to DOST’s Lab-in-Mug project.
The possibility of bringing IMBUE to the regions
Dr. Yap and his team went to Xavier University, Mindanao State University, and UP Cebu last November 17 to 21 to further increase awareness on the availability of this
training program, and to also generate more applicants from the regions. With the fixed stipend of ₱19,000 to help cover the intern’s travel and living expenses over the six-week internship in UP-PGC located in Diliman Campus, collaboration with potential co-hosts were also being explored.
Capability building activities in Visayas, Mindanao and beyond
Apart from IMBUE, the Department of Science and Technology also funded the “Enhanced Capability Building in R&D in Genomics” last year. It is instrumental in setting up PGC’s satellite facility in Visayas, and in Mindanao. Dr. Cynthia P. Saloma, the program leader, and PGC executive director shared “the availability of tools, experts, addressing the learning gaps of the students, and providing an enabling atmosphere are very crucial in rolling out training programs”. “Thankfully DOST and the University see the value in our activities and project proposals, the science that we do and the direction R&D is heading, ‘translational research’, data-driven analysis and decision-making is now becoming the norm”, added Saloma. As a molecular biologist, Dr. Saloma is also aware of the enormous demand for skilled bioinformaticians here and abroad. The fast-paced upgrades of Next Generation Sequencing technologies in sequencing genomes of any organism somehow sets the pace for bioinformatics as a field.
UP System-wide MS in bioinformatics
Since it was established in UP in 2009, the Philippine Genome Center has long been active in offering training programs in bioinformatics. For long-term yield in increasing bioinformaticians nationwide, Dr. Yap also formed a UP System-wide committee to develop the curriculum for the MS in Bioinformatics in UP. Currently, the proposal is undergoing a review process in each participating campus. DOST Usec. Guevara is also looking forward to the offering of the MS Bioinformatics program in UP as early as August 2020.
About the Philippine Genome Center
The Philippine Genome Center is a genomics-focused and multidisciplinary institution which combines basic and applied research for the development of health and therapeutic products and services, improve the competitiveness of our agriculture and aquatic resources through research. It was established to facilitate the translation of knowledge in genomics into applications beneficial to the Filipinos, to the Philippines. Its main headquarters is located at Ma. Regidor St., National Science Complex, University of the Philippines, Diliman, Quezon City. Visit www.pgc.up.edu.ph for more information about IMBUE and other upcoming capacity building activities. (JORELLE R. SAN JOSE-BONIFACIO, Office of the Undersecretary for Research and Development, Department of Science and Technology)