IPB University Bioinformatics Experts Share Knowledge Regarding the Role of High-Performance Computing in the Field of Bioinformatics

Three work units at IPB University, namely the Department of Computer Science, Leading Research Laboratory Unit, and the Faculty of Mathematics and Natural Sciences (FMIPA), collaborated to hold the 7th High Performance Computing (HPC) Webinar Series with the theme “HPC in Bioinformatics,” Tuesday (30/30). 11). In this activity, IPB University bioinformatics experts were present to share knowledge related to HPC applications in the bioinformatics field.

Dr. Wisnu Ananta Kusuma, Secretary of the Tropical Biopharmaca Research Center (Trop BRC) IPB University, explained the role of HPC in the process of aligning DNA sequences. He said that one of the DNA sequences helped calculate the value of sequence similarity.
“The results of this alignment are not only needed for the field of bioinformatics but other fields. This process is also useful for mapping DNA, searching databases, predicting protein function, searching for genes, and identifying genetic variations,” he said.

An example of the research he carried out was the alignment of protein sequences on Drug Target Proposing for COVID-19. The goal is to explore other benefits of various herbs that the public has consumed. The trick is to build a model comparing herbal compounds and conventional drugs on the target protein.
However, he continued that it is not enough to compare the similarity values of herbal compounds and conventional drugs. The similarity value of the target protein is also essential to study.

“Then we will get results that may have more potential than just calculating the similarity value of the compounds,” he said. He added that one of the similarity values could be calculated by performing sequence alignment. The use of HPC or High Performance Computing is one technology that can efficiently perform this alignment.

The research he did relate to this alignment was a calculation using Dynamic Time Wrapping in parallel. This technique is used for the non-linear alignment of two signals with time series units. Of course, this technique requires sophisticated computing, so that the role of HPC is needed.
In addition to sequence alignment, HPC also plays a role in parallelizing the pairwise alignment (PA) algorithm.

Auriza Rahmad Akbar, IPB University Lecturer from the Department of Computer Science FMIPA, added that this advanced technology is needed to produce significant data and perform fast processing.
According to him, there are already many algorithms that have been developed. However, it is unknown which scheme produces the best performance on systems sharing the same memory.

“The more data, the more effective it looks. Because if there is less data, the time needed for processing will be longer. Parallel programs will be more beneficial for large data,” he said. Good parallel algorithm performance also depends on an efficient data partitioning scheme. (MW/Zul) (IAAS/ERN)

Published Date : 02-Dec-2021

Resource Person : Dr Wisnu Ananta Kusuma

Keyword : High Performance Computing (HPC) Webinar Series, IPB University Lecturer, bioinformatics