Bogor Agricultural University (IPB) launched five open applications in the field of computational science. The launch of this university’s work application is in the context of developing computational science as a research tool.
Not only that, this activity seeks to reach out to various universities in collaboration with the National Research and Innovation Agency (BRIN) to launch various researches that are useful for researchers and the public. IPB University researcher from the Tropical Biopharmaceutical Study Center (Trop BRC) Dr. Wisnu Ananta Kusuma introduced two applications, namely IJAH Analytics and Integrated Single Nucleotide Polymorphism Pipelien (ISNIP).
Both of these applications have been used in various researches, especially in the pharmaceutical field. Wisnu explained that the IJAH Analytics application is a drug target interaction (DT) prediction application.
The application uses the semi-supervised learning method BLM-NII (Bipartite Local Model-Network Interaction Profile Inferring) between compounds and proteins. He admitted, this application was expanded so that it is not only used in research about DT, but also to the efficacy of plants and the composition of herbal medicine.
“This application aims to find the efficacy of a plant or plant composition as well as to find potential formulas for certain diseases,” he explained.
With this application, he said, he could find alternative plants that previously had no history as herbal medicine compositions. The results of the analysis using machine learning BLM-NII are then stored and displayed in the IJAH analytics database.
The IPB University researcher continued, the ISNIP pipeline application functions to detect variants or single nucleotide polymorphisms. The application requires data fragments sequencing results using Next generation Sequencing (NGS).
“SNIP is one of the latest molecular markers that has begun to be widely studied, in the form of changes or variations of one nucleotide base in DNA sequences,” said Wisnu in his written statement, Friday, August 19, 2022.
Use of SNIP
He continued, SNIP can be used to research the genome of plants to humans using statistics or machine learning. The data results will be annotated and then assembled into a pipeline. “These steps can use open software so that researchers will find it easier to use because it is freely available,” he added.
The IPB University lecturer continued, an example of the IJAH application is to analyze bitter melon plants. The results of the analysis found that bitter melon can target 62 compounds, five proteins, and 13 diseases.
“The relationship between compounds in bitter melon and disease can be linked directly to database sources which are also freely available. However, further validation is needed in the laboratory to really prove this prediction,” said Wisnu Ananta.
Meanwhile, SNIP can be used to analyze a disease, such as analyzing the Omicron variant of the COVID-19 virus. The tool can also be used to make primers or marker genes which are then used for PCR tests.