Bioinformatics education course on gene networks reconstruction using online tools

Abstract

Bioinformatics education requires the use of online computer tools for modeling protein-protein interactions, visual presentation of the networks, access to open databases. The usage of online bioinformatics tools makes it possible to reconstruct both protein and genes networks, and develop modeling skills for students. We consider the issues of computer reconstruction of gene networks - complexes of interacting macromolecules - using a list of genes associated with a particular disease, or a complex disorder based on public online bioinformatics tools - STRINGDB, GeneMANIA, Metascape, Cytoscape applications. Examples of computer reconstruction and visualization of gene networks of oncological diseases including glioma, breast cancer, as well as complex mental disorders such as Parkinson’s disease, schizophrenia, were recently published in co-authorship with the students. The use of only online bioinformatics tools is educational in nature, focused on students, both in mathematics and in natural sciences and medical disciplines, who do not have enough skills in computer science, programming, and writing their own code. Automatic construction of lists of genes associated with a disease using open databases (OMIM, GeneCards, MalaCards), computer reconstruction of gene networks, calculations of enrichment statistics for gene ontology categories have been successfully mastered by students. The educational bioinformatics materials designed for the students and with the students were tested at several universities in Russia, including courses in English for foreign students studied in Russia. The tasks of digitalization of medicine, the development of IT technologies are in the priority. The epidemic situation that has existed in recent years and the forced transition to distance learning had accelerated the adoption of measures to change the formats of education, the emergence of new learning platforms. Note a number of qualitatively new tasks of education in the field of digital healthcare, such as the use of blockchain technologies, the use of Artificial Intelligence (AI) methods in support of medical decision-making. Overall, the educational course developed includes a theoretical part (video lessons) and a practical part - performing tasks on the use of computer programs and databases that have found a number of applications for medical problems in the reconstruction and analysis of networks of interactions of macromolecules.