Biophysics education section and computational training discussion at VII Congress of Russian Biophysicists

Abstract

We present commentaries on the section “Biophysical education” of the VII Congress of Russian Biophysicists. Presentations are briefly introduced along with the current problems of biophysical education and the educational approach development. We discuss educational course on bioinformatics based on the integration of online databases and the usage of internet platforms for functional annotation of genes and proteins.

VII Congress of Russian Biophysicists was organized on 17–23 April 2023 in Krasnodar at the Kuban State Technological University (Anashkina et al. 2022). The Congress held several science sections on Molecular biophysics, Biophysics of the Cell, Bioenergetics, Biomechanics, Medical Biophysics, and Bioinformatics, as well as Biophysical education (Rubin et al. 2023). Professor Valeriy G. Artyukhov chaired the education section leading the discussion on the problems and perspectives of new education technologies in biophysics and related fields.

Biophysical education experiences new challenges related to the extension and wide distribution of new computer and information technologies. It was noted at the Section by Professors I. I. Digurova and T. V. Machneva in their invited talks (Rubin et al. 2023). High demand for IT specialists for modern industry and healthcare system reorients young scientists from biological background. Distant mode of education in recent years also has limited classical education standards pushing all the universities worldwide for distant education mode. Another challenge for biophysical education is access to modern experimental equipment (Sorokin et al. 2023). Computational models should be used for students to help better understand biophysical experiments. Thus, education in computer science, developing computer skills, programming, and general informatics is a necessary background for the students. The task of digitalization in medicine is a priority for medical universities in Russia followed by reorganization of educational standards. The problems of new educational approaches in medical biophysics and informatics have been discussed at the events organized at First Sechenov Moscow State Medical University of the Russian Ministry of Health (Sechenov University) in Moscow, at the series of international conferences BGRS\SB (Bioinformatics of Genome Regulation and Structure\Systems Biology) in Novosibirsk (https://bgrssb.icgbio.ru/2022/) (Orlov et al. 2023; Anashkina et al. 2023).

The automation of teaching informatics-related disciplines is of special interest for computer scientists. It includes the areas of telemedicine, e-health, and pharmaceutics (Lebedev et al. 2021; Koshechkin et al. 2022). The students studying biophysics have different educational backgrounds—from specialized mathematics schools to biological and socio-humanitarian backgrounds. The issues of developing the biophysics and bioinformatics courses are related to the adaptation of the training to the educational profile of the students with engineering, mathematical, or medical backgrounds. The problem of differences in student backgrounds and future specializations was noted at the Biophysical Education Session VII Congress of Russian Biophysicists by representatives of several universities in Russia. We acknowledge the educational courses in Russia developing at Voronezh State University, Novosibirsk State University, Irkutsk State University, Far Eastern Federal University, Immanuel Kant Baltic Federal University, and Peoples’ Friendship University of Russia (RUDN University). We discussed the bioinformatics course prepared for students at Sechenov University in Moscow (Orlov and Orlova 2022). It was available at the university website and at the site of the Digital Chair of the Digital Health Institute (https://dk.sechenov.ru/).

The educational course aimed for students to learn basic bioinformatics knowledge, and to be able to make their own data processing and coding of complex bioinformatics pipelines. The course content includes the fundamentals of bioinformatics databases, online tools, and web services for medical consultations. The access to various online bioinformatics databases could be integrated using specialized visual online tools not demanding programming skills for the students such as BioGraph (Veljkovic et al. 2023), ANDSystem, and ANDDigest (Ivanisenko et al. 2022).

Examples of the tasks in medical informatics include the creation of the list of genes associated with the given disease (using online databases and resources such as OMIM.org, dbSNP, GeneCards.org, STRING-DB), reconstruction and visualization of the gene network (protein interaction network), analysis of the gene ontologies enrichment, and prediction of the protein secondary and domain structure (Orlov and Orlova, 2022). Reconstruction of a gene network for a given disease using online bioinformatics tools is the key task resulting as the outcome of the bioinformatics training. Such tasks were published in a series of papers co-authored by students. Note the work on gene network models for glioblastoma (Gubanova et al. 2021), schizophrenia (Dokhoyan et al. 2022), Parkinson’s disease (Orlov et al. 2021), and metabolic syndrome (Tiis et al. 2021). The reconstruction of regulatory gene networks in plants using transcription factor binding data was considered by Dergilev et al. (2022). Overall, the computational training based on online bioinformatics tools focused on gene network reconstruction and annotation has been effective for the education of medical students (Orlov and Orlova 2022).

Author contributions

Yuriy Orlov reviewed the Biophysical education section; Vasilisa Turkina and Nina Orlova presented the online education course. Vasilisa Turkina wrote the draft of the manuscript, edited by Yuriy Orlov. All the authors read and approved the final manuscript.

Funding

The publication was prepared with the support of the RUDN University Strategic Academic Leadership Program (YO).

Data availability

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Code availability

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Declarations

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Conflict of interest

Yuriy Orlov is a member of the National Committee of Russian Biophysicists and the guest editor of the special journal issue.