Master’s student from Altai State University develops a virtual laboratory - "Vecherny Barnaul"

23 December 2022 Text: Svetlana Ermoshina / "Vecherny Barnaul"
The newspaper "Vecherny Barnaul" reported about the IT development of a talented student from AltSU. “Virtual laboratory for processing and analyzing data on the biodiversity of plant species and bioclimatic modeling” - this is the full name of the development of Zakhar Pokalyakin, a master’s student at the Institute of Mathematics and Information Technology of Altai State University and the REC of Altaistics and Turkology “The Greater Altai”. The interdisciplinary project is designed to help not only the scientists of Altai Krai.

As a reminder, AltSU scientists have developed a “smart” plant monitoring system together with Yandex Cloud.

The virtual laboratory project took third place in the competition "The Best Informatization Projects in Altai" named after V.I. Beregovoy" in the nomination Student apportunITy.

Estimates and forecasts

In the service created at AltSU, you can enter data on the location of plant species in order to analyze and predict the area of growth. It is a kind of digital inventory of the flora of the Greater Altai, and with assumptions where this species can be found in a few years. There are already systems in the world that perform similar functions, but they are either in English or they lack data on Russia. There are scientific articles, databases, but the question of biodiversity has not yet gone beyond the research field to a general user. They decided to fill this gap with their own development of mathematicians and biologists of Altai State University. The former are responsible for the software part, the latter for the actual content. Accordingly, the work has two supervisors: this is an associate professor of the Department of Theoretical Cybernetics and Applied Mathematics Lyubov Khvorova and a senior researcher of the South Siberian Botanical Garden, an associate professor of the Department of Botany Alexei Vaganov.

“We want to create a portal with a number of services for working with geographic information systems, that is, big data on the biodiversity of plants of any territory of your choice will be connected here, ecological niches will be built based on this data, and their areas will be calculated,” specifies Alexey Vaganov. “Another functionality will allow us to evaluate bioresources, the volumes of various groups of plants: medicinal, technical, fodder, and forecasts of their distribution. In the future, anyone will be able to use the browser or mobile version of the portal, regardless of the power of the computer or phone. Scientists and conservation institutions will be able to obtain data on the distribution of species of interest to them: rare, endemic, scientifically promising. The forecast can be carried out up to 2080 - climate data is available until this period. It  assume where the species can spread when the temperature regime changes. Farmers may also be interested in such information in order to predict the spread of weeds. And, for example, allergy sufferers, going on vacation to another region, using our application will be able to assess whether there are allergens there.

Points of Presence

Zakhar Pokalyakin began work on the project to create a virtual laboratory while still studying for a bachelor's degree. He does deal with entering data: he is responsible for writing the program code.

- It took about a year from the idea to the current stage, says the developer. The project is still far from the final form, but already now there is a certain working build, that is, the product has certain functionality and it is possible to use it. The user can specify the points of presence of the species and environmental factors - humidity, temperature, precipitation, and so on - and then use them to model the distribution area of the plant. Neural networks are already working on this, which are trained on data provided by the user, and as a result, the model is able to independently identify the ecological niche of a certain plant species. And the researcher gets the opportunity to assess the potential habitat of this species, to understand how rare it is in this area, where it can be found, where it will take root, and where it will not. Range estimates can be obtained, as well as metrics indicating the validity of these results. Reports are displayed in the form of graphs, charts, maps.

Altai Krai is interested in this service. Data on the resource potential of medicinal, food and rare species of plants in the Greater Altai will serve as a serious basis for assessing the economic potential of the region. There are no plans yet to include animals in the development: they migrate faster, and the dynamics of the range is more difficult to predict.

It is worth noting that a similar development has already shown its value, however, in a different area. Alexey Vaganov explains:

- In Australia, they created a laboratory similar to ours with three global tasks. The first is tracking the dynamics of the ranges of animals and plants with the possible appearance of infrastructure facilities. Simply put, if there are Red Book species at the future construction site, then what will happen to them - will they migrate, disappear? The program calculates these scenarios. The second task is to assess the epidemiological species, that is, those that are the hosts of infections. And the third is the study of alien species that behave aggressively, like our maple: having arrived to us from the North American flora, it began to displace native plants. There are many species that can behave in the same way, and this too can be calculated. We have partly adopted some of these tasks, but we are trying to find an even wider range of applications for the virtual laboratory.

Alpha testing will begin in the first quarter of 2023. The university's partners will be the first users: the Tigirek Nature Reserve, environmental organizations of the Republic of Altai and Kazakhstan.

A virtual laboratory is software that allows research and experiments to be carried out without direct contact with the object of study or laboratory equipment. Most often, experiments are modeled using modern computer algorithms. Such laboratories can serve both for teaching students and for real research activities of scientists without causing harm to the objects of research. Therefore, a virtual laboratory is essential for studying rare plants or animals.

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