Noah’s Ark launched at Moscow State University

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Noah’s Ark launched at Moscow State University

The large-scale electronic database is designed to work with a wide variety of biological information – from the diet of single-celled organisms to sequenced genomes.

We recently wrote that work on creating a digital herbarium is in full swing at the Moscow State Institute. However, the digital herbarium is only part of a huge information system called Noah’s Ark, which contains data on specimens from the biological collections of the university and its partners involved in the project.

Some collections of microalgae are stored in special refrigerators at a temperature of +10°C. (Photo: Peter Kamensky.) The information system was developed by programmers from the Research Institute of Physical and Chemical Biology named after. A.N. Belozersky Moscow State University together with scientists from the “Microorganisms and Fungi” direction of the “Noah’s Ark” project. (Photo: Peter Kamensky.) Today the information system includes 19 different collections of biological material. The list of collections and samples is constantly updated. Soon all samples will have an individual barcode, which will make them much easier to find. (Photo: Peter Kamensky.) Suspension cultures of microalgae after reseeding must be grown on special “rocking chairs”. (Photo: Peter Kamensky.) ‹ › Open full size

For each sample, MSU staff create detailed passports containing comprehensive information about each of the “collection” organisms. It is important not only the presence of the sample itself, but also its detailed description: what kind of organism it is, by whom, where and when it was collected, what is remarkable about it, and why it can be used in science and practice.

According to the head of the Microorganisms and Fungi department, Alexey Solovchenko, the information system has everything to become a real knowledge base about living organisms. In the “Noah’s Ark” (which is being created within the framework of the Russian Science Foundation grant “Scientific foundations for the creation of the National Depository Bank of Living Systems”), you can save not only a description of the organisms themselves, but also all the methods of working with them: how to cultivate them, study them and preserve them for a long time time. This is especially important for collections of single-celled organisms such as bacteria and microalgae.

“The main operating principle of the system is an adaptive sample passport form, which initially contains a minimum of information describing each sample, regardless of the type of biomaterial and collection: data on where and how the sample was obtained, as well as information about the living organism from which the material was taken . The rest of the passport is configured so as to optimally and completely reflect information specific to different living beings and storage units, from bacteria to animals,” says the scientific coordinator of the Noah’s Ark project, leading researcher at the Faculty of Biology of Moscow State University Petr Kamensky.

One of the main “advantages” of the system is the ability to automatically download information about stored organisms from authoritative international databases, such as Catalog of Life, NCBI GenBank, etc. Thus, a sample passport can contain a wide variety of information, up to the DNA sequence. Some genomes were sequenced specifically as part of the project, while other samples require access to external databases.

For now, the genomic browser built into the system is under development, but in addition to it, the system will eventually have other bioinformatics services, with the help of which users of the depository will be able to extract the maximum benefit from the information stored in it.

The number of digitized samples is constantly increasing due to the uploading of new collections and the addition of information from existing electronic databases. “Noah’s Ark” was developed in such a way as to collect information from collections not only from Moscow University, but also from other scientific organizations – thus, for the first time, a prototype of a system capable of connecting together all Russian biocollections was created.

“At the moment, about 510 thousand samples are loaded into the system, 500 thousand of which are herbarium samples, and about 10 thousand are detailed characterized microorganisms. For them, in addition to microphotographs, detailed descriptions are loaded into the system, down to the preferred “menu” and “fingerprints” (genome fragments). By the end of 2018, we plan to upload into the information system all the samples that are in the collections of Moscow State University,” continues Pyotr Kamensky. “Currently there are 19 collections in the system, the process of inventory, digitization and data downloading continues.

Physically, the collections of the Moscow State University Depository are located in those laboratories in which they are worked with. If we take the biology department, there are at least a hundred collections there. Previously, the owners of collections knew little about each other, and, accordingly, only those people who directly worked with them could use the collections. With the advent of our information system, the situation has changed dramatically.”

The creation of such a large-scale electronic system requires strict ordering of samples. This was achieved by providing each sample with a unique barcode: by photographing the barcode with a regular smartphone, in a split second you can find in the database all available information about this sample and download its passport. The developers plan to create convenient tools for working with the information contained in the system and make it possible to submit online applications for obtaining biological material. The current version of the system is available at depo.msu.ru.

Biological collections are needed not only and not so much so that there is something to show to students and other public. First of all, they store material for a wide variety of research – the collections are used by biologists of various specialties, from botanists and zoologists to geneticists and ecologists. In addition, they serve to preserve biodiversity, if we are not talking about dried samples, but about “living” collections, such as a seed storage or microorganism bank. (Details about why biobanks are needed and how the biological collections of Moscow State University were formed can be found in the article by the rector of Moscow State University V.A. Sadovnichy, published in the December 2015 issue of Science and Life.) Digital technologies not only make the collection more convenient and accessible, but also allow scientific research to be carried out at a qualitatively new level. The new database is already being actively used in research work – the information that was obtained with its help can be found in recent articles published by project participants in the journals PLOS ONE, Molecular Phylogenetics and Evolution and Photosynthesis Research.

There is no doubt that “Noah’s Ark” has a great scientific future ahead of it – there is no analogue of such an information system in the world that allows one to operate with information about biological samples of a wide variety of nature, as well as manage storage facilities for biomaterial.

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Nicholas Ross

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