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<article article-type="research-article" dtd-version="1.3" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xml:lang="ru"><front><journal-meta><journal-id journal-id-type="publisher-id">vavilov</journal-id><journal-title-group><journal-title xml:lang="ru">Вавиловский журнал генетики и селекции</journal-title><trans-title-group xml:lang="en"><trans-title>Vavilov Journal of Genetics and Breeding</trans-title></trans-title-group></journal-title-group><issn pub-type="epub">2500-3259</issn><publisher><publisher-name>Institute of Cytology and Genetics of Siberian Branch of the RAS</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="doi">10.18699/VJGB-23-103</article-id><article-id custom-type="elpub" pub-id-type="custom">vavilov-3991</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="section-heading" xml:lang="ru"><subject>КОМПЬЮТЕРНАЯ БИОЛОГИЯ РАСТЕНИЙ</subject></subj-group><subj-group subj-group-type="section-heading" xml:lang="en"><subject>COMPUTATIONAL PLANT BIOLOGY</subject></subj-group></article-categories><title-group><article-title>DyCeModel: программное средство для одномерного моделирования распределения гормонов растений, контролирующих образование структуры ткани</article-title><trans-title-group xml:lang="en"><trans-title>DyCeModel: a tool for 1D simulation for distribution  of plant hormones controlling tissue patterning</trans-title></trans-title-group></title-group><contrib-group><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0009-0006-2030-6842</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Азарова</surname><given-names>Д. С.</given-names></name><name name-style="western" xml:lang="en"><surname>Azarova</surname><given-names>D. S.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Новосибирск</p></bio><bio xml:lang="en"><p>Novosibirsk</p></bio><xref ref-type="aff" rid="aff-1"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0003-3438-0147</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Омельянчук</surname><given-names>Н. А.</given-names></name><name name-style="western" xml:lang="en"><surname>Omelyanchuk</surname><given-names>N. A.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Новосибирск</p></bio><bio xml:lang="en"><p>Novosibirsk</p></bio><xref ref-type="aff" rid="aff-1"/></contrib><contrib contrib-type="author" corresp="yes"><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Миронова</surname><given-names>В. В.</given-names></name><name name-style="western" xml:lang="en"><surname>Mironova</surname><given-names>V. V.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Неймеген</p></bio><bio xml:lang="en"><p>Nijmegen</p></bio><xref ref-type="aff" rid="aff-2"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0009-0005-7316-7690</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Землянская</surname><given-names>Е. В.</given-names></name><name name-style="western" xml:lang="en"><surname>Zemlyanskaya</surname><given-names>E. V.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Новосибирск</p></bio><bio xml:lang="en"><p>Novosibirsk</p></bio><xref ref-type="aff" rid="aff-3"/></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0001-8813-8941</contrib-id><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Лавреха</surname><given-names>В. В.</given-names></name><name name-style="western" xml:lang="en"><surname>Lavrekha</surname><given-names>V. V.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Новосибирск</p></bio><bio xml:lang="en"><p>Novosibirsk</p></bio><email xlink:type="simple">vvl@bionet.nsc.ru</email><xref ref-type="aff" rid="aff-3"/></contrib></contrib-group><aff-alternatives id="aff-1"><aff xml:lang="ru">Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук<country>Россия</country></aff><aff xml:lang="en">Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences<country>Russian Federation</country></aff></aff-alternatives><aff-alternatives id="aff-2"><aff xml:lang="ru">Университет Неймегена<country>Нидерланды</country></aff><aff xml:lang="en">Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University<country>Netherlands</country></aff></aff-alternatives><aff-alternatives id="aff-3"><aff xml:lang="ru">Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Новосибирский национальный исследовательский государственный университет<country>Россия</country></aff><aff xml:lang="en">Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University<country>Russian Federation</country></aff></aff-alternatives><pub-date pub-type="collection"><year>2023</year></pub-date><pub-date pub-type="epub"><day>12</day><month>12</month><year>2023</year></pub-date><volume>27</volume><issue>7</issue><fpage>890</fpage><lpage>897</lpage><permissions><copyright-statement>Copyright &amp;#x00A9; Азарова Д.С., Омельянчук Н.А., Миронова В.В., Землянская Е.В., Лавреха В.В., 2023</copyright-statement><copyright-year>2023</copyright-year><copyright-holder xml:lang="ru">Азарова Д.С., Омельянчук Н.А., Миронова В.В., Землянская Е.В., Лавреха В.В.</copyright-holder><copyright-holder xml:lang="en">Azarova D.S., Omelyanchuk N.A., Mironova V.V., Zemlyanskaya E.V., Lavrekha V.V.</copyright-holder><license license-type="creative-commons-attribution" xlink:href="https://creativecommons.org/licenses/by/4.0/" xlink:type="simple"><license-p>This work is licensed under a Creative Commons Attribution 4.0 License.</license-p></license></permissions><self-uri xlink:href="https://vavilov.elpub.ru/jour/article/view/3991">https://vavilov.elpub.ru/jour/article/view/3991</self-uri><abstract><p>Для изучения механизмов роста и развития необходимо анализировать динамику распределения регуляторов по ткани во времени и пространстве и учитывать их влияние на клеточную динамику внутри ткани. Растительные гормоны являются основными регуляторами динамики клеток в тканях растений; они образуют градиенты и максимумы и контролируют молекулярные процессы в зависимости от концентрации. Мы представляем DyCeModel, программный инструмент, реализованный в среде MATLAB для одномерного моделирования ткани с динамическим клеточным ансамблем, где изменения концентрации гормона (или другого активного вещества) в клетках описываются обыкновенными дифференциальными уравнениями. Мы применили DyCeModel для моделирования динамики клеток в меристемах растений с различной клеточной структурой и продемонстрировали, что DyCeModel помогает выявить взаимосвязь между концентрацией гормонов и поведением клеток. Инструмент визуализирует ход моделирования и предоставляет видео, полученное в ходе расчета. Важно отметить, что инструмент способен автоматически подбирать параметры, подгоняя распределение концентраций веществ, предсказанное в модели, к экспериментальным данным, полученным по изображениям с микроскопа. Примечательно, что DyCeModel позволяет строить модели для различных типов меристем растений на основе одних и тех же обыкновенных дифференциальных уравнений, используя для каждой меристемы специфические входные характеристики. Эффективность инструмента продемонстрирована путем моделирования влияния распределения ауксина и цитокинина на формирование паттерна ткани в двух типах ниш стволовых клеток Arabidopsis thaliana: апикальных меристемах корня и побега. Полученные модели представляют собой перспективный фреймворк для дальнейшего изучения роли контролируемых гормонами генных регуляторных сетей в динамике клеток.</p></abstract><trans-abstract xml:lang="en"><p>To study the mechanisms of growth and development, it is necessary to analyze the dynamics of the tissue patterning regulators in time and space and to take into account their effect on the cellular dynamics within a tissue. Plant hormones are the main regulators of the cell dynamics in plant tissues; they form gradients and maxima and control molecular processes in a concentration-dependent manner. Here, we present DyCeModel, a software tool implemented in MATLAB for one-dimensional simulation of tissue with a dynamic cellular ensemble, where changes in hormone (or other active substance) concentration in the cells are described by ordinary differential equations (ODEs). We applied DyCeModel to simulate cell dynamics in plant meristems with different cellular structures and demonstrated that DyCeModel helps to identify the relationships between hormone concentration and cellular behaviors. The tool visualizes the simulation progress and presents a video obtained during the calculation. Importantly, the tool is capable of automatically adjusting the parameters by fitting the distribution of the substance concentrations predicted in the model to experimental data taken from the microscopic images. Noteworthy, DyCeModel makes it possible to build models for distinct types of plant meristems with the same ODEs, recruiting specific input characteristics for each meristem. We demonstrate the tool’s efficiency by simulation of the effect of auxin and cytokinin distributions on tissue patterning in two types of Arabidopsis thaliana stem cell niches: the root and shoot apical meristems. The resulting models represent a promising framework for further study of the role of hormone-controlled gene regulatory networks in cell dynamics.</p></trans-abstract><kwd-group xml:lang="ru"><kwd>компьютерное моделирование</kwd><kwd>траектория развития</kwd><kwd>входные данные</kwd><kwd>генетический алгоритм</kwd><kwd>фитогормоны</kwd></kwd-group><kwd-group xml:lang="en"><kwd>computer modeling</kwd><kwd>developmental trajectory</kwd><kwd>input data</kwd><kwd>genetic algorithm</kwd><kwd>phytohormones</kwd></kwd-group><funding-group xml:lang="en"><funding-statement>The model development was supported by the budget project FWNR-2022-0020. 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