Solving the problem of storing trajectories of molecular dynamics in a DBMS
https://doi.org/10.15514/ISPRAS-2022-34(1)-12
Abstract
The paper solves the problem of storing molecular dynamics trajectories in relational and non-relational databases. The traditional approach to organizing the structure of relational tables is not suitable for storing trajectories due to the appearance of a large number of records in one table. It is described how best to place data in the NoSQL class DBMS. These ideas are then transferred to the MySQL relational DBMS.
Keywords
DBMS,
SQL,
NoSQL,
MongoDB,
MySQL,
molecular dynamics simulation,
molecular dynamics trajectories,
TAMD,
Trajectory Analyzer of Molecular Dynamics,
Big Data
Supporting agencies: The author thanks Balabaev N.K. for critical remarks, as well as Sychugov A.A. and Sulimova V.V. for being entrusted to conduct the course "Technology of storage and processing of big data" at Tula State University.
About the Author
Ilya Vyacheslavovich LIKHACHEV
The Institute of Mathematical Problems of Biology RAS - the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences
Russian Federation
Russian Federation
PhD in Physics and Mathematics, Senior Researcher
References
1. W. Humphrey, A. Dalke, and K. Schulten. VMD: Visual molecular dynamics. Journal of Molecular Graphics, vol. 14, issue 1, 1996, pp. 33-38.
2. J. Hsin, A. Arkhipov et al. Using VMD: an introductory tutorial. Current Protocols in Bioinformatics, issue Suppl. 24, 2008, pp. 5.7.1-5.7.48.
3. I.V. Likhachev, N.K. Balabaev, and O.V. Galzitskaya. Available Instruments for Analyzing Molecular Dynamics Trajectories. The Open Biochemistry Journal, vol. 10, 2016, pp.1-11.
4. I.V. Likhachev, N.K. Balabaev. Trajectory analyzer of molecular dynamics. Mathematical Biology and Bioinformatics, vol. 2, issue 1, 2007, pp. 120-129.
5. I.V. Likhachev, N.K. Balabaev. Construction of Extended Dynamical Contact Maps by Molecular-Dynamics Simulation Data. Mathematical Biology and Bioinformatics, vol. 4, issue 1, 2009, pp. 36-45.
6. The PyMol Molecular Graphics System, Version 2.0. Schrödinger, 2015.
7. R.E. Rigsby, A.B. Parker. Using the PyMOL application to reinforce visual understanding of protein structure. Biochemistry and Molecular Biology Education, vol. 44, issue 5, 2016, pp. 433-437.
8. Т. Кайт, Д. Кун. Oracle для профессионалов. Архитектура, методики программирования и основные особенности. Вильямс, 2020 г., 960 стр. / T. Kyte, D. Kuhn. Expert Oracle Database Architecture 3rd ed. Edition. Apress, 2014, 857 p.
9. Р. Шелдон, Д. Мойе, MySQL. Базовый курс. Диалектика, 2007 г., 880 стр. / R. Sheldon, G. Moes. Beginning MySQL. Wrox, 2005, 864 p.
10. Ш. Чаллавала, Дж. Лакхатария и др. MySQL 8 для больших данных. ДМК-Пресс, 2019 г., 226 стр. / Sh. Challawala, J. Lakhatariya et al. MySQL 8 for Big Data. Packt, 2017, 266 p.
11. Р.М. Михеев. MS SQL Server 2005 для администраторов. BHV, 2007 г., 534 стр. / R.M. Mikheev. MS SQL Server 2005 for administrators. BHV, 2007, 534 p. (in Russian).
12. Г.-Ю. Шениг. PostgreSQL 11. Мастерство разработки. ДМК-Пресс, 2019 г., 352 стр. / H.-J. Schönig. Mastering PostgreSQL 11. Packt Publishing, 2018, 446 p.
13. А.А. Зоткина, И.А. Подопригора, Е.И. Маркин. Сравнительный анализ NoSQL баз данных. Вестник современных исследований, вып. 9.1 (24), 2018 г., стр. 146-148 / A.A. Zotkina, I.A. Podoprigora, and E.I. Markin. Comparative analysis of NoSQL databases. Bulletin of Modern Research, issue. 9.1 (24), 2018, pp. 146-148 (in Russian).
14. О.Н. Чопоров, О.Е. Работкина, А.Е. Капишников, Разработка баз данных в среде Субд Ms Access и Ms Visual FoxPro. Учебное пособие. Воронежский государственный технический университет, 2004 г., 171 стр. / O.N. Choporov, O.E. Rabotkina, A.E. Kapishnikov, Development of databases in the environment of DBMS Ms Access and Ms Visual FoxPro. Tutorial. Voronezh State Technical University, 2004, 171 p. (in Russian).
15. Д.А. Шорохов. Создание меню и отчётности для информационной системы учёта игроков и тренеров футбольного клуба „Калининград“ в среде разработки Microsoft Visual Foxpro 9.0. Актуальные научные исследования в современном мире, вып. 7–1 (63), 2020 г., стр. 227-232 / D.A. Shorokhov. Creating a menu and reporting for the information system of accounting of players and trainers of the football club “Kaliningrad” in the environment of Microsoft Visual Foxpro 9.0 development. Actual scientific research in the modern world, vol. 7–1 (63), 2020, pp. 227-232 (in Russian).
16. Top 5 NoSQL databases for Data Scientists in 2020. URL: https://content.techgig.com/top-5-nosql-databases-for-data-scientists-in-2020/articleshow/78330888.cms, accessed 29.09.2021.
17. Ю.С. Порохненко, П.Н. Полежаев. Сравнительный нализ NoSQL баз данных. Актуальные направления научных исследований XXI века: теория и практика, т. 5, вып. 9 (35), 2017 г., стр. 25-30 / Yu.S. Porokhnenko, P.N. Polezhaev. Comparative analysis of NoSQL database. Actual Directions of Scientific Research of the 21st Century: Theory and Practice, vol. 5, no. 9 (35), 2017, pp. 25-30.
18. К. Бэнкер. MongoDB в действии. ДМК Пресс, 2017 г., 394 стр. / K. Banker. MongoDB in Action. Manning Publications, 2011, 312 p.
Review
For citations:
LIKHACHEV I.V. Solving the problem of storing trajectories of molecular dynamics in a DBMS. Proceedings of the Institute for System Programming of the RAS (Proceedings of ISP RAS). 2022;34(1):161-172. (In Russ.) https://doi.org/10.15514/ISPRAS-2022-34(1)-12
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