Thesis/Dissertation: Filip Múdry: User Interface for Molecular Dynamics Data Repository
Bachelor's thesis
User Interface for Molecular Dynamics Data Repository
Abstract
Simulácie molekulovej dynamiky (MD) sú pre moderné vedy o živej prírode (life sciences) kľúčové, najmä v oblasti návrhu liečiv a modelovania vírusov, čo sa potvrdilo aj počas pandémie COVID-19. Táto oblasť však čelí výzve týkajúcej sa správy dát. Cenné súbory dát trajektórií často nie sú systematicky uchovávané, čo bráni reprodukovateľnosti a budúcim metaanalýzam. V dôsledku toho vyvstáva potreba repozitárov …more
Abstract
Molecular dynamics (MD) simulations are essential for modern life sciences, particularly in drug design and viral modelling, as demon- strated during the COVID-19 pandemic. However, the field faces a challenge regarding data management. Valuable trajectory datasets are often not systematically preserved, which hinders reproducibility and future meta-analyses. Consequently, there is a need for repositories …more
Thesis description
The aim of the thesis is to design and develop a proof-of-concept interface for a data repository of molecular dynamics (MD) datasets. As part of the work, a user interface design will be created in Figma and subsequently implemented as a web application built with React and TypeScript.
The development will focus on:
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designing and implementing the repository homepage,
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displaying and enabling search and filtering of the list of data records,
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providing an interface for interactive data deposition using forms,
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components for filtering search results and repository records based on a defined metadata schema,
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containerization of the user interface,
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preparing the solution for easy deployment to the e-INFRA CZ cloud infrastructure.
The solution will be based on the API, and model architecture of the open-source system InvenioRDM, which is also used by the general-purpose data repository Zenodo operated by CERN. The thesis will focus on adapting the general repository to the needs of the molecular dynamics domain and creating a modern, visually attractive design that subtly reflects the life-science orientation of the project.
19/12/2025 13:36, Mgr. Adrián Rošinec, UČO 469240
Consultant
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