The Biological Data Management and Analysis Core Facility offers project and thesis topics for students of various academic expertise – from high school students to prospective postgraduate students.
Semestral projects
Semestral projects typically span a single semester and are suitable for university students and talented high school students. Each project is supervised by a supervisor, which also serves as the primary contact for students interested in a project.
Students can be rewarded for working on a semestral project with three credits. After completing a project, the solver must write a three-page summary of the project and its results and present it at a lab meeting if the three credits are to be awarded. Competent students may also be offered part-time employment. This option also applies to students not studying at Masaryk University (e.g. still attending high school or studying at another university).
Currently offered semestral projects are listed below. If you are interested in a project, don't hesitate to get in touch with the supervisor of the project you are interested in.
Migration of web services to the MetaCentrum virtual environment
Supervisor: Mgr. Vladimír Horský, Ph.D. (e-mail, CEITEC)
Synopsis: Various research projects have resulted in the creation of several web services (e.g. PatternQuery, MotiveValidator, ValidatorDB, and ValTrendsDB) that have been published in impacted scientific journals. These services are currently running on end-of-life infrastructure. Some of the services were programmed in an older version of .NET as one monolithic solution and deployed on the Microsoft Internet Information Services web server. Therefore, this legacy software needs to be migrated elsewhere. Our goal is to containerise our legacy web services and run them on the computing resources of the MetaCentrum virtual organisation.
Goals:
- Learn about the web services that need to be migrated.
- Get familiar with the MetaCentrum environment, especially running applications in containers in this environment.
- Perform containerisation of the migrated web services.
- Create documentation describing the containerisation process and the procedure for deploying the application in the container to the MetaCentrum environment.
Prerequisites: Basic command line skills in Linux (a higher level of knowledge and skills is an advantage). Knowledge of C# and .NET and experience using MetaCentrum resources is also an advantage. However, a willingness to learn new skills is key.
Bachelor’s theses
The Biological Data Management and Analysis Core Facility offers thesis topics for bachelor's theses, both at the Faculty of Science and the Faculty of Informatics of Masaryk University. Each topic has a supervisor contact and a link to its listing in the Masaryk University Information System. Some thesis topics are offered at both faculties mentioned above, while others are only offered at one of them. A part-time employment may also be offered to competent students.
The topics currently offered are listed below. If you are interested in any of them, please do not hesitate to contact the topic supervisor.
Deployment of the OMERO system as a part of a comprehensive laboratory data workflow
Supervisor: Mgr. Ing. Tomáš Svoboda (e-mail, MUNI)
Topic description: The CELLIM laboratory (CEITEC) produces a large number of experimental datasets that need to be further processed. The OMERO system provides tools for visualization, annotation, and management of scientific image data, which use can benefit the laboratory.
The objective of this bachelor's thesis: The student will learn about the OMERO system and propose a way in which the system could be optimally deployed and operated for use by the operators and users of this laboratory. In addition, the thesis will address the interconnection between the OMERO system and Onedata, the general distributed data management system. If the analysis results show that the interconnection of the systems is beneficial, the student will propose a procedure or implement a connector that will allow the processing (import) of data stored in the Onedata system in the OMERO system.
Link to this topic in the topic list in the IS MUNI:
Enhancing the FAIRness of Gromacs: Adding Metadata support to dump metadata of dataset in JSON/YAML
Supervisor: Mgr. Ing. Tomáš Svoboda (e-mail, CEITEC)
Consultant: RNDr. Tomáš Raček, Ph.D. (e-mail, CEITEC)
Consultant: Mgr. Adrián Rošinec (e-mail, CEITEC)
Topic description: Gromacs is a popular open-source software tool used by biologists and chemists to simulate molecular dynamics. It is widely used for simulating complex biological processes, including protein folding and drug interactions. However, despite its popularity and usefulness, Gromacs lacks proper support for the FAIR (Findable, Accessible, Interoperable, and Reusable) principles when publishing output datasets. Specifically, it lacks support for generating a proper metadata set for each dataset, which can make it difficult for researchers to find and reuse the data.
The objective of this bachelor's thesis is to analyse the Gromacs dump tool gmx dump and try to add support for outputting metadata in JSON or YAML data file format. This will help improve the FAIRness of Gromacs output datasets by making it easier for researchers to find and reuse the data. The expected outcomes of this thesis are:
- A comprehensive analysis of the current state of metadata support in Gromacs and the gaps that need to be addressed.
- An updated gmx dump tool that supports metadata generation in JSON or YAML data file format.
- Contribute changes to the Gromacs tool community
- A testing report of the updated gmx dump tool and its effectiveness in generating metadata for Gromacs output datasets.
- A set of recommendations for future work to improve the FAIRness of Gromacs output datasets.
Prerequisites: Knowledge of C/C++ programming and the ability to understand existing code (i.e. "software archaeology").
Link to this topic in the topic list in the IS MUNI:
Making data stored in Onedata accessible using a Windows application
Supervisor: Mgr. Ing. Tomáš Svoboda (e-mail, MUNI)
Topic description: The Onedata data management system provides comprehensive distributed data storage, sharing and access capabilities. Because it supports FAIR principles and HPC data processing, it is also suitable for storing scientific research data. For this purpose, it is used to manage experimental data generated on scientific instruments within the Central European Research Institute CEITEC operating within MU.
The aim of this thesis: The student will learn about the architecture and capabilities of the Onedata system, analyse the tools provided by the Windows operating system (e.g. Cloud Sync Engine), and design and implement a proof-of-concept application that will make remotely stored data available to the user. The practical goal of this thesis is to create a native application running under the Windows operating system that will make data stored in Onedata accessible to users. The developed solution can be inspired by the functionality of existing applications that access data from public or private clouds (e.g. ownCloud, Google Drive).
Link to this topic in the topic list in the IS MUNI:
Dissertation theses
Dissertation thesis topics are agreed upon by a prospective PhD student and the leader of The Biological Data Management and Analysis Core Facility. They reflect the prospective student's abilities and research interests and the direction of the core facility. Dissertation thesis topics tend to relate to the offered services of the core facility or these fields of research:
- Development of tools for analysis and visualization of protein.
- Development of methods for extraction and processing of metadata.
If you are interested in a dissertation topic, don't hesitate to get in touch with the core facility leader.
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