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In July 2022, Radka Svobodová was appointed as the official head of the Biological Data Management and Analysis core facility at CEITEC Masaryk University (MU). The new core facility was established in January 2022 and focuses on storing and analysing various types of biological data. Radka Svobodová is leading a team of eight members at the youngest of all CEITEC’s core facilities. Her core facility offers services in data annotation and repository systems, access to computing and storage resources, structural bioinformatics support and services connected to the ELIXIR project. Radka is responsible for setting the portfolio of relevant technological services and adequate resource planning. She ensures top services and their implementation at the world-class standard and provides resources in biological data management and analysis.
What is the added value of the Biological Data Management and Analysis Core Facility for researchers? Who are the typical customers of her core facility, and what are their needs? What are the most significant challenges in data management and data analysis? And how will her core facility address those challenges? Read the following interview with Radka Svobodová to get answers to those questions!
Radka, you are now leading the new Biological Data Management and Analysis core facility for several months. What is the added value of your facility for researchers?
Nowadays, most of the researchers produce data. It can be raw data directly from an experiment, results of analyses or final data for publication. Many great ideas, efforts, time and money, were invested to reach this data, and the data are precious to the research community. This data should and deserves to be archived. And not only archived, but it should also be findable, accessible, interoperable and reusable (FAIR) for other scientists because only in this way can we fully exploit data. Moreover, the legislation of the EU countries motivates us step-by-step to make the data FAIR. Our core facility helps the researchers to perform this task.
Moreover, the BioData core facility provides a gate to ELIXIR CZ bioinformatics infrastructure expertise and IT resources and to the IT infrastructure of the Institute of Computer Science (ICS). Last but not least, our core facility offers validation and analysis of structural bioinformatics data.
What do you like the most about working with biological data?
It is possible to reach precious and interesting results by analysing biological data. For example, many great articles in top-class journals were prepared based on structural bioinformatics data. Currently, we have a supercritical amount of data, and we have computational resources to interconnect and combine them. And most of the data is waiting for our deeper analysis. I enjoy the potential hidden in the biological data that we can uncover. The core facility allows me to touch various biological data types and support researchers in their analyses and archiving.
Who are the typical customers of your core facility, and what are their needs?
Typical users are researchers who would like to archive their data. We offer archiving of the data to all CEITEC core facilities – their data and their users’ data. In parallel, we provide this support also for CEITEC research groups.
Typical users are also researchers who need to use advanced IT resources. For example, they developed some software and needed to run it on powerful virtual servers. Or they want to use high performing compute resources. Our users are also researchers dealing with biomacromolecular structures and who need support with their analyses.
What are the most significant challenges in biological data management and data analysis?
The first challenge is the data size – from MBs to thousands of TBs. And the size of the data is still rapidly growing. The second challenge is the variability of the data and also the variability of metadata describing the data. Data standards are often missing or just partially present.
How is your core facility addressing those challenges?
Members of our core facility are skilled informaticians and bioinformaticians with an experience in complex life science projects. Therefore, they can design, develop and operate advanced workflows, databases and tools.
Moreover, our core facility is a part of the ELIXIR infrastructure for processing and storing bioinformatics data. Therefore, we have access to ELIXIR expertise and contacts with the ELIXIR research community. Last but not least, we can use robust and rich IT resources of ELIXIR CZ and ICS.
Is your core facility offering any courses or workshops for researchers that would expand their data management and analysis skills? What particular course would you recommend and why?
Yes, we offer training. Specifically, training focused on our structural bioinformatic tools and databases (Mol*, MOLE, 2DProts, ACC2, ValTrendsDB, …); protein structure deposition, validation and analyses; and advanced usage of PDB and related tools (PDBe-KB, AlphaFoldDB, CATH, ...). We can also offer training about ELIXIR and ICT resources. Moreover, we prepare training focused on archiving data generated by certain core facilities or measurement tools.
About Radka Svobodova
Radka Svobodova studied Biochemistry and, in parallel, informatics at Masaryk University. She holds a PhD in Biomolecular Chemistry and spent ten years in the industry. She worked as a researcher and section lead in Life Science Division at Siemens. During her career at Siemens, she spent several months in Ireland, Austria and Germany. Then, she received a job offer from Professor Koca and returned to academia and became an employee of NCBR and CEITEC. Here, she used her IT and management experience from the industry within the creative and open-minded environment of the university. She built a team of several skilled and enthusiastic informaticians and bioinformaticians. Together, they have produced software tools and databases, which are now integrated into essential bioinformatics data resources (e.g., Protein Data Bank, CATH) and used by thousands of researchers. Radka Svobodova is the author of 50 publications cited more than 2,000 times, and her h-index is 20. Radka is also the Head of Node at ELIXIR CZ research infrastructure and strongly cooperates with EMBL-EBI. In 2021, Radka accepted the possibility of establishing a BioData core facility, and from July 2022, she became the official head of this core facility. In parallel, Radka is also involved in academia and teaches at the Faculty of Science and Faculty of Informatics of Masaryk University. She supervises several undergraduate, graduate and doctoral students.
Radka is married and has one daughter (10 years old). She and her family like cats; therefore, they host three of them in their home. Radka enjoys cycling, walking in nature and reading. She is also active in her church and enjoys bringing Communion to sick people or preparing children for their first Communion.
