Autumn 2023 Program

This is the program of the Sitola seminar in autumn 2023. Presentations for the current semester are available here.

• 14.9. – 16.9. 2023
  SitSem seminar at Telč
  Program and presentation slides

• 20.9.2023
  RNDr. Petra Němcová
  Caverdock 2.x: Multi-receptor approach
  Abstract: The receptor-ligand interactions are an essential part of many biologically relevant processes. The small ligand molecule needs to pass via a tunnel into a receptor before the interaction of interest begins. Both receptor-ligand interaction and ligand pathway need to be studied. CaverDock is a computational tool that simulates the transport of the ligand in a tunnel. CaverDock 1.0. works with one receptor’s conformation.
  Since then, we have made several improvements. CaverDock 2.0 can work with multiple receptors and, therefore, can better simulate natural receptor behavior. However, when implemented naively, the multi-receptor approach may break continuous movement. I will present the definition of the problem, its possible solutions, and the computationally lightweight solution we have implemented.
• 27.9.2023
  Ing. Václav Oujezský, Ph.D.
  Habilitation lecture, Ústav telekomunikací, zasedací místnost SC7.53, 7. patro, blok C, Technická 12, Brno
  Invitation
• 4.10.2023
  Juha Törnroos
  Building services to enable world-class research
  Abstract: With over 100 thousand lakes, the most metal bands per capita and one of the world’s best education system Finland has a unique state owned enterprise CSC – IT Center for Science Ltd that is responsible for developing and operating services for Finnish research. This insider view gives an insight to some of the successes and challenges of data management and compute service development in Finland in the past 10 years. Unique national setting has enabled significant contribution to European research infrastructures and services, such as ELIXIR, EuroHPC LUMI and European Open Science Cloud.
• 11.10.2023
  Mgr. Viktória Spišaková
  Internship in the US: Is it better across the big pond?
  Abstract: It is compulsory to participate in at least one monthly internship abroad during doctoral studies. There appeared an opportunity to spend a semester at Carnegie-Mellon University (CMU), PA, USA, in a Cloud Computing lab led by Prof. Majd Sakr. CMU is a prestigious university ranked (in the US) #2 in the undergraduate CS program and #4 in the graduate CS program and has high expectations both from students and faculty members. I will present my impressions of the faculty, lab, university, working environment, approach to doctoral students, and overall style of education. Moreover, internships are meant to broaden cultural horizons, so I will present the city of Pittsburgh, the living standard in the US in the year 2023, and places I visited across the country. Lastly, I will state not only whether I was able to fulfill the expectations of CMU but also if CMU and the United States of America met mine.
• 18.10.2023
  RNDr. Lukáš Hejtmánek, Ph.D., RNDr. Tomáš Rebok, Ph.D.
  New technology course at FI MU
  Abstract: As the use of large infrastructures such as e-INFRA CZ increases, so does the need for knowledge to use them efficiently. We are in the process of preparing a new technology course at FI MU, which will provide an overview of the available resources (cloud, Kubernetes, batch system), how to access them, and how to use them. The course will include a lab where students will practically train to use the infrastructure and perform some simple tasks. The presentation will outline the course, and we will discuss our ideas for the practical exercises.
  Slides in PDF, video
• 25.10.2023
  RNDr. Matej Antol, Ph.D.
  The EOSC initiative in the Czech Republic from the perspective of the EOSC-CZ project
  Abstract: The European Open Science Cloud (EOSC) initiative seeks to create an infrastructure for publishing, searching, and reusing data, tools, and services for research. European countries are in different stages of national implementations, and this talk will present the Czech approach. More specifically, it will focus on the EOSC-CZ project: a systemic, strategic project that will develop a foundation for adopting EOSC on the national level in three directions: supporting national and international cooperation, providing a technological foundation for „next-gen“ national data infrastructure, and supporting development of necessary research data-related competencies. Moreover, the role of Czech national e-infrastructure e-INFRA CZ (a consortium of CESNET, CERIT-SC, and IT4Innovations) in the EOSC implementation will also be presented. A following discussion about such efforts‘ impact on the everyday conduct of research will be most welcome.
• 1.11.2023
  prof. RNDr. Luděk Matyska, CSc.
  EOSC — what is actually planned?
  Abstract: While starting with a short overview of the Europan Open Science Cloud and FAIR data initiatives, the presentation will mainly focus on the specific components of the planned implementation of EOSC in Czechia. The expected architecture of the National Metadata Directory (NMA), the National Repository Platform (NRP) concept, the role of AAI, and the actual repository platforms to be provided and managed will be presented and discussed. The technology challenges, visions, and expectations will also be commented on.

• 7.11.2023
  RNDr. Jan Fousek, Ph.D.
  Pioneering digital brain research: hands-on experience
  Abstract: Data-driven virtual brain models lie at the center of a push towards interpretable, mechanistic approaches to studying brain states, brain health trajectories, and clinical applications. This talk provides an overview of the science behind the recent advances and achievements, together with the peek under the hood of the EBRAINS research infrastructure, which was built to support such endeavors. Specific focus will be given to the Human Brain Project showcases, which, besides their neuroscientific value, helped to shape and integrate the EBRAINS tools and services through collaborative co-design.
• 15.11.2023
  Seminar canceled due to many other events/conferences this week
  
• 22.11.2023
  Mgr. et Mgr. Jaroslav Oľha
  Towards practical usage of dynamic autotuning
  Abstract: In this overview of my dissertation thesis, I will present a sample of the last few years of my work and place them in the broader context of the current state of the art in the field of autotuning. From traditional offline autotuning, through real-time source code optimization unlocked by dynamic autotuners, to sophisticated systems for prediction of tuning efficiency, it is a story that has been in the making for far too long.
• 29.11.2023
  Mgr. Jaroslav Juráček, Ph.D.
  Genomic data II – The secrets of analysis
  Abstract: In the first lecture on genomic data at SitSem in Telč, we learned what the genome is, why it is worth studying, and how to process the data in the form of a nucleotide sequence to extract information. This follow-up lecture will focus on genomic data analysis in more detail, providing a comprehensive overview of the structure and significance of sequencing data files, processing methodologies, and demonstrating practical applications of nucleic acid sequencing, which has become an indispensable tool in modern medicine.
• 6.12.2023
  Student presentations with ongoing work (organized by Adrian Rošinec and Tomáš Svoboda)

  Jozef Sabo
  Wireguard provisioning system for SensitiveCloud
  Annotation: The system helps with the secure distribution of Wireguard VPN configurations which are needed to set up the tunnel between the client and the SensitiveCloud environment. The SensitiveCloud is an environment developed at the CERIT-SC to secure the processing and storage of sensitive data, such as medical records.

  Jakub Čillík
  Implementing an interface for protein similarity search in the AlphaFold database
  Annotation: This thesis project aims to contribute to the scientific community by implementing a robust similarity search tool for the AlphaFold protein database, emphasizing its significance in empowering biologists with efficient access to protein structural information, thereby advancing research and discoveries in the field of biology.

  Andrej Gáfrik
  Windows client for Onedata research data management system
  Annotation: The objective is to enable users to seamlessly work with data stored on Onedata directly within the Windows environment, streamlining accessibility and functionality. The focus will be on detailing the steps and features that will be incorporated to ensure a native and user-friendly experience, ultimately facilitating efficient data management on the Onedata platform for Windows users.

  Boris Jurič
  Optimizing data transfers for workload orchestrators Galaxy and TESP
  Annotation: Task Execution Service (TES) API is an effort to define a standardized schema and API for describing batch execution tasks. Galaxy is an open-source platform for FAIR data analysis. This effort is aimed at optimizing TESP (implementation of a task execution engine based on the TES standard distributing executions to services exposing Pulsar application) data management, and Galaxy runner for TES API.

• 13.12.2023 15:00
  AI jokes and Christmas Sitola
  With all AI around, we would like to give you an opportunity to prepare some short AI jokes for our Christmas meeting. Let’s surprise us! If you have any ideas, we will be happy to discuss it. If you have an idea and want to prepare a Christmas surprise, don’t hesitate! Just send Hanka your name, and that’s it.
• Examination period
  Meetings devoted to state exam rehearsals are scheduled mostly. State exam rehearsals are in Czech mostly.

• 31.1.2024
  State exam rehearsals (master and bachelor)
  Markéta Křenková: Using knowledge graphs for predicting food supplement interactions with drugs
  Supervisor: Vít Nováček
  Reader: Mohan Timilsina
• 7.2.2024
  State exam rehearsals (bachelor)
  Martin Janů: Setup utility for Datavideo DAC-70 cross-converter
  Supervisor: Lukáš Ručka
  Reader: Martin Piatka

  Jakub Kováč: Reimplementation of Live555 plugin for UltraGrid
  Supervisor: Lukáš Ručka
  Reader: Martin Pulec

  Ján Repka: Scientific network tags (scitags) implementation using P4 language
  Supervisor: Miloš Liška
  Reader: Lukáš Ručka

Contact: Hana Rudová