Autumn 2016 Program

This is the programme of the Sitola seminar in autumn 2016. Presentations for the current semester are available here.

• 28.9.2016
  Holiday

• 5.10.2016
  Ing. Jana Pazúriková
  How less is more, even when you are computing atomic charges
  Abstract: Calculation of empirical atomic charges presents an optimization problem: we are looking for parameters that would lead to approximately the same charges as those obtained by quantum mechanics. Traditional least squares method is heavily used, but stochastic methods as genetic or evolutionary algorithms have been emerging in last years.
  I have found out that the results of stochastic methods largely depend on extensive application of local optimization method. With systematic analysis, I effectively combined simple global and standard local method. It reaches the same (or even better) accuracy than state-of-the-art approaches and shorter computation time.

• 12.10.2016
  doc. Ing. Vojtěch Spiwok, Ph.D., Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague
  Simulating long time scale by short simulations
  Abstract: Molecular simulations show a great potential in drug discovery and similar fields. However, progress in this area is limited by the fact that biologically interesting processes are often much slower than nanosecond to microsecond time scales we can currently simulate. In principle it is possible to place a drug and the protein to be influenced by the drug into the same box and simulate their binding. Such simulations were successful for selected systems, however they are far from being routinely used. This problem can be addressed by enhanced sampling techniques introduced in the presentation.

• 19.10.2016
  RNDr. Vít Rusňák, Ph.D.
  Remote sign language interpretation with CoUnSiL
  Abstract: More than three years ago, SITOLA laboratory started cooperation with Teiresiás Centre on the project which resulted in CoUnSiL — a video conferencing environment for remote interpreting of sign language. In the talk, we will present the motivation for this work and its brief history. We will discuss the CoUnSiL features compared to regular video conferencing environments and on-line translation services. In the end of the talk, we would like to mention several observations from such an unusual multidisciplinary teamwork.

• 26.10.2016
  RNDr. David Sehnal, Ph.D.
  Data delivery and visualisation of 3D macromolecular structures in the browser
  Abstract: Recent advances in Cryo-EM and other structure determination techniques enabled a rapid increase in the complexity and size of biomacromolecular structures available in the Protein Data Bank (PDB). A great challenge is to deliver and visualize this data to the user in a reasonable time.
  We have developed a comprehensive solution for both efficient delivery of large data sets and interactive visualisation of macromolecular structures. First, the CoordinateServer provides functionality for dynamic selection of a subset of structural data (backbone, ligand binding sites, etc.) that is of interest to the user. Second, the amount of transferred data is further reduced using binary representation of the standard mmCIF data format called BinaryCIF. The CoordinateServer thus provides a complete solution for efficient transfer of data to user interface. Finally, LiteMol is an interactive browser based 3D viewer, designed using HTML5 and WebGL technologies that provides all key structural visualisation modes.
  In the talk, I will go through some of the theoretical and practical aspects of the solution and outline possible future developments.

• 2.11.2016 15:00
  RNDr. Jiří Filipovič, Ph.D.
  Using molecular docking to analyze transport processes in proteins
  Abstract: Modeling the protein-ligand interactions has many practical applications in e.g. drug discovery or toxic substance decomposition. Computer simulations address the binding of ligand into protein active site and transportation of ligand between protein surface and active site, which can be hidden inside the protein’s cavity. The molecular docking has been developed to predict ligand binding in protein active site. However, with several modifications, it can be used to analyze energy required to transport ligand through tunnels in protein from/to active site. Unlike geometrical analysis, our method gives qualitative results. On the other hand, it is faster, easier to setup and easier to interpret results than molecular dynamics. In this talk, I will focus mainly to algorithmic and implementation challenges related to transport process analysis with molecular docking.

• 9.11.2016
  Next discussion about future SITOLA

• 16.11.2016
  Vinh Quang Dang, Ph.D.
  Scheduling of mobile robots in manufacturing systems
  Abstract: The current manufacturing systems have a tendency to become more and more flexible to adapt to the needs of product diversification. These systems consists of a number of automatic machines, material handling devices, e.g. automatic guided vehicles (AGVs) or mobile robots, and a central control computer. Likewise AGVs, mobile robots not only can move around within their working space to transport parts/components among machines but also can execute various value-added activities without human intervention thanks to their manipulation arms. To utilize these manufacturing systems in an efficient manner it is necessary to schedule transportation of product components by mobile robots and to schedule processing of products on machines posssibly by mobile robots. The motivations for this problem comes from the company Grundfos.
  In this work, a computationally effective hybrid heuristic method combining genetic algorithm and tabu search is developed to solve the problem considering makespan minimization. A mixed-integer programming (MIP) model is also proposed. The quality of hybrid method’s solutions are compared and evaluated by using those of the MIP model as reference points.

• 23.11.2016
  RNDr. Jan Fousek
  Devectorization of array expressions for selective just in time specialization
  Abstract: The scientific software performing numerical analysis is generally written at first in productivity-oriented languages and environments to speed up the development. Often the computational core of these applications is composed of series of element-wise operations and reductions on multidimensional arrays. Later, when performance and scaling become priority, selective specialization can be used to translate computationally intensive parts of the computation to efficiency level language with the information on both target architecture and problem structure being available at compile time.
  In this talk, we show how to extract the structure of the computation from the high-level array expressions notation and translate it to nests of (potentially parallel) loops in C. The benefits of the performed optimizations will be demonstrated on benchmark codes derived from selected real-life applications, showing considerable speedup.

• 30.11.2016
  Ing. RNDr. Barbora Bühnová, Ph.D.
  Smart grids, smart homes, smart cities
  Abstract: The talk will present an overview of current research directions of the Lab of Software Architectures and Information Systems (LaSArIS, FI MU), connected to the simulation and analysis of critical infrastructures in the domains of Smart Grids, Smart Homes and Smart Cities. It will discuss the goals and challenges of such analysis, looking into both design-time predictive analysis and run-time monitoring, with special emphasis of the benefits of data analysis along the way.

• 7.12.2016 15:00
  Mgr. Boris Parák
  Virtualization and containers (tutorial, 45 minutes)
  Abstract: The tutorial will introduce basic concepts behind virtualization, including specific virtualization technologies such as hypervisors and containers. It will present differences between these technologies and motivation for using them as tools to aid development, testing, and in building isolated experimental environments. The tutorial will focus on practical application and examples using Docker [1] and Docker-related tools [2]. Attendees are encouraged to install this platform and actively participate in the tutorial.

  [1] https://www.docker.com/products/overview#/install_the_platform
  [2] http://docs.master.dockerproject.org/compose/install/

• 14.12.2016 16:00
  Christmas meeting

• 21.12.2016
  No meeting

• Examination period 2.1. – 19.2.2017
  Only meetings devoted to state exam training below are scheduled. More days can be added if needed by students.

• 25.1.2017
  State exam training

  Gabriela Podolníková: Plánovací modul pro cloudový middleware OpenNebula
  Vedoucí: Dalibor Klusáček
  Oponent: Martin Kuba

  Matúš Moravčík: Použití neuronových sítí pro doplňování chybějících dat meteorologických měření
  Vedoucí: Tomáš Rebok
  Oponent: Tomáš Brázdil

• 1.2.2017
  State exam training

  Miloš Selečéni: Paralelizace intra-frame kódování v H.265 pro architektury grafických karet
  Vedoucí: Petr Holub
  Oponent: Jiří Matela

  Adam Zemek: Vizualizace pro simulaci diskretizovaného neuronálního pole
  Vedoucí: Miloš Liška
  Oponent: Jiří Filipovič

  András Ürge: Správa férovosti uživatelů v cloudových výpočetních systémech
  Vedoucí: Dalibor Klusáček
  Oponent: Martin Kuba

• 8.2.2017
  State exam training

  Lukáš Sukeník: Reimplementace výpočtu hrubozrnné simulace peptidů
  Vedoucí: Aleš Křenek
  Oponent: Jana Pazúriková

  Dominik Toušek: Frontend pro databázi parciálních atomových nábojů
  Vedoucí: Tomáš Raček
  Oponent: Radka Svobodová Vařeková

  Miroslava Voglová: Backend pro databázi parciálních atomových nábojů
  Vedoucí: Tomáš Raček
  Oponent: Vladimír Horský

Contact: Hana Rudová