{"id":3043,"date":"2017-02-07T10:32:16","date_gmt":"2017-02-07T09:32:16","guid":{"rendered":"http:\/\/www.sitola.cz\/wordpress\/?page_id=3043"},"modified":"2020-09-19T18:34:34","modified_gmt":"2020-09-19T17:34:34","slug":"autumn-2016-programme","status":"publish","type":"page","link":"https:\/\/www.sitola.cz\/wordpress\/seminar\/autumn-2016-programme\/","title":{"rendered":"Autumn 2016 Program"},"content":{"rendered":"<p>This is the programme of the Sitola seminar in autumn 2016. Presentations for the current semester are available <a href=\"https:\/\/www.sitola.cz\/wordpress\/seminar\">here<\/a>.<\/p>\n<ul>\n<li><strong>28.9.2016<\/strong><br \/>\nHoliday<\/p>\n<\/li>\n<li><strong>5.10.2016<\/strong><br \/>\nIng. Jana Paz\u00farikov\u00e1<br \/>\n<strong>How less is more, even when you are computing atomic charges <\/strong><br \/>\nAbstract: 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.<br \/>\nI have found out that the results of stochastic methods largely depend on extensive application of local optimization method. With systematic analysis, I&nbsp;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.<\/p>\n<\/li>\n<li><strong>12.10.2016<\/strong><br \/>\ndoc. Ing. Vojt\u011bch Spiwok, Ph.D., Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague<br \/>\n<strong>Simulating long time scale by short simulations<\/strong><br \/>\nAbstract: 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.<\/p>\n<\/li>\n<li><strong>19.10.2016<\/strong><br \/>\nRNDr. V\u00edt Rus\u0148\u00e1k, Ph.D.<br \/>\n<strong>Remote sign language interpretation with CoUnSiL<\/strong><br \/>\nAbstract: More than three years ago, SITOLA laboratory started cooperation with Teiresi\u00e1s Centre on the project which resulted in CoUnSiL \u2014 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.<\/p>\n<\/li>\n<li><strong>26.10.2016<\/strong><br \/>\nRNDr. David Sehnal, Ph.D.<br \/>\n<strong>Data delivery and visualisation of 3D macromolecular structures in the browser<\/strong><br \/>\nAbstract: 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. <br \/>\nWe have developed a comprehensive solution for both efficient delivery of large data sets and interactive visualisation of macromolecular structures. First, the <a href=\"http:\/\/webchemdev.ncbr.muni.cz\/CoordinateServer\">CoordinateServer<\/a> 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, <a href=\"http:\/\/ncbr.muni.cz\/LiteMol\">LiteMol<\/a> is an interactive browser based 3D viewer, designed using HTML5 and WebGL technologies that provides all key structural visualisation modes.<br \/>\nIn the talk, I will go through some of the theoretical and practical aspects of the solution and outline possible future developments.<\/p>\n<\/li>\n<li><strong>2.11.2016 15:00<\/strong><br \/>\nRNDr. Ji\u0159\u00ed Filipovi\u010d, Ph.D.<br \/>\n<strong>Using molecular docking to analyze transport processes in proteins<\/strong><br \/>\nAbstract: 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&#8217;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. <\/p>\n<\/li>\n<li><strong>9.11.2016<\/strong><br \/>\n<strong>Next discussion about future SITOLA<\/strong><\/p>\n<\/li>\n<li><strong>16.11.2016<\/strong><br \/>\nVinh Quang Dang, Ph.D.<br \/>\n<strong>Scheduling of mobile robots in manufacturing systems<\/strong><br \/>\nAbstract: 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 <a href=\"http:\/\/dk.grundfos.com\/\">Grundfos<\/a>. <br \/>\nIn 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&#8217;s solutions are compared and evaluated by using those of the MIP model as reference points. <\/p>\n<\/li>\n<li><strong>23.11.2016<\/strong><br \/>\nRNDr. Jan Fousek<br \/>\n<strong>Devectorization of array expressions for selective just in time specialization<\/strong><br \/>\nAbstract: 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.<br \/>\nIn 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.<\/p>\n<\/li>\n<li><strong>30.11.2016<\/strong><br \/>\nIng. RNDr. Barbora B\u00fchnov\u00e1, Ph.D.<br \/>\n<strong>Smart grids, smart homes, smart cities<\/strong><br \/>\nAbstract: 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. <\/p>\n<\/li>\n<li><strong>7.12.2016 15:00<\/strong><br \/>\nMgr. Boris Par\u00e1k<br \/>\n<strong>Virtualization and containers<\/strong> (tutorial, 45 minutes)<br \/>\nAbstract: 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.<\/p>\n<p>[1] <a href=\"https:\/\/www.docker.com\/products\/overview#\/install_the_platform\">https:\/\/www.docker.com\/products\/overview#\/install_the_platform<\/a><br \/>\n[2] <a href=\"http:\/\/docs.master.dockerproject.org\/compose\/install\">http:\/\/docs.master.dockerproject.org\/compose\/install\/<\/a><\/p>\n<\/li>\n<li><strong>14.12.2016 16:00<\/strong><br \/>\n<strong>Christmas meeting<\/strong><\/p>\n<\/li>\n<li><strong>21.12.2016<\/strong><br \/>\nNo meeting<\/p>\n<\/li>\n<li><strong>Examination period 2.1. &#8211; 19.2.2017<\/strong><br \/>\nOnly meetings devoted to state exam training below are scheduled. More days can be added if needed by students.<\/p>\n<li><strong>25.1.2017<\/strong><br \/>\n<strong>State exam training<\/strong><\/p>\n<p><strong> Gabriela Podoln\u00edkov\u00e1: <a href=\"https:\/\/is.muni.cz\/auth\/th\/396214\/fi_m\/\">Pl\u00e1novac\u00ed modul pro cloudov\u00fd middleware OpenNebula<\/a><\/strong><br \/>\nVedouc\u00ed: Dalibor Klus\u00e1\u010dek<br \/>\nOponent: Martin Kuba<\/p>\n<p><strong> Mat\u00fa\u0161 Morav\u010d\u00edk: <a href=\"https:\/\/is.muni.cz\/auth\/th\/374160\/fi_m\/\">Pou\u017eit\u00ed neuronov\u00fdch s\u00edt\u00ed pro dopl\u0148ov\u00e1n\u00ed chyb\u011bj\u00edc\u00edch dat meteorologick\u00fdch m\u011b\u0159en\u00ed<\/a><\/strong><br \/>\nVedouc\u00ed: Tom\u00e1\u0161 Rebok<br \/>\nOponent: Tom\u00e1\u0161 Br\u00e1zdil<\/p>\n<\/li>\n<li><strong>1.2.2017<\/strong><br \/>\n<strong>State exam training<\/strong><\/p>\n<p><strong>Milo\u0161 Sele\u010d\u00e9ni: <a href=\"https:\/\/is.muni.cz\/auth\/th\/374402\/fi_m\/\">Paralelizace intra-frame k\u00f3dov\u00e1n\u00ed v H.265 pro architektury grafick\u00fdch karet<\/a><\/strong><br \/>\nVedouc\u00ed: Petr Holub<br \/>\nOponent: Ji\u0159\u00ed Matela <\/p>\n<p><strong>Adam Zemek: <a href=\"https:\/\/is.muni.cz\/auth\/th\/374459\/fi_m\/\">Vizualizace pro simulaci diskretizovan\u00e9ho neuron\u00e1ln\u00edho pole<\/a><\/strong><br \/>\nVedouc\u00ed: Milo\u0161 Li\u0161ka<br \/>\nOponent: Ji\u0159\u00ed Filipovi\u010d <\/p>\n<p><strong>Andr\u00e1s \u00dcrge: <a href=\"https:\/\/is.muni.cz\/auth\/th\/373859\/fi_m\/\">Spr\u00e1va f\u00e9rovosti u\u017eivatel\u016f v cloudov\u00fdch v\u00fdpo\u010detn\u00edch syst\u00e9mech<\/a><\/strong><br \/>\nVedouc\u00ed: Dalibor Klus\u00e1\u010dek<br \/>\nOponent: Martin Kuba\n<\/li>\n<li><strong>8.2.2017<\/strong><br \/>\n<strong>State exam training<\/strong><\/p>\n<p><strong>Luk\u00e1\u0161 Suken\u00edk: <a href=\"https:\/\/is.muni.cz\/auth\/th\/376267\/fi_b\/\">Reimplementace v\u00fdpo\u010dtu hrubozrnn\u00e9 simulace peptid\u016f<\/a><\/strong><br \/>\nVedouc\u00ed: Ale\u0161 K\u0159enek<br \/>\nOponent: Jana Paz\u00farikov\u00e1<\/p>\n<p><strong>Dominik Tou\u0161ek: <a href=\"https:\/\/is.muni.cz\/auth\/th\/422385\/fi_b\/\">Frontend pro datab\u00e1zi parci\u00e1ln\u00edch atomov\u00fdch n\u00e1boj\u016f<\/a><\/strong><br \/>\nVedouc\u00ed: Tom\u00e1\u0161 Ra\u010dek<br \/>\nOponent: Radka Svobodov\u00e1 Va\u0159ekov\u00e1<\/p>\n<p><strong>Miroslava Voglov\u00e1: <a href=\"https:\/\/is.muni.cz\/auth\/th\/382579\/fi_b\/\">Backend pro datab\u00e1zi parci\u00e1ln\u00edch atomov\u00fdch n\u00e1boj\u016f<\/a><\/strong><br \/>\nVedouc\u00ed: Tom\u00e1\u0161 Ra\u010dek<br \/>\nOponent: Vladim\u00edr Horsk\u00fd<\/p>\n<\/li>\n<\/ul>\n<p>Contact: <a href=\"http:\/\/www.fi.muni.cz\/~hanka\">Hana Rudov\u00e1<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>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 Paz\u00farikov\u00e1 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 [&hellip;]<\/p>\n","protected":false},"author":42,"featured_media":0,"parent":2896,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"_links":{"self":[{"href":"https:\/\/www.sitola.cz\/wordpress\/wp-json\/wp\/v2\/pages\/3043"}],"collection":[{"href":"https:\/\/www.sitola.cz\/wordpress\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.sitola.cz\/wordpress\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.sitola.cz\/wordpress\/wp-json\/wp\/v2\/users\/42"}],"replies":[{"embeddable":true,"href":"https:\/\/www.sitola.cz\/wordpress\/wp-json\/wp\/v2\/comments?post=3043"}],"version-history":[{"count":10,"href":"https:\/\/www.sitola.cz\/wordpress\/wp-json\/wp\/v2\/pages\/3043\/revisions"}],"predecessor-version":[{"id":3502,"href":"https:\/\/www.sitola.cz\/wordpress\/wp-json\/wp\/v2\/pages\/3043\/revisions\/3502"}],"up":[{"embeddable":true,"href":"https:\/\/www.sitola.cz\/wordpress\/wp-json\/wp\/v2\/pages\/2896"}],"wp:attachment":[{"href":"https:\/\/www.sitola.cz\/wordpress\/wp-json\/wp\/v2\/media?parent=3043"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}