Work Experience

  • Present 2016

    Senior Researcher

    Masaryk University, Institute of Computer Science

  • 2017 2016

    Postdoc Researcher

    University of Vienna, Faculty of Computer Science

  • 2015 2013

    Postdoc Researcher

    Masaryk University, Faculty of Informatics

  • 2013 2006

    Researcher

    CESNET

  • 2011 2006

    Specialist

    Masaryk University, National Centre for Biomolecular Research

Education & Training

  • Ph.D. 2013

    Ph.D. in Informatics

    Masaryk University, Faculty of Informatics

  • M.Sc. 2008

    Mgr. (M.Sc. equivalent) in Applied Informatics

    Masaryk University, Faculty of Informatics

  • B.Sc. 2006

    Bc. (B.Sc. equivalent) in Applied Informatics

    Masaryk University, Faculty of Informatics

News

  • July 2019
    Exploiting historical data: pruning autotuning spaces and estimating the number of tuning steps will be presented at HeteroPar 2019
    Our paper "Exploiting historical data: pruning autotuning spaces and estimating the number of tuning steps" has been accepted and will be presented on HeteroPar 2019 workshop (co-located with Euro-Par 2019 conference).
  • May 2019
    Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport is published in Nucleid Acids Research
    Our paper Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport has been published in Nucleid Acids Research. The paper introduces Caver Web 1.0, a service for comprehensive analysis of protein tunnels and channels, and study of the ligands’ transport through these transport pathways. It provides easy-to-use web-based interface allowing calculations with Caver 3.02 and CaverDock 1.0.
  • May 2019
    CaverDock: A Molecular Docking-Based Tool to Analyse Ligand Transport through Protein Tunnels and Channels is published in Bioinformatics
    Our paper CaverDock: A Molecular Docking-Based Tool to Analyse Ligand Transport through Protein Tunnels and Channels has been published in Bioinformatics. The paper extensively evaluates CaverDock and is therefore complementar to IEEE/TCBB paper. CaverDock implements a novel method for the analysis of transport processes in proteins.
  • April 2019
    Kernel Tuning Toolkit 1.1 has been released
    We have released Kernel Tuning Toolkit 1.1. The latest version newly supports Vulcan API, together with already supported OpenCL and CUDA. It is also capable of profiling CUDA kernels, so a developer has detailed feedback on tuning parameters effect.
  • March 2019
    CaverDock: A Novel Method for the Fast Analysis of Ligand Transport is published in IEEE/ACM TCBB
    Our paper CaverDock: A Novel Method for the Fast Analysis of Ligand Transport has been published in IEEE/ACM Transactions on Computational Biology and Bioinformatics. The paper introduces a novel method for the analysis of transport processes in proteins and its implementation called CaverDock. Our method uses a restrained molecular docking, allowing it to compute energy of transport processes much faster than molecular dynamic-based methods. CaverDock have broad applications in the fields of computational enzymology, drug design and protein engineering.
  • March 2019
    GPU acceleration of 3D Fourier reconstruction is published in Sage IJHPCA
    Our paper A GPU acceleration of 3-D Fourier reconstruction in cryo-EM has been published in The International Journal of High Performance Computing Applications. The paper introduces a novel GPU-friendly algorithm for 3D Fourier reconstruction (a computationaly-demanding part of reconstruction pipeline in cryo-electron microscopy). We have used our Kernel Tuning Toolkit to auto-tune the code for various GPU architectures. The code presented in the paper is integrated in a Xmipp 3.19.
  • October 2018
    Autotuning of cuFFT setup is to be presented at ANDARE 2018
    Our paper Performance analysis and autotuning setup of the cuFFT library is to be presented on ANDARE workshop (part of PACT conference). The paper evaluates the performance of cuFFT library and introduces a method to speed it up by introducing small changes in input data size. The cuFFTAdvisor tool, introduced in the paper, is available here.
  • September 2018
    Preprint discussing the implementation of CaverDock is available
    We have published a preprint of our paper "CaverDock: A Novel Method for the Fast Analysis of Ligand Transport", describing an implementation of the novel method for analysis of tunnels in proteins.
  • July 2018
    Kernel Tuning Toolkit 1.0 has been released
    We have released Kernel Tuning Toolkit 1.0. Version 1.0 is capable of performing dynamic tuning (i.e. just in time recompilation of tunable kernels) and global optimizations of sets of kernels, where tuning parameters affect multiple kernels and/or host code.
  • March 2018
    GPU-accelerated 3D Fourier Reconstruction has been integrated into Xmipp
    We have successfully implemented the autotuned and GPU-accelerated version of 3D Fourier Reconstruction. Our implementation is integrated into Xmipp. The paper will follow.).
  • October 2017
    CaverDock 1.0 has been released
    Our tool for evaluation of ligand's binding or unbinding trajectory with molecular docking has been released. It can be downloaded at https://loschmidt.chemi.muni.cz/caverdock/. The papers describing CaverDock functionality and evaluating it are in preparation.
  • August 2017
    Autotuning of OpenCL/CUDA with global kernel optimization will be presented at ANDARE 2017
    Our paper "Autotuning of OpenCL Kernels with Global Optimizations" has been accepted on ANDARE workshop (part of PACT conference).
  • July 2017
    CaverDock will be presented at ISMB/ECCB 2017
    We are currently finishing CaverDock tool for release. I will present poster focused on basic principles of novel transport method analysis implemented in CaverDock as well as preliminary evaluation of the tool at ISMB/ECCB conference.
  • May 2017
    CERIT-SC HPC Research Group has been established
    The CERIT-SC Centre is a Czech national centre operating computing and storage infrastructure for research and development. The centre cooperates on many interdisciplinary research projects for a couple of years. There are two newly established research groups in the centre, focusing on High Performance Computing and Big Data. Those research groups will focus on general, but still widely applicable research topics, helping infrastructure and their partners to solve challenging research questions requiring huge amount of computation or non-trivial data analysis.
  • January 2017
    This website has been created
    I have finally found some time to create my personal web-site!