UP Faculty of Mathematics, Natural Sciences and Information Technologies

Laboratory of Bioinformatics

It is equipped with a computing cluster:

• 21 x Intel(R) Xeon(R) CPU E5-2630 v4
• 32 GB RAM, 2 TB HD
• Total 840 cores, 42 TB of disk space

A computing cluster is used for:

• ProBis identification of protein binding sites
• ProBiS H2O detection of conserved waters at interprotein surfaces
• Molecular dynamics (Charm, Amber, Gromacs)
• Anchoring (OE, GOLD, ProBiS)

Blockchain and Language Technology Laboratory

The laboratory is primarily engaged in researching the possible applications of technology, such as smart homes and sensor networks.

The computing cluster consists of 24 computers with 16 CPU cores each, 32 parallel thread capability, 32 GB of RAM, and a GPU unit. A total of 768 parallel processes can be handled by the cluster. Each node has an AMD Threadripper CPU, 32GB of RAM, an NVME disk, and an NVIDIA GTX 1080ti GPU.

The range of calculations on a computer cluster is quite broad:

• Machine translation using deep neural networks on the Neural Monkey platform
• Image recognition using deep neural networks
• Molecular simulations using LAMMPS, GROMACS, and GAMESS-US
• Game theory (Nash equilibrium)

The laboratory also has a modular smart system installed - a smart floor (space, runway), which is designed to detect signs of certain neurological diseases based on gait analysis, and a sensor network with its own control system.

HICUP/Design studio

The Design Studio is dedicated to studying and analyzing the built environment and various objects that integrate computational and communication skills. Through this approach, the Studio provides new opportunities to improve our daily lives and address contemporary challenges.

The design studio houses equipment and tools for: prototyping, designing, and developing electronic circuits, various crafts, creating 3D virtual worlds, making 3D prints, studying human-computer interaction, and designing and creating multimedia content.

The following equipment set is available:

• Tools for prototyping, designing, and developing electronic circuits (oscilloscope, spectrum analyzer, LCR meter, multimeter, power supply, desoldering station, robot kit, graphics tablet with pen)
• Tools for various hand jobs (Trotec speedy 400 laser cutter, extraction system, set of various hand tools, rotary laser, table band saw, 6-piece cordless tool set, electric carpentry face, table belt sander, portable thickness planer, industrial vacuum cleaner, silent piston compressor, pull-type miter saw, electric file)
• Equipment for creating 3D virtual worlds (photo studio, DSD sound recorder, 360 degree camera and 3D camera, camera and two lens set, handheld 3-axis gimbal with stabilizer and double handle, A2 printer)
• Equipment for producing 3D prints (3D printer - desktop, FDM 3D printer Stratasys F170 and Ultimaker 5s, 3D printer Stratasys PolyJet Object 260 CONNEX 3, advanced 3D printing system (with water jet), advanced 3D printing system (dissolving in a hot bath))
• Equipment for studying human-computer interaction (professional drone, compact drone (smaller), drone with "first person view" option)
• Equipment for designing and creating multimedia content (Mac 15" and Mac 13", iPad Pro, Space Gray, 256 GB, 12.9 inch, height-adjustable desks)

   

HICUP/Laboratory for studying cognitive, perceptual, and behavioural processes

The research equipment of the laboratory enables the study of a wide range of cognitive, perceptual, and behavioural processes, from understanding the perception and processing of perceptual stimuli to the structure of decision-making and memory processes, and to understanding the conversion of brain information into actions.

The following set of equipment is available:

• The EEG system with wet and dry electrodes - G-tec Nautilus 64
• TOBII 2 eye tracking glasses
• On-screen Eye Tracking, TOBII Pro, nano, and 4C
• HTC Vive with Tobii tracking integration for VR eye tracking
• EMG, EKG, and galvanic sensors for the Shimmer skin response
• iMotions and Tobii Pro Lab to capture and analyze data
• Smartphones and Smart Tablet
• Industrial Dual Camera System
• Thermal Camera
• Workbench for Prototyping Computer Vision Systems

HICUP/Laboratory for immersion analytics

The Immersive Analytics Laboratory includes Immersive Analytics (IA) research equipment, which is a new interdisciplinary research area focused on exploring new interaction techniques for data analysis.

The key equipment used in these investigations is:

• A virtual reality space (CAVE Virtual Reality) constructed from a motion tracking system and head-mounted displays
• Touch screen (approx. 4.4 m × 2.4 m)
• Tracking and multi-user VR system
• VR glasses with integrated vision tracking with software
• Augmented Reality Head-mounted Display with Wide Viewing Angle
• Stereoscopic Camera
• Smartphone Illumini Room
• Projection System
• Complete: Projector, Mirror Head, MDX Server System
• Fast Projector
• Surround Sound System 

Genetic laboratories for biodiversity and environmental research

The laboratories work towards the preservation of biodiversity, improvement of management, and knowledge of the ecological, genetic, and genomic properties of protozoa and domesticated animals and plants, as well as the development of sustainable conservation and agricultural practices

There are several different genetic laboratories on the premises:

• For isolation of genetic material, amplification with PCR/qPCR, gel electrophoresis, for sequencing (post-PCR)
• For the analysis of ancient DNA, environmental DNA
• For cell culture analysis

The main activities of the laboratories are:

• Study of genetic and genomic properties of protozoa and domesticated animals and plants, microorganisms, and other organisms
• Studying the biodiversity of animals and plants, which is based on an approach called metabarcoding (i.e., identification of organisms based on nucleotide sequences of DNA, obtained with high-throughput sequencing technology)
• Analysis of environmental DNA (non-invasive samples from the environment, such as finger, water, air, etc.)
• Ancient DNA analysis to study the spatial distribution of ancient and recent protozoa
• Transcriptome analysis, with sequencing of total RNA with RNA-Seq of animals and plants
• Study of plant species, interesting for transfer to agricultural ecosystems
• Characterization of agricultural plants at the level of DNA and RNA to determine the most suitable genotypes for cultivation and to optimize the technology of cultivation

Equipment of the laboratory:

• NGS sequencer (Ion S5 with Ion Torrent technology) and equipment for NGS library preparation (Ion OTS and Ion ES) (Thermo Fisher Scientific)
• SeqStudio sequencer for fragment analysis Sanger sequencing (Thermo Fisher Scientific)
• Agilent BioAnalyzer 2100 for quantification of the library
• qPCR (LightCycler 96 Instrument, Roche LifeSciences)
• PCR (SimpliAmp, Thermo Fisher Scientific)
• MagPix (Luminex)
• Plant growing chambers
• Epoch spectrophotometer (Agilent, BioTek)
• Precision XS Automated Pipetting System
• Fluorescent Microscope

Technology laboratory

The Technology laboratory is equipped for research in the field of fundamental and applied botany. The laboratory has basic literature (plant identification keys, pollinator identification keys), which serves to assist employees and students in their daily work in the aforementioned fields. Research is carried out in the following areas: research into plant anatomy, morphological and morphometric analyses, research into pollination biology and pollinators, research into germination ecology, laboratory steam distillation of medicinal and aromatic plants, identification of pests and diseases of cultivated plants, and preparation of herbarium specimens. 

Research equipment:

• Growth chamber POLEKOP ST500
• Growth chamber MEMMERT HPP260
• Microtone LEICA RM2125 RTS
• Extraction arm Alsident Systems 50 - 63 – 75
• Magnifying glass LEICA S100
• Analytical balance - Kern ABJ320-4NM
• Digester Waldner SCALA Secuflow

Chemistry and Food Science Laboratory

The Chemistry and Food Science Laboratory is dedicated to the study of terrestrial and aquatic animals, their ecology, systematics, and evolution. In addition to various tools and devices, the laboratory also has basic literature (keys for identifying animals) available to assist employees and students in their daily work in the aforementioned fields.

The laboratory conducts various research activities such as:

• Macroscopic and microscopic analysis of animal tissues and organs
• Comparative animal morphology, where body structures between different species are studied and compared for the purpose of understanding evolutionary changes and connections between different species
• Systematic studies - classifying species based on morphological characteristics and determining new species or revising existing classifications
• Morphometric analyses, where morphological characteristics of animals are precisely measured and analyzed using computer software

Research equipment:

• Suction arm Alsident Systems 50 - 63 – 75
• Magnifying glass LEICA S100
• Digester Waldner SCALA Secuflow

Botany practice room

The practice room is intended primarily for subjects in the field of plant biology. The lab allows simultaneous playback of images from a microscope or stereo magnifier (live) and a PPT presentation. The lab has two sinks, which allows for simpler experiments.

Research equipment:

• School Microscopes DM300
• School Stereo Magnifiers Leica EZ4
• Camera Microscope Leica DM500
• Computer with Projector and Wall LCD Display
• Logitech StreamCam Webcam and Headphones

Zoology practice room

The practice room is intended primarily for subjects in the field of zoology. The lab allows simultaneous playback of images from a microscope or stereo magnifier (live) while simultaneously playing a PPT presentation. The lab has two sinks, which allows for simpler experiments.

Research equipment:

• Leica BME School Microscopes
• Leica EZ4 School Stereo Magnifiers
• Leica DM500 Camera Microscope
• Leica EZ4W Camera Stereo Microscope
• Logitech StreamCam Webcam and Headset

Chemistry practice room

The practice room is intended primarily for chemistry subjects, but is occasionally used for other subjects that require laboratory use. It is used for the preparation of chemical samples (measuring, weighing, and preparing chemicals), various analytical techniques (titration, chromatography, spectroscopy, mass spectrometry, etc.). It is equipped with advanced laboratory equipment and tools that allow students to learn and perform various chemical analyses in a controlled environment. 

Research equipment:

• TKA Smart2Pure Standard 6l/h water distiller
• Iskra HP 1502 electric cooker
• Julabo SW22 water bath with shaker
• Kambič EasyOven SP-55 dryer
• Asecos type 90 fireproof industrial hazardous materials cabinet
• Waldner SCALA Secuflow fume hood
• SevenGo Duo SG23-FK2-Kit pH meter
• Kern EMB 600 scale
• Kern EMB 500 scale
• Kern EMB 100 scale
• Alsident Systems 50 - 63 - 75 suction arm
• Desktop computer with projector and wall-mounted LCD screen

Genetics and Biochemistry practice room

The practice room is primarily intended for genetics courses, but is occasionally used for other courses that require laboratory use. It is used for the preparation of genetic samples (isolation of DNA, RNA, or proteins from various biological materials), various molecular techniques (polymerase chain reaction, DNA sequencing, nucleotide sequence analysis, etc.). It is equipped with advanced laboratory equipment and tools that allow students to learn and perform various genetic analyses in a controlled environment.

Research equipment:

• Refrigerator (Gorenje, RK62FSY2W) for sample storage
• Protective microbiological chamber MC 9-2
• Fume hood Waldner SCALA Secuflow
• Transilluminator UVP Stainless Steel M-26V
• Shaker IKA HS 260 basic
• IKA magnetic stirrer with heating, RH basic 2
• Water bath Memmert WNB 10
• Centrifuge Eppendorf 5430R
• Vortex shaker Vibromix 10
• Mini centrifuge Labnet C1301-230V
• Laboratory balance Kern ALS 160
• Balance Kern EMB 100
• VisPerkinElmer Lambda 25 UV/Vis spectrophotometer
• Pipettes BRAND Transferpette S (10 µl, 100 µl, and 1000 µl)
• Desktop computer with wall-mounted LCD