Lead Partner

Sofia University
"St. Kliment Ohridski"
Faculty of Physics

"We are at the dawn of a new industrial revolution of the twenty-first century, and the future will show how molecular machinery can become an integral part of our lives. The advances made have also led to the first steps can become an integral part of our lives. The advances made have also led to the first steps towards creating truly programmable machines, and it can be envisaged that molecular robotics will be one of the next

Being the first school of higher education in Bulgaria, the Sofia University "St. Kliment Ohridski" is nowadays the largest and most prestigious educational and scientific centre of the country. The Group on Biosimulations stems from the Particle Physics Group (PPG) at the Physics Faculty, Atomic Physics Department (which is responsible for the curriculum in Medical Physics). The members of the group have the opportunity to gain experience in respectable European research institutions as CERN (European Laboratory for Particle Physics, Geneva, Switzerland) and JINR (Joint Institute for Nuclear Research, Dubna, Russia). The PPG's expertise is in physical modelling, experiment R&D, data acquisition and analysis, big data, IT approaches in high-energy physics. An example of knowledge transfer from natural to life sciences is the group activity in simulations of biological molecule interactions and in silico drug design by means of high-performance computing and parallel processing. The PPG has established and now operates the Grid cluster at Sofia University. It participated in EGEE (Enabling Grid for E-science), SEE-GRID and LCG (LHC Computing Grid) projects. It has been performing research on projects of the Ministry of Education and Science, the Bulgarian National Science Fund, the European Commission, CERN and JINR and has strong relations with a number of research institutions in Europe and in the US. The group is running a cluster for parallel computing (the BioSim HPC cluster) equipped with GPUs.

Partners

Institute of Molecular Biology "Acad. Roumen Tsanev" Bulgarian Academy of Sciences

The Institute of Molecular Biology "Roumen Tsanev" (IMB-BAS) at the Bulgarian Academy of Sciences is a leading scientific institution in the field of molecular and cell biology in Bulgaria. The research in IMB is focused on the study of the processes and phenomena of living nature at molecular level, including basic and applied research in molecular biology and related disciplines such as structural and cellular biology, molecular genetics and bioorganic chemistry with potential applications in medicine and pharmacy. IMB is well equipped for molecular biology experiments with equipment such as: water baths, shakers, electrophoretic equipment, balances, pH meters, refrigerators, freezers incl. deep freezers, vacuum oven, vacuum pumps, Speed Vac, gel dryer, centrifuges, thermal cycler, ultrasonic disintegrators, FPLC and HPLC systems, 2L and 12L fermenters, chemical fume hoods and two specialized laboratories for bacterial and eukaryotic cell cultures. The shared rooms include autoclaving equipment, centrifuge room, radioactivity counters, spectro(fluoro)photometers and Nanodrop, real time PCR, Phospho Imager, fully equipped fluorescence microscopes, system for spinning-disk confocal microscopy, flow cytometer, system for fluorescent analyses Odyssey, dark room with film developing equipment, and a mechanic workstation. During the last few years IMB obtained Single Molecule Detection Platform (Leica), isotherm microcalorimeter iTC200 (GE Healthcare), and mass spectrometer Thermo Scientific Orbitrap Elite (OTELITE-10000), Next-generation sequencing platform (Illumina) and peptide synthesizer. The Centre for Advanced Microscopy at IMB is part of the Euro-BioImaging consortium (http://www.eurobioimaging.eu/).

Institute of Information and Communication Technologies Bulgarian Academy of Sciences

The Institute of Information and Communication Technologies (IICT-BAS) at the Bulgarian Academy of Sciences is the leading Bulgarian research organization in ICT with internationally-recognized expertise in HPC and supercomputing, artificial intelligence, optimization and intelligent control, robotics and cybersecurity. IICT hosts the largest supercomputer in South-East Europe Avitohol with a total of 20700 cores and 9.6 TB memory, (412 Tflop/s peak performances). Avitohol is part of the Advanced Computing and Data Centre (ACDC) operated by IICT-BAS, together with another HPC system – a heterogeneous HPCG cluster with 22.83 Tflop/s peak performance (total 576 CPU cores, total 8192 GPU cores, and total 540 coprocessor's cores). IICT-BAS is the coordinator of the 6-year project "Center of Excellence in Informatics and Information and Communication Technologies", funded under the Operational Programme "Science and Education for Smart Growth" for enlarging ACDC in the institute with more than 3 Petaflop/s peak performance (HPC/cloud computing) and with 5-7 Petabytes storage, as well as developing and supporting generic and thematic services for open research data and open science on national level. The biomodelling and biocomputing research at IICT is supported under a number of national and international research projects, among them the National Research Programme "Innovative low-toxic substances for precision medicine (BioActiveMed)", research projects with the National Science Fund on in silico studies of antimicrobial peptides and engineering of immunomodulating biologicals, as well as on topological aspects of biopolymers' structure and dynamics within the EC-supported COST Action "European Topology Interdisciplinary Action".

Stephan Angeloff Institute of Microbiology Bulgarian Academy of Sciences

The Stephan Angleoff Institute of Microbiology (IMicB-BAS) at the Bulgarian Academy of Sciences is the leading national center in all branches of microbiological science. Laboratories of the Department of Immunology, where part of the projected laboratory investigations will be performed, are equipped with a flow cytometer with 4 lasers (LSR II, Becton Dickinson), PCR equipment, ELISA plate reader, UV/Vis spectrophotometer, microscopes, incl. fluorescent and confocal, centrifuges, gel electrophoresis devices, microtomes, freezers at -20 and -80C.There is a fully equipped laboratory for cell culture, a GenePix4000A micromatrix scanner (Molecular Devices) is available and a procedure for purchasing of InnoScan1100 is underway. The microarray scanners are used for antibody repertoire studies based on antigen and peptide microarrays. Most types of immunochemical analyses are performed in the laboratories, including two-dimensional gel electrophoresis and HPLC analysis. There is also a refrigerated room and a fully equipped cell culture room. Special emphasis is placed on in vitro validation of in silico models and prognostic results, as well as on the development of bioinformatics techniques based on experimental studies.