Uniwersytet Jagielloński Collegium Medicum Zakład bioinformatyki i telemedycyny

EuChina

EuChina (2006 - 2008)

The bioinformatics team participated in the project called EuChinaGrid. The unification of the European grid system with the one in China was the main purpose of the Project. The participants: Beihang University, Beijing (China), CNIC (China), IHEP, Beijing (China),·Peking University, Beijing (China), GRnet (Greece),·Consortium GARR (Italy), Department of Biology, Università di Roma3 (Italy), INFN (Italy), Jagiellonian University in Krakow (Poland), CERN (Switzerland).

The task for Krakow team was the large-scale calculation to test the newly organized, unified grid system. The calculations were focused on the structural analysis of proteins. The University RomaTre team and our team were involved in prediction of the 3-D structure of proteins of 60 aa polypeptide chain length. The Rome team performed calculations exploiting ROSETTA program, while Krakow team performed calculations using the “fuzzy oil drop” model. The objects of calculations were Never Born Proteins (aa sequence generated randomly) which were assumed to carry the biological activity unknown so far. The prospective pharmacological application was expected. The set of 10 000 sequences were analysed in the project.

eViP

eViP (2007-2010)

The main purpose of his educational Project was the generation of database with so called “Virtual Patients”. The Internet repository with 320 medical cases for international educational use were generated. The adaptation of foreign virtual patients to national standards made the collection applicable to international medical student (http://www.virtualpatients.eu/referatory). Virtual patients generated by eViP project are available in common format for MedBiquitous Virtual Patient and compatible with European databases like Campus, CASUS, OpenLabyrinth i Web-SP.

The partners: St George's University of London (United Kingdom) – coordynator, Karolinska Institutet (Sweden), Ludwig-Maximilians-Universität München (Germay), University of Warwick (United Kingdom), Maastricht University (Netherlands), University of Heidelberg (Germany), University "Iuliu Hatieganu" Cluj-Napoca (Rumania), Universität Witten/Herdecke (Germany).

The eViP was accomplished in 2010. However the collaboration with project’s partners , Departament of Bioinformatics and Telemedicine has been continued in generation eViP.  

COST

COST(2008-2011).

The COST BM0601 NeuroMath in the Department of Bioinformatics and Telemedicine was implemented the project “The role of dorsolateral prefrontal cortex in saccadic eye movement. Multiresolution analysis of event-related potentials using wavelet transform.” The main objective of the COST Action BM0601: Advanced Methods for the Estimate of Human Brain Activity and Conectivity (NeuroMath) is to increase the knowledge on the mathematical methods able to estimate the cortical activity and connectivity in the human brain from non invasive neuroelectric and hemodynamic measurements. Additional objectives include the developing of new techniques for the multimodal integration of neuroelectromagnetic and hemodynamic measurements, and their application in several contexts, from the study of human cortical activity during cognitive tasks to the field of the brain computer interface. Studies on voluntary eye movements have been largely focused on the relation between the dorsolateral prefrontal cortex, caudate nucleus, globus pallidus, substantia nigra pars reticulate and superior colliculus. This neuroanatomical circuit by serial inhibitory connections controls the oculomotor function of the saccadic omnipause and burst neurons (caudate inhibits the substantia nigra pars reticulata, which in turn inhibits the superior colliculus). Neuroanatomical studies measured cerebral blood flow has documented abnormalities in brain regions such as dorsolateral prefrontal cortex, caudate nucleus, globus pallidus for adults and children with ADHD. We analyzed such parameters of saccades as duration, amplitude, fixation, peak velocity, slope, sharpness, position profile, velocity profile, phase profile and relation between peak velocity and amplitude. In present research we analyzed event-related potentials by wavelet decomposition. We used the discrete wavelet transform DWT (Daubechies with 20 coefficients, i.e., Daub20, and Haar). The discrete wavelet transform (DWT) is an implementation of the wavelet transform using a discrete set of the wavelet scales and translations obeying some defined rules. In other words, this transform decomposes the signal into mutually orthogonal set of wavelets, which is the main difference from the continuous wavelet transform (CWT), or its implementation for the discrete time series sometimes called discrete-time continuous wavelet transform (DT-CWT). The NEUROMATH Action aimed to develop an European networks in the neuroscience field which, if possible, should become reference in Europe and contribute to the scientific development of the domain. Scientific research will address questions in the areas listed below. 1. Development of new techniques for the estimation of brain activity and connectivity One of the main objective of this area of research is to increase the knowledge about the accuracy that is possible to obtain for the estimation of brain activity from separate neuroelectric and hemodynamic non invasive recordings. In particular, the possibility is addressed to estimate the cortical activity in selected cortical regions of interest from non invasive scalp EEG recordings. This objective is fundamental since the activity of the brain is generated from the brain and not from the scalp, where it is usually represented. Definitive measure of estimation errors for cortical estimation from non-invasive EEG measurements are to be obtained. Another important goal of this area of research is to increase the knowledge about the estimation of the functional brain connectivity, i.e. how and how much particular regions of the brain cooperate together during cognitive and motor tasks.

We also participated in:

COST Action Action B27: Electric Neuronal Oscillations and Cognition (ENOC)

COST Action BM0605: Consciousness: A Transdisciplinary, Integrated Approach

Consortium TIM (2011 -)

Department of Bioinformatics and Telemedicine UJCM participate in consortium TIM initiative activities ("Information Technologies in Medicine").
The consortium was established by agreement of four Polish University:

  • Military University of Technology in Warsaw – project coordinator
  • Military Institute of Medicine in Warsaw
  • University of Information Technology and Management in Rzeszow
  • Jagiellonian University, Medical College in Krakow.

The aim of the consortium is to take common research and development activities that would be applicable in health care by using current medical knowledge and innovative information technology supporting disease prevention, diagnosis and treatment in clinical practice.

POLONIUM (2012 – 2014)

Project of the category of bilateral collaboration between Poland (Jagiellonian University) and France (Marie et Pierre Curie University – Paris).

The task of the Project is the generation of tools for in silico identification of hydrophobic core. The mutants and the influence of mutation on hydrophobic core were are the main objects of analysis.