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Services

Management of ELIXIR CZ

Life science experiments generate an immense and exponentially increasing volume of data. It is necessary to store the data, make them accessible, interoperable and safe. The mission of ELIXIR CZ is to create a sustainable infrastructure for storing, processing and analysing life science data in the Czech Republic and to provide an access to tools and training to facilitate these activities. Uniqueness of the ELIXIR CZ lies in the expertise provided by specialized groups at significant Czech life research organizations – members of ELIXIR CZ consortium. Jointly they create a bioinformatics platform offering services for wide research community in the open access regime. ELIXIR CZ participates in the pan-European research infrastructure ELIXIR and Laboratory of Bioinformatics at IOCB is the central node responsible for management of the Infrastructure.

Bioinformatic Services for IOCB labs

We offer professional support for institutional users in analysis of protein sequences, modeling of protein structures, prediction of protein-protein interactions and utlization of standard bioinformatics analysis and tools. We offer consulatation on problems in life science disciplines requiring bioinformatics and we provide user-tailored scripts and programs upon requests.

Training and teaching

In collaboration with EBI,SIB and other institutions within and ELIXIR infrastructure we organize trainings and workshops on specific bioinformatics subject on IOCB users demand. In last two years we trained users on Chipster, methods of genom assembly and annotation, Galaxy platform, structural biology databases, chemical databases and proteomic,

Running chemistry and molecular biology databases and tools in chosen regimes

We maintain „ Integrated Database of Small Molecules (IDSM)“ which is aimed to provide connections between chemical and biological space. The database is national contribution to the pan-European ESFRI project ELIXIR – the infrastructure for biological data.
We provide web interface to our tool „INTAA“. The application is aimed to make the calculation of interaction energies between amino acids in proteins easily available for public. The IEM methods are useful to determine the key residues that are important for stability and correct formation of a protein fold.
In collaboration with EBI we offer 3DPAtch. I tis an application facilitating residue-level information content calculations, homology searches, and 3D structure conservation level-based mark-up for protein sequence or profile hidden Markov model (HMM) queries.
Efficient unbiased data analysis is a major challenge for laboratories handling large flow cytometry datasets. We developer special software - EmbedSOM, a non-linear embedding algorithm based on FlowSOM that improves the analyses by providing high-performance visualization of complex single cell distributions within cellular populations and their transition states.