Other International Projects

General information about H2020 EuroHPC (The European High Performance Computing) grants:
eurohpc-ju.europa.eu

IO - Software for Exascale Architecture

• Principal Investigator: Jiří Nováček, Ph.D.
• Acronym: IO-SEA
• Project role: Partner
• Project coordinator: Commissariat à l'énergie atomique et aux énergies alternatives (CEA), France
• Project partners: BULL SAS (BULL), France; Forschungszentrum Jülich GmbH (JUELICH), Germany; European Centre for Medium-range Weather Forecasts (ECMWF), United Kingdom; Seagate Systems (UK) Limited (SEAGATE), United Kingdom; National University of Ireland, Galway (NUI GALWAY), Ireland; Vysoka Skola Banska – Technicka Univerzita Ostrava (IT4I), Czech Republic; Royal Institute of Technology (KTH), Sweden; Johannes Gutenberg-Universitat Mainz (JGU MAINZ), Germany; ParTec Cluster Competence Center GmbH (ParTec), Germany
• Investor: H2020 (EuroHPC-RIA) & MEYS
• Implementation period: 1. 4. 2021 – 31. 03. 2024
• Budget: 7 995 952.50 EUR (128 750 EUR for CEITEC MU)
• Web: TBD

IO-SEA aims to provide a novel data management and storage platform for exascale computing based on hierarchical storage management (HSM) and on-demand provisioning of storage services. The platform will efficiently make use of storage tiers spanning NVMe and NVRAM at the top all the way down to tape-based technologies. System requirements are driven by data intensive use-cases, in a very strict co-design approach. The concept of ephemeral data nodes and data accessors is introduced that allow users to flexibly operate the system, using various well-known data access paradigms, such as POSIX namespaces, S3/Swift Interfaces, MPI-IO and other data formats and protocols. These ephemeral resources eliminate the problem of treating storage resources as static and unchanging system components – which is not a tenable proposition for data intensive exascale environments. The methods and techniques are applicable to exascale class data intensive applications and workflows that need to be deployed in highly heterogeneous computing environments. 

Together with its partner, IT4I, CEITEC Cryoelectron microscopy core facility will focus on the implementation of the workflow which comprises transfer of the electron microscopy data to remote computational infrastructure and real-time processing of the data. In addition, the data analysis will generate feedback information for the instruments running at CEITEC and allow for optimization of data acquisition parameters or data collection strategy in real time.

General information about Instruct-ERIC grants:
www.instruct-eric.eu

Enabling user access to bioreactors for real-time in-cell NMR

• Principal Investigator: Lukáš Trantírek, Ph.D.
• Project partners: CERM/CIRMMP, Italy (coordinator), Weizmann Institute/Philipp Selenko Lab; Bruker UK Ltd. (Industrial Partner)
• Investor: Instruct-ERIC
• Funding program: R&D Pilot Projects, Joint Research Action (JRA)
• Implementation period: 1. 10. 2019 – 30. 9. 2021
• Budget: 20 000 EUR

NMR applications to living cells requires that the cells remain viable and metabolically active during the duration of the NMR measurement to preserve the biological significance of the experiment. Typical in-cell NMR experiments are performed under static sample conditions, and are limited to few hours of experimental time to avoid compromising cell viability. Moreover, even in that short time frame, the metabolic homeostasis of the cells is not maintained, due to changes in the chemical composition of the external medium. To overcome this limitation, NMR bioreactors have been developed, in which a flow system provides fresh nutrients and removes metabolic by-products while the cell sample is kept confined within the NMR active volume. In addition to the existing custom-made designs, a modular design was developed at CERM/CIRMMP in collaboration with Bruker UK Ltd. that allows multiple flow unit configurations, including in-cell NMR bioreactor suitable for a high density of cells, either in suspension or immobilized in a gel matrix. The main technical limitations of current bioreactor designs are: a reduced sample volume / number of cells compared to static in-cell NMR, leading to decreased S/N ratio and prolonged acquisition times, and a relatively long and complex assembly procedure, which can cause cellular stress prior actual in-cell NMR measurements, compromising metabolic homeostasis and cell viability. These aspects need to be optimized to allow widespread application of in-cell NMR bioreactors to real-time monitoring of biological processes. The ultimate goal of this JRA is to implement and standardise a bioreactor setup that is broadly applicable (i.e. can be adapted to any type of in-cell NMR sample) and routinely accessible by non-expert users.