Work Packages

WP1 focuses on the development of algorithms essential for MALDIBANK which aims to support the broad-based integration, processing, quality control, and detailed analysis of MALDI-TOF MS spectra. It aims to develop algorithms for automatic processing of spectra uploaded to MALDIBANK by external users, automated spectra curation pipeline, and novel AI-based architecture for MALDIBANK spectra analysis pipeline.

WP 2 is dedicated to implementing a robust data warehouse for MALDI-TOF spectra and trained AI models, and integrating innovative AI tools developed in WP1 to provide comprehensive business intelligence support. The approach involves establishing an advanced High-Performance Computing (HPC)-cloud convergence infrastructure developed in alignment with Open Science best practices. This hybrid infrastructure aims to enhance system utilisation by leveraging the strengths of both architectures, with the cloud offering scalable services and HPC handling resource-intensive tasks. Emphasis is also placed on data interoperability, involving the development of protocols for efficient data exchange across project components and research infrastructures, and implementing data quality AI tools for continuous monitoring of spectral data stored in the bank.

The general objective of WP3 is to build a global database covering different types of microorganisms including bacteria, cyanobacteria, yeasts, moulds and microalgae. The database will be organised by types of microorganisms and will integrate, in a standardised manner, spectra of strains from various habitats. It specifically aims to acquire data through the selection of existing reference spectra, to extend the coverage of the database through targeted generation of new reference spectra, to develop best practices and an operational framework by defining standard operating procedures (SOPs) for the creation of new spectra and for the identification of isolates, and to investigate new approaches to improve identification.

WP 4 aims to apply the innovative tools for databasing, strain identification, detection of phenotypic characters (e.g., AMR, toxins) and AI algorithms developed in WP1, to demonstrate their relevance and feasibility using world class data generated in
WP3 (previous and new data) and protocols (manuals and videos) provided in WP5 through the IT platform (system and access) provided by WP2. Use cases selected to represent different areas (Health, Food and Environment) will be utilised to test MALDIBANK as a platform for microbial identification. Results derived from WP4 will be used as feedback to refine developments in WP1, WP2, WP3 and WP5. WP4 will contribute to the growth of the MALDIBANK databank and refinement of the tools developed.

This WP will focus on identifying Infrastructure Training Staff and equipping them with state of the art train-the-trainer skills, and developing contents for the daily routine of RI Staff using MALDI-TOF spectra for sample characterisation and analysis, as well as for data curation. It aims to develop and deliver a training programme for RIstaff to enhance their skills in using MALDI-TOF spectra for different applications, according to WP1 and WP4 outcomes, also capacitating them to provide user support namely in TNAs, and deliver tutorials that enable external users to adopt the newly developed services in their daily practice. A specific task will be dedicated to assess and adjust the training programme developed is compatible with ISO17043 requirements.

WP6 will develop a comprehensive DCP to promote the innovative solutions developed within the project, thereby enhancing the visibility and competitive edge of European RI. The project is committed to bolstering European and global collaboration through a series of online and in-person activities, promoting the integration of RI and the solutions developed into wider innovation ecosystems, contributing to the wider dissemination of technology.

WP7 will develop the strategy to ensure the long-term continuity and exploitation of MALDIBANK while maintaining open access for the research community. It aims to create a dynamic resource that not only serves the current needs, but is also capable of evolving with the changing landscape of scientific research and societal demands. WP7 will establish the long-term MALDIBANK governance and exploitation plan aligned with both RIs and users’ interests (T7.1, T7.2), foster an entrepreneurial and innovation culture by strengthening ties with the private sector, particularly SMEs (T7.2), implement a novel ISO technical standard for microbial identification (T7.3).

WP8 oversees the project execution ensuring the project goals are fully and timely delivered respecting the foreseen budget and scope, with the required quality standards by effective project management. It will provide the needed efficient coordination to facilitate the articulation between all project activities and participants, namely the different RIs. It will also develop the project DMP, monitor project risks and opportunities, socioeconomic impact.

WP9 ensures compliance with the ‘ethics requirements’ set out in this work package.

WP 1 - SU

WP 2 - UNITO

WP 3 - Sciensano

WP 4 - UVEG-CECT

WP 5 - WI-KNAW

WP 6 - SPI

WP 7 - INRAE

WP 8 - MIRRI-ERIC

WP 9 - MIRRI-ERIC

Coordinator

Follow us