COBRA - COmputer Based RNA Analysis and prediction

Title COBRA – COmputer Based RNA Analysis and prediction

Project Type National Recovery and Resilience Plan

Call for tender
Rectoral Decree no. 750 of 02/28/2024 of the University of Bari Aldo Moro – Public notice relating to the cascade call for the project entitled “National Center for Gene Therapy and Drugs based on RNA Technology” – identification code MUR CN00000041 financed in scope of Notice no. 3138 of 16.12.2021 National Recovery and Resilience Plan (PNRR), Mission 4 Component 2 Investment 1.4 “Strengthening research structures and creation of “national R&D champions” on some Key Enabling Technologies” – NextGenerationEU

Identification code CN_00000041 UNIBA_TRACKA1

CUP H93C22000430007

Fund grant deed UNIBA R.D. no. 3096 of 08/28/2024

Purpose
This project has two main aims:
1) to implement a powerful and scalable Compute and storage platform supporting the Omics data-analysis.
In particular, INFN will buy new hardware resources and integrate in the already available Cloud and HPC
installation that is already in production at INFN-Bari, called ReCaS-Bari data center.
Moreover, we will implement new analytics services to support the Omics community and to implement
the services provided within the project.
2) Development of advanced computational tools for the analysis and interpretation of omics data, focused on modeling the structure of RNAs and RNA-DNA interactions using algorithms guided by artificial intelligence. In this WP, we aim to integrate data generated by recent omics platforms with robust theoretical models, based on polymer physics theory.

Methodology:

The INFN-Bari group will initially work on the definition of the technical requirements for the new
hardware to be acquired, with a close interaction with the scientific activities that will provide information about the typology and quantity of resources needed. After the acquisition of the resources they will be installed and configured accordingly with the need of the scientific use cases, and the end users services will be made available to the general Omics community.

The methodology we plan to employ for this WP is a combination of Machine Learning techniques and
numerical simulations. Specifically, as first step we will analyze by means of AI-driven inference publicly
available omics data to identify the molecules and the interaction network necessary to simulate the system
including RNA molecules and RNA-DNA. Once this is achieved, we will make large use of Molecular
Dynamics, mainly using classical potentials, to deepen the understanding of molecular dynamics of the
system, thus enhancing the accuracy and effectiveness of the developed tools.

Scientific coordinator of the project – INFN Scientific Manager – Local Scientific Manager-INFN Bari
Giacinto Donvito

INFN Administrative manager of the project – Local Administrative Contact – INFN Bari
Addolorata Macina

Duration
12 months
Starting Date 09/01/2024
End Date 10/31/2025

Financing Contribution for INFN € 721.950,00