Periodic Reporting for period 2 - PHINDaccess (Strengthening Omics data analysis capacities in pathogen-host interaction)
Période du rapport: 2020-01-01 au 2022-09-30
Needless to say that Omics science has dramatically shifted the way pathogen-host interaction could be approached. The advent of next-generation sequencing (NGS) allows generating massive Omics data (genomics, transcriptomics, proteomics, and metabolomics) of both pathogen and host, thus enabling to get a refined and exploitable picture of the molecular circuitries induced by the pathogen to ensure its survival. To be able to benefit of such an exciting era, any research institution has to offer an optimized informatics environment enabling proper handling, processing, and analyzing the huge load of Omics data derived from the host and its invading pathogen. PHINDaccess (Pathogen-Host INteraction Data access) has been conceived so that the Institut Pasteur de Tunis (IPT), a research institution chiefly involved in infectious disease research, ensures such a prerequisite and becomes able to discern the multiple facets of the evolutionary arms race occurring between pathogen and host. However, as an emerging research field, Omics science and its immediate applications for a better control of infectious diseases, has to be introduced to the society, which is increasingly aware of the threat posed by emerging pathogens and their intercontinental expansion.
The overall objective of PHINDaccess is threefold: (i) endow IPT researchers with advanced knowledge and skills in Omics science, (ii) provide IPT with an efficient high-performance bioinformatics environment, and (iii) make IPT a regional flagship for excellence in innovative Omics research with increased networking and openness to the socioeconomic sector. Towards this end, IPT has teamed up with world-renowned European centers, namely the Institut Pasteur, the Max Planck Institute for Molecular Genetics, the Center for Genomic regulation, and the Robert Koch Institute, with whom previously EC-funded collaborations have been successfully achieved.
As a first project funded by the EC that is coordinated by a Tunisian Institution since Tunisia has accessed the status of an EC-associated country. PHINDaccess aims to serve as a success story for other Tunisian institutions, and to introduce new governance attitudes and practices.
Thanks to PHINDaccess, members of our financial services and grant offices have been acquainted with the requirements for the role of a coordinator, as they have been fully involved in the management of project and benefited from trainings in the management of EC-funded projects. Furthermore, PHINDaccess is unique in that it embraces RRI principal and endeavors to embed them at the institutional level. Therefore, PHINDaccess would have at term contributed to, (i) establish a structural institutional change leading to a better governance and adhesion to RRI principals; (ii) accompany young researchers at their early career steps; (iii) popularize Omics science and update ethics- and legislation-related issues; and (iv) create a thriving Omics environment, setting IPT on the path of excellence in infectious diseases research.
The overall objective of PHINDaccess is threefold: (i) endow IPT researchers with advanced knowledge and skills in Omics science, (ii) provide IPT with an efficient high-performance bioinformatics environment, and (iii) make IPT a regional flagship for excellence in innovative Omics research with increased networking and openness to the socioeconomic sector. Towards this end, IPT has teamed up with world-renowned European centers, namely the Institut Pasteur, the Max Planck Institute for Molecular Genetics, the Center for Genomic regulation, and the Robert Koch Institute, with whom previously EC-funded collaborations have been successfully achieved.
As a first project funded by the EC that is coordinated by a Tunisian Institution since Tunisia has accessed the status of an EC-associated country. PHINDaccess aims to serve as a success story for other Tunisian institutions, and to introduce new governance attitudes and practices.
Thanks to PHINDaccess, members of our financial services and grant offices have been acquainted with the requirements for the role of a coordinator, as they have been fully involved in the management of project and benefited from trainings in the management of EC-funded projects. Furthermore, PHINDaccess is unique in that it embraces RRI principal and endeavors to embed them at the institutional level. Therefore, PHINDaccess would have at term contributed to, (i) establish a structural institutional change leading to a better governance and adhesion to RRI principals; (ii) accompany young researchers at their early career steps; (iii) popularize Omics science and update ethics- and legislation-related issues; and (iv) create a thriving Omics environment, setting IPT on the path of excellence in infectious diseases research.
Main key performance of PHINDaccess project were:
- Implementation and initiation of the training portfolio.
The course portfolio implemented with partners, mainly IPP (Institut Pasteur in Paris, France) and CRG (Center of Genomics Regulation, Barcelona, Spain) consisted of a series of 24 events, totaling 650 hours deployed during 16 weeks between January 2020 and July 2022. The total number of participants reached 33 trainees, among them 19 participants were constantly present as a core set of trainees, and 13 occasional trainees from Pasteur International Network institutes (Iran, Morocco and Algeria). Internal assessment related to the course's implementation was conducted throughout the project with both trainers and trainees, and submitted to the EC participant portal as a milestone (M2.3).
- Finalization of the informatics architecture installation.
Following the adoption by all participant institutions’ experts of the architecture of the informatics infrastructure to be implemented at IPT, an invitation to tender has been launched for the acquisition of equipment (on IPT own budget).
- Pathogen-host interaction pilot projects and establishment of a dynamic synergy with partners.
Eight ongoing projects on infectious diseases (HPV and, Poliovirus infections, Leishmaniasis, Mycoplasmosis, tuberculosis, candidiasis, theileriosis), which already generated big amounts of NGS data, have benefited from PHINDaccess in terms of data analyses in participants’ labs. Thanks to expert meetings, the scientific pertinence of these projects has been discussed in details and a collaborative program has been agreed upon and initiated.
-Gaining access to Omics platforms.
Given the absence of an Omics platform at IPT, the opportunity to generate additional Omics data derived from IPT’s PHI research was sought during expert meetings. During an expert meeting at IP, the Biomics platform (IP) was interested in PHINDaccess, and is now an integral part of it. Biomics offered IPT researchers privileged access to its sequencing platform. In addition, Biomics has allowed IPT to benefit from the sponsoring of Illumina, the major global actor in NGS technology worldwide, thus tightening a private-public partnership.
- Implementation and initiation of the training portfolio.
The course portfolio implemented with partners, mainly IPP (Institut Pasteur in Paris, France) and CRG (Center of Genomics Regulation, Barcelona, Spain) consisted of a series of 24 events, totaling 650 hours deployed during 16 weeks between January 2020 and July 2022. The total number of participants reached 33 trainees, among them 19 participants were constantly present as a core set of trainees, and 13 occasional trainees from Pasteur International Network institutes (Iran, Morocco and Algeria). Internal assessment related to the course's implementation was conducted throughout the project with both trainers and trainees, and submitted to the EC participant portal as a milestone (M2.3).
- Finalization of the informatics architecture installation.
Following the adoption by all participant institutions’ experts of the architecture of the informatics infrastructure to be implemented at IPT, an invitation to tender has been launched for the acquisition of equipment (on IPT own budget).
- Pathogen-host interaction pilot projects and establishment of a dynamic synergy with partners.
Eight ongoing projects on infectious diseases (HPV and, Poliovirus infections, Leishmaniasis, Mycoplasmosis, tuberculosis, candidiasis, theileriosis), which already generated big amounts of NGS data, have benefited from PHINDaccess in terms of data analyses in participants’ labs. Thanks to expert meetings, the scientific pertinence of these projects has been discussed in details and a collaborative program has been agreed upon and initiated.
-Gaining access to Omics platforms.
Given the absence of an Omics platform at IPT, the opportunity to generate additional Omics data derived from IPT’s PHI research was sought during expert meetings. During an expert meeting at IP, the Biomics platform (IP) was interested in PHINDaccess, and is now an integral part of it. Biomics offered IPT researchers privileged access to its sequencing platform. In addition, Biomics has allowed IPT to benefit from the sponsoring of Illumina, the major global actor in NGS technology worldwide, thus tightening a private-public partnership.
Implementation of PHINDaccess has considerably impacted on the institutional R&I environment. In fact, empowerment of knowledge and resources in Omics science and technologies became accessible to the IPT scientific community. The initiation of the training portfolio, coupled with the selection of pilot PHI projects provided immediate concrete measures, which have been felt by researchers as an effective shift allowing exploitation of Omics technologies in the ongoing research activities. A new generation of young researchers benefiting from the training portfolio and NGS facilities brought by the PHINDaccess consortium will undoubtedly step up the R&I potential of IPT.
PHINDaccess, through its WP4 and the selected pilot projects, is on the path to step up IPT’s R&I potential thanks to the use of state-of-the-art Omics-based approaches in several biomedical and healthcare research fields. The use of such approaches will facilitate the understanding of disease mechanisms and identification of molecular targets, as well as specific biomarkers for therapeutic, early screening and rapid diagnostic kits development.
In addition,the implementation of an OMICS facility with a training capacities at Institut Pasteur de Tunis leads it to have national and regional position as hub of competencies that have a direct impact on improving human resources qualification, guaranteeing jobs for highly qualified personnel, improving regional development in the fields of PHI research field and improvement of healthcare and public health at regional level and beyond. Henceforth IPT has a HPC cluster that includes a master node and 5 computing nodes including a high memory node with 96To of storage capacity and a backup server with similar capacity. This operational HPC cluster allows IPT scientists and researchers to store, manage, handle and analyze their OMICS data in a secure manner respecting all the international standards
PHINDaccess, through its WP4 and the selected pilot projects, is on the path to step up IPT’s R&I potential thanks to the use of state-of-the-art Omics-based approaches in several biomedical and healthcare research fields. The use of such approaches will facilitate the understanding of disease mechanisms and identification of molecular targets, as well as specific biomarkers for therapeutic, early screening and rapid diagnostic kits development.
In addition,the implementation of an OMICS facility with a training capacities at Institut Pasteur de Tunis leads it to have national and regional position as hub of competencies that have a direct impact on improving human resources qualification, guaranteeing jobs for highly qualified personnel, improving regional development in the fields of PHI research field and improvement of healthcare and public health at regional level and beyond. Henceforth IPT has a HPC cluster that includes a master node and 5 computing nodes including a high memory node with 96To of storage capacity and a backup server with similar capacity. This operational HPC cluster allows IPT scientists and researchers to store, manage, handle and analyze their OMICS data in a secure manner respecting all the international standards