Institut Pasteur de Tunis - Actualités

PHINDaccess Course « Introduction to R and R Studio » January 30-Feb 01, 2020

R phindWith an ever-expanding number of users, R is one of the leading programming languages used worldwide. Its popular use in statistics and data science is mainly due to the wide range of open source packages that are offered for a wide range of applications, including Omics-related analysis and visualization of high-throughput datasets. This course will take participants to their first steps in R and RStudio environments, by presenting them the core fundamentals of R and RStudio. Participants are expected to use it interactively to explore, analyse and visually interpret a set of model high-throughput datasets. The use of R as a programming language will be partially covered in this course and during the upcoming NGS-RNASeq course, and should be envisioned as a subsequent best practice that would improve participants daily research.

This course is restricted to the young researchers previously selected from IPT's research labs and to 6 candidates from the Institut Pasteur International Network

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PHINDaccess Course « NGS-DNASeq for WGS, Wes and de novo genome sequencing » January 27-29, 2020

dna seq phind FINAL nouveauNext Generation Sequencing (NGS) is a catch-all-term widely used nowadays to refer to a wide range of high-throughput technologies devoted to many areas of research relevant to Biology. This course will be focusing on Genomics analysis using NGS solutions, and will essentially cover Whole Genome Sequencing (WGS), with a glimpse on Whole Exome Sequencing (WES) and de novo Genome Sequencing. Participants are expected to use it to explore, analyse and interpret their high-throughput genomic datasets.


Upon completion of this course you should be able to:

Understand the basics of the experimental design for WGS in general, with a glimpse on WES and de novo Genome Sequencing.
Understand the methods for library generation, and the potential consequences of errors occurring at the level of library generation.
Use and interpret the wide range of file formats generated.
Use streamlined available pipelines or design specific pipelines

This course is restricted to the young researchers previously selected from IPT's research labs and to 6 candidates from the Institut Pasteur International Network.


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PHINDaccess seminar: Strengthening best practices for biospecimen collection, Omics data sampling and handling, November 14-15, 2019

14-15-Novembre-2019Pursuing PHINDaccess's objectives of Excellence, a seminar titled "Strengthening best practices for biospecimen collection, Omics data sampling and handling" was organized at the Institut Pasteur de Tunis (IPT), November 14-15, 2019.

The seminar, organized by Pr Houda Yacoub, involved 65 participants consisting of PhD students, Post-docs and researchers from IPT and from other universities in Tunis.

During his introductory talk, Pr Samir Boubaker, Head of Public Health department at IPT, paid tribute to the late Pr. Amor Chadly, who led IPT for 25 years.

The seminar, which was competently facilitated by Marie-Noelle Ungeheuer and Dominique Clermont (IP, Paris, PHINDaccess partner), covered several aspects, such as (i) ethical, legal and regulatory issues related to biobanks, (ii) good practices for the collection, preparation, storage and distribution of human biological resources, (iii) the Nagoya Protocol for microorganisms handling, (iv) governance of biobanks, (v) challenges of personal data protection associated to human specimens; and (vi) examples of national (IPT, Tunis) and international (IP, Paris) biobanks. A debate revolving around the aforementioned aspects took place in an interactive manner and with concrete cases studies. The seminar was ended with examples on public and African databases as a prelude to PHINDaccess's forthcoming event.

The seminar also involved Tunisian esteemed experts, namely Pr Hend Bouacha, President of the National Medical Ethics Committee, Drs Fatma Guerfali and Kais Ghedira (PHINDaccess members), Pr Anis Klouz, Director General of SIPHAT, and Mr Chawki Gaddes, president of the National Body for the Protection of Personal Data (INPDP)

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PHINDaccess course on Database Development, Nov 18-21, 2019

18-21-Novembre-FINAL-petitThe advent of Omics science has resulted in the generation of a tremendous amount of data, which makes database development a crucial requirement. PHINDaccess, which is striving for an easy access to Omics data at the Institut Pasteur de Tunis (IPT), is strongly committed to enhance all aspects relating to data stewardship, including databases. Toward this end, a course dealing mainly with SQL Relational Databases was organized at IPT premises, November 18-21, 2019. The course was delivered to nineteen selected young researchers, representatives of IPT's research labs. They have been brought through different steps for database conception and modeling, got acquainted with entity relationship diagram, developed a relational biological database from scratch, learned how to deal with MySQL queriesand how to use PHPMyadmin to manage the database and users. Trainees have also been introduced to good practices to ensure the security and integrity of a database.

Theoretical courses were alternated by practical sessions, which allowed the participants to appreciate their newly acquired skills. The course ended up with an overview on back end and front end web application development.

This course was nicely and competently organized by Dr. Kais Ghedira (PHINDaccess WP3 Leader), with the kind help of Dr. Fatma Guerfali (PHINDaccess WP2 Coordinator) and Mr Wahbi Belhadj (PHINDaccess system administrator).

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PHINDaccess second consortium meeting (October 30-31, 2019)

The first annual meeting of PHINDaccess, a twinning project funded the European Commission-H2020 program, took place in the coastal city of Monastir (160 km south east of Tunis), October 30-31, 2019.

During this meeting, PHINDaccess partners discussed the first-year achievements and the activities to be implemented in the second year.
In his talk, the project coordinator, Pr Helmi Mardassi, insisted upon the ultimate objective of the project, which consists to "make IPT a regional flagship for excellence in Omics-based research pertaining to Pathogen-Host Interaction.

The first year of the project allowed PHINDaccess team laying the ground for the effective implementation of the project by achieving the following critical preparatory steps:

Preparation of an implementation plan agreed upon after four expert visits in partners institutions (March to july, 2019)
Organization of five key events (conferences, workshops and seminars)
Endowment of PHINDaccess with a graphic identity, a website with social networks accounts, and different communication material
Finalization of IPT's IT platform architecture designed for a fluent OMICS data stewardship and analysis
Selection of 19 young researchers to be future experts in OMICS data analysis
Allocation of a new spacious and commodious room for training activities
Refinement of the objectives of OMICS-based pilot projects to be implemented in 2020-2021
Involvement of BIOMICS platform of the Institut Pasteur, Paris, as an integral PHINDaccess partner

During the second year, PHINDaccess team will endeavor to:

Set up of the OMICS training curriculum
Implement all components of IPT's IT infrastructure
Ensure the generation of high-quality OMICs data and initiate analysis
Undertake the "Science with and for Society" program

The Scientific Advisory Board esteemed members, Pr. Jessica Kissinger and Pr Toni Gabaldon, acknowledged the tremendous amount of work performed during this first year, and provided a number of specific recommendations to make PHINDaccess a highly successful initiative.

annual meeting phind october 30-31 2019

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