Institut Pasteur de Tunis - Actualités

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)

Read the program of the seminar

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).

Read the program of the course

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

January, 13-17, 2020: PHINDaccess Course "Introduction to Python"


The Big Data era has created the necessity to manage high-throughput data files and data analysis with renewed and improved approaches. Scripting languages are nowadays an integral component of this landscape and their daily use leverages and grows the analytical capabilities by integrating complex operations. This course introduces the Python programming language, as an easy-to-use interpreted language, providing a rich and robust programming environment. Participants are expected to use it to explore, analyse and interpret their high-throughput datasets.

Upon completion of this course you should:

  1. Understand the basics of Python programming.
  2. Understand data types, control flow, object-oriented programming.
  3. Be able to use state-of-the-art scientific packages (Pandas library).
  4. Be able to execute a code in a jupyter notebook.

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



January 2-4, 2020: PHINDaccess Course "Introduction to Linux"


This course explores the various advantages of using the Linux environment to work with complex or big file systems. Main commands used to create, manipulate and navigate through directories and files will be covered.

The main objective of this course is to help participants become able to achieve their upcoming high-throughput data analysis under the Linux environment. Upon completion of this course you should:

  1. Understand the advantages of Linux OS vs Windows OS.
  2. Have a good working knowledge of Linux from a command line perspective.
  3. Be able to easily navigate through a directory/file system tree.
  4. Be able to use basic & complex command-line operations
  5. Have a basic knowledge of Bash scripting

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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