Bioinformatics program for PhD students 2023 2024

This training program in statistics, bioinformatics and image analysis, financed by INCEPTION program, begins with a mandatory common core during which we will present all the tracks, and follow short courses on computer science, reproducible research, experimental design and ethics, plagiarism and good scientific conduct.

Each student then can choose to follow one or several track of  modules — R and Statistics, Bioinformatics, or Image Analysis— according to their background and field of research. A certificate of attendance will be delivered to each student at the end of each track session.

Agenda

Next key dates for this year’s session :

• Common core :
  • Session 1 – on campus session – October 23, 2023, from 9:30 AM to 5:30 PM – Room Retrovirus Lwoff building (program)
  • Session 2 – on campus session – March 8, 2024, from 9:30 AM to 5:30 PM – Room Retrovirus Lwoff building (program)

• R Programming and Statistics: Session 1 in French
  • RS1, Introduction to R and Statistics: October 26, 27, 30 and 31 (mornings only) on Teams. Note that for this course, the teachers ask to the participants to read the material before the starting of the course (see https://hub-courses.pages.pasteur.fr/R_pasteur_phd/index.html).
  • RS2, Hypothesis testing: November 6 (all day) and November 8 (afternoon only) and November 9 (afternoon only) in Retrovirus room
  • RS3, Linear models: November 13 (Retrovirus room) and 15 (Salle 4 of the teaching center Pavillon Emile roux)
  • RS4, Multivariate analyses: November 16 and 17 (Salle 4 of the teaching center Pavillon Emile roux)
• Bioinformatics – on campus Room 6 (computer room at the basement of the Education Center)
  • B1, Unix basic commands: March 21 and 22 (Room 5 – under the canteen – all day)
  • B2, Introduction to sequence analysis: Marche 27 and 28 (Room 6 – all day)
  • B3, Refresher on utilities for HTS data analysis: March 29 (Room 6 – all day) 
  • B4, Basic concepts in HTS data analysis: April 2 (Room 6 – all day)
  • B5, (requires B3 and B4), Expression, quantification, differential analysis: April 3 (Room 6 – all day)
  • B6, (requires B3 and B4), Variant calling: April 4 (Room 6 – all day)
  • B7, (requires B3 and B4), Genotype data and association studies: April 5 (Room 6 – all day)
  • B8, (requires B3 and B4), ChiP-seq data analysis: April 30 (Room 6 – all day)
  • B9, (requires B5), Single cell analysis: April 23 and 24 (Room 6 – all day)
  • B10, (requires B5), Functional analysis: April 25 and 26 (Room 6 – all day)
  • B11, Metagenomics: April 29 (Room 6 – all day)
  • B12, Advanced UNIX commands: May 16 and 17 (Room 6 – all day)
• R Programming and Statistics : Session 2 – on campus in English
  • RS1, Introduction to R and Statistics: April 8, 9 and 10, 2024 (all day) – rooms 2 and 3 of the Teaching Center Pavillon Emile Roux
  • RS2, Hypothesis testing: April 11 and 12, 2024 (all day) – rooms 2 and 3 of the Teaching Center Pavillon Emile Roux
  • RS3, Linear models: April 15 and 16, 2024 (all day) – rooms 2 and 3 of the Teaching Center Pavillon Emile Roux
  • RS4, Multivariate analyses: April 18 and 19, 2024 (all day) – rooms 2 and 3 of the Teaching Center Pavillon Emile Roux

• Image Analysis : Session 5 (June 2023)- on campus Room 5 (“module” under the cantine)
  • IA1, Getting started in BioImage Analysis with Fiji: TBD (all day)
  • IA5, Using Machine Learning for BioImage Analysis: TBD (morning)
  • IA6, Analysis of histopathology images with QuPath: TBD (afternoon)
  • IA7, Bioimage analysis with Python: TBD (all day)
• Image Analysis : Session 6 (January 2024) – on campus Room 5 (“module” under the cantine)
  • IA1, Getting started in BioImage Analysis with Fiji: TBD (all day)
  • IA5, Using Machine Learning for BioImage Analysis: TBD (morning)
  • IA6, Analysis of histopathology images with QuPath: TBD (afternoon)
  • IA7, Bioimage analysis with Python: TBD (all day)

A detailed description of the next Common Core day is available here. First year PhD students will receive information from the Graduate Office. For an overview of all the courses and sessions of the program and a detailed description of each module, you can access the Course Content.

The bioinformatics program is also a Pasteur course. For more information, follow this link : www.pasteur.fr/en/bioinformatics-program-phd-students

How to enrol

Register on Moodle

To register and connect to Hub-Moodle, go to the moodle login page. If you have a Pasteur account (meaning if you have a @pasteur.fr mail address), click on PasteurID authentification method, and use your usual short login and password if prompted.

Otherwise, if you don’t have a Pasteur account, contact the track managers and we will manually create an account for you. Then you will be able to log in using Manual login.

Enrol to a course

Use the links below to register to the modules that you want to attend. You will need the password communicated during the Common Core to enroll. Once done, you should receive a confirmation by e-mail. Registration to the modules are opened a few weeks before the beginning of the course, and closed (usually) one week before the starting date of each module. If you experience any difficulties with the registration system, please contact the teaching team: bioinfo-program@pasteur.fr.

The course is opened to Pasteur collaborators and to INCEPTION program partners. For the latter, we must apply a delay of 2 months before the start of the course, in order to proceed internally of the enrollment.