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 – 21st of October 2024, from 9:30 AM to 16:00 PM – Room Retrovirus Lwoff building (program)
- Session 2 – on campus session – 6th of February 2025, from 9:30 AM to 16:00 PM – Room Jules Bordet Metchnikoff building (program)
- R Programming and Statistics: Session 1 in French
- RS1, Introduction to R and Statistics: October 30, 31 and November 4, 5, 2024 (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 and 7, 2024 – Salle 4 (Batiment 6, under the canteen)
- RS3, Linear models: November 12 and 13, 2024 – Salle 4 (Batiment 6, under the canteen)
- RS4, Multivariate analyses: November 14 and 15, 2024 – Salle 4 (Batiment 6, under the canteen)
- Note: Due to the administrative procedure for entering the Pasteur campus as an external member, the deadline for external application is the 15th of September for this 1st session of RS.
- Bioinformatics – on campus Room 6 (computer room at the basement of the Education Center)
- B1, Unix basic commands: March 24 and 25, 2025 (Room 5 – under the canteen – all day)
- B2, Introduction to sequence analysis: March 26 and 27, 2025 (Room 5 – under the canteen – all day)
- B3, Refresher on utilities for HTS data analysis: March 28, 2025 (Room 5 – under the canteen – all day)
- B4, Basic concepts in HTS data analysis: March 31, 2025 (Room 5 – under the canteen – all day)
- B5, (requires B3 and B4), Expression, quantification, differential analysis: April 1st, 2025 (Room 5 – under the canteen – all day)
- B6, (requires B3 and B4), Variant calling: April 2nd, 2025 (Room 5 – under the canteen – all day)
- B7, (requires B3 and B4), Genotype data and association studies: April 3rd, 2025 (Room 5 – under the canteen – all day)
- B8, (requires B3 and B4), ChiP-seq data analysis: April 4, 2025 (Room 5 – under the canteen – all day)
- B9, (requires B5), Metagenomics : April 28, 2025 (Room 5 or 6 – teaching center – all day)
- B10, (requires B5), Single cell analysis: April 22 and 23, 2025 (Room 6 – teaching center – all day)
- B11, Functional analysis : April 24 and 25, 2025 (Room 6 – teaching center – all day)
- B12, Advanced UNIX commands: May 22 and 23 (Room6 – teaching center – all day)
- NEW, Introduction to Artificial Intelligence : April 29 (and maybe 30) (Room 5 or 6 – teaching center – all day)
- Note: Due to the administrative procedure for entering the Pasteur campus as an external member, the deadline for external application is the 14th of January 2025 for bioinformatics courses.
- R Programming and Statistics : Session 2 – on campus in English
- RS1, Introduction to R and Statistics: April 7, 8 and 9, 2025 (all day) – rooms 2 and 3 of the Teaching Center Pavillon Emile Roux
- RS2, Hypothesis testing: April 10 and 11, 2025 (all day) – rooms 2 and 3 of the Teaching Center Pavillon Emile Roux
- RS3, Linear models: April 14 and 15, 2025 (all day) – rooms 2 and 3 of the Teaching Center Pavillon Emile Roux
- RS4, Multivariate analyses: April 16 and 17, 2025 (all day) – rooms 2 and 3 of the Teaching Center Pavillon Emile Roux
- Note: Due to the administrative procedure for entering the Pasteur campus as an external member, the deadline for external application is the 14th of January 2025 for this 2nd session of RS.
- Image Analysis : Session 5 (January 6-10, 2025)- on campus Room 5 (“module” under the cantine)
- IA1, Getting started in BioImage Analysis with Fiji: January 7th, 2025 (all day)
- IA2, Using Machine Learning for BioImage Analysis: January 8th, 2025 (morning)
- IA3, Quantification of large 2D images using QuPath: January 8th, 2025 (afternoon)
- IA4, Tracking Cells and Organelles with TrackMate: January 9th, 2025 (morning)
- IA5, Bioimage analysis with Python: January 10th, 2025 (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.
| Session | Course | Course Dates | Room | Enrolment Link |
|---|---|---|---|---|
| Common core | ||||
| Session 1 | CC – Mandatory common core | 21st October, 2024 | Retrovirus Lwoff | Enroll here |
| Session 2 | CC – Mandatory common core | 6th February, 2025 | Jules Bordet – Metchnikoff | Enroll here |
| Bioinformatics track | ||||
| Session 1 | B1 – Unix basic commands | March 24 and 25, 2025 (all day) | Room 5 – Bellow canteen | Enroll here (opens on 1st January 2025) |
| Session 1 | B2 – Introduction to sequence analysis | March 26 and 27, 2025 (all day) | Room 5 – Bellow canteen | Enroll here (opens on 1st January 2025) |
| Session 1 | B3 – Refresher on utilities for HTS data analysis | March 28, 2025 (all day) | Room 5 – Bellow canteen | Enroll here (opens on 1st January 2025) |
| Session 1 | B4 – Basic concepts in HTS data analysis | March 31, 2025 (all day) | Room 5 – Bellow canteen | Enroll here (opens on 1st January 2025) |
| Session 1 | B5 – Expression, quantification, differential analysis | April 1, 2025 (all day) | Room 5 – Bellow canteen | Enroll here (opens on 1st January 2025) |
| Session 1 | B6 – Variant calling | April 2, 2025 (all day) | Room 5 – Bellow canteen | Enroll here (opens on 1st January 2025) |
| Session 1 | B7 – Genotype data and association studies | April 3, 2025 (all day) | Room 5 – Bellow canteen | Enroll here (opens on 1st January 2025) |
| Session 1 | B8 – ChiP-seq data analysis | April 4, 2025 (all day) | Room 5 – Bellow canteen | Enroll here (opens on 1st January 2025) |
| Session 1 | B9 – Metagenomics | April 28, 2025 (all day) | Room 5 or 6 – Teaching center or canteen | Enroll here (opens on 1st January 2025) |
| Session 1 | B10 – Single-cell analysis | April 22 and 23, 2025 (all day) | Room 6 – Teaching center | Enroll here (opens on 1st January 2025) |
| Session 1 | B11 – Functional analysis | April 24 and 25, 2025 (all day) | Room 6 – Teaching center | Enroll here (opens on 1st January 2025) |
| Session 1 | B12 – Advanced Unix Commands | May 22 and 23, 2025 (all day) | Room 6 – Teaching center | Enroll here (opens on 1st January 2025) |
| Image analysis track | ||||
| Session 1 | IA1 – Getting started in BioImage Analysis with Fiji | January 7, 2025 (all day) | Room 5 – Below canteen | Enroll here |
| Session 1 | IA2 – Using Machine Learning for BioImage Analysis | January 8, 2025 (morning) | Room 5 – Below canteen | Enroll here |
| Session 1 | IA3 – Quantification of large 2D images using QuPath | January 8, 2025 (afternoon) | Room 5 – Below canteen | Enroll here |
| Session 1 |
IA4 – Tracking cells and organelles with TrackMate |
January 9, 2025 (morning) | Room 5 – Below canteen | Enroll here |
|
Session 1 |
IA5 – Bioimage analysis with Python | January 10, 2025 (all day) | Room 5 – Below canteen | Enroll here |
| Statistics track | ||||
| Session 1 | RS1 – Introduction to R and Statistics | October 30 and 31, November 4 and 5, 2024 (mornings only) | Online – Teams | Enroll here |
| Session 1 | RS2 – Hypothesis testing | November 6 and 7, 2024 (all day) | On campus – Room 4 (Batiment 6, under the canteen) | Enroll here |
| Session 1 | RS3 – Linear Models | November 12 and 13, 2024 (all day) | On campus – Room 4 (Batiment 6, under the canteen) | Enroll here |
| Session 1 | RS4 – Multivariate Analysis | November 14 and 15, 2024 (all day) | On campus – Room 4 (Batiment 6, under the canteen) | Enroll here |
| Session 2 | RS1 – Introduction to R and Statistics | April 7, 8 and 9, 2025 (all day) | On campus – Rooms 2 and 3 of the Teaching Center Pavillon Emile Roux | Enroll here |
| Session 2 | RS2 – Hypothesis testing | April 10 and 11, 2025 (all day) | On campus – Rooms 2 and 3 of the Teaching Center Pavillon Emile Roux | Enroll here |
| Session 2 | RS3 – Linear Models | April 14 and 15, 2025 (all day) | On campus – Rooms 2 and 3 of the Teaching Center Pavillon Emile Roux | Enroll here |
| Session 2 | RS4 – Multivariate Analysis | April 16 and 17, 2025 (all day) | On campus – Rooms 2 and 3 of the Teaching Center Pavillon Emile Roux | Enroll here |