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 – TBD, from 9:30 AM to 5:30 PM – Room Retrovirus Lwoff building (program)
- Session 2 – on campus session – TBD, 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 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 of the teaching center Pavillon Emile Roux
- RS3, Linear models: November 12 and 13, 2024 – Salle 4 of the teaching center Pavillon Emile Roux
- RS4, Multivariate analyses: November 14 and 15, 2024 – 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 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 21, 2025 (Room 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: TBD (all day)
- 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
- Image Analysis : Session 5 (TBD)- 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 (TBD) – 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.
| Session | Course | Course Dates | Room | Enrolment Link |
|---|---|---|---|---|
| Common core | ||||
| Session 1 | CC – Mandatory common core | TBD | Retrovirus Lwoff | Enroll here (opens on 1st October 2024) |
| Session 2 | CC – Mandatory common core | TBD | Retrovirus Lwoff | Enroll here (opens on 1st October 2024) |
| 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 21, 2025 (all day) | Room 6 – Teaching center | 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 | TBD | TBD | Enroll here (opens on 1st January 2025) |
| Image analysis track | ||||
| Session 5 | IA1 – Getting started in BioImage Analysis with Fiji | TBD | Room 5 | Enroll |
| Session 5 | IA5 – Using Machine Learning for BioImage Analysis | TBD | Room 5 | Enroll |
| Session 5 | IA6 – Analysis of histopathology images with QuPath | TBD | Room 5 | Enroll |
| Session 5 | IA7 – Bioimage analysis with Python | TBD | Room 5 | Enroll |
| Session 6 | IA1 – Getting started in BioImage Analysis with Fiji | TBD | Room 5 | Enroll |
| Session 6 | IA5 – Using Machine Learning for BioImage Analysis | TBD | Room 5 | Enroll |
| Session 6 |
IA8 – Tracking cells and organelles with TrackMate |
TBD | Room 5 | Enroll |
|
Session 6 |
IA7 – Bioimage analysis with Python | TBD | Room 5 | Enroll |
| 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 (opens on 1st October 2024) |
| Session 1 | RS2 – Hypothesis testing | November 6 and 7, 2024 (all day) | On campus – Room 4 of the teaching center Pavillon Emile Roux | Enroll here (opens on 1st October 2024) |
| Session 1 | RS3 – Linear Models | November 12 and 13, 2024 (all day) | On campus – Room 4 of the teaching center Pavillon Emile Roux | Enroll here (opens on 1st October 2024) |
| Session 1 | RS4 – Multivariate Analysis | November 14 and 15, 2024 (all day) | On campus – Room 4 of the teaching center Pavillon Emile Roux | Enroll here (opens on 1st October 2024) |
| 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 (opens on 1st October 2024) |
| 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 (opens on 1st October 2024) |
| 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 (opens on 1st October 2024) |
| 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 (opens on 1st October 2024) |