This training program in statistics, bioinformatics and image analysis 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 21, 2022, from 9:30 AM to 5:30 PM – Room Retrovirus Lwoff building
- Session 2 – on campus session – February 17, 2023, from 9:30 AM to 5:30 PM – Room Retrovirus Lwoff building
- R Programming and Statistics: Session 1 – virtual session (on Teams) in French
- RS1, Introduction to R and Statistics: November 7, 8, 9, 10, 2022 (mornings)
- RS2, Hypothesis testing: November 14, 15, and 17, 18, 2022 (mornings)
- RS3, Linear models: November 28, 29 and December 1, 2, 2022 (mornings)
- RS4, Multivariate analyses: December 5, 6 and 8, 9 2022 (mornings)
- Bioinformatics – on campus Room 6 (computer room at the basement of the Education Center)
- B1, Unix basic commands: March 20, 21, 2023 (all day)
- B2, Introduction to sequence analysis: March 22, 23, 2023 (all day)
- B3, Refresher on utilities for HTS data analysis: March 24, 2023 (all day)
- B4, Basic concepts in HTS data analysis: March 27, 2023 (all day)
- B5, Expression, quantification, differential analysis: March 28, 2023 (all day)
- B6, Variant calling: March 29, 2023 (all day)
- B7, Genotype data and association studies: March 30, 2023 (all day)
- B8, ChiP-seq data analysis: March 31, 2023 (all day)
- B9, Single cell analysis: April 17, 18, 2023 (all day)
- B10, Functional analysis: April 19, 20, 2023 (all day)
- B11, Advanced UNIX commands: May 11, 12, 2023 (all day)
- R Programming and Statistics : Session 2 – on campus (Teaching Center) in English
- RS1, Introduction to R and Statistics: April 3, 4, 5, 2023 (all day) – rooms 2 and 3
- RS2, Hypothesis testing: April 6, 7, 2023 (all day) – rooms 2 and 3
- RS3, Linear models: April 11, 12, 2023 (all day) – rooms 2 and 3
- RS4, Multivariate analyses: April 13, 14, 2023 (all day) – rooms 2 and 3
- Image Analysis : Session 5 (January 2023) – on campus Room 5 (“module” under the cantine)
- IA1, Getting started in BioImage Analysis with Fiji: Tuesday January, 10, 2023 (all day)
- IA5, Using Machine Learning for BioImage Analysis: Wednesday January, 11, 2023 (morning)
- IA6, Analysis of histopathology images with QuPath: Wednesday January, 11, 2023 (afternoon)
- IA7, Bioimage analysis with Python: Thursday January, 12, 2023 (all day)
- Image Analysis : Session 6 (June 2023)- on campus Room 5 (“module” under the cantine)
- IA1, Getting started in BioImage Analysis with Fiji: Tuesday June, 27, 2023 (all day)
- IA5, Using Machine Learning for BioImage Analysis: Wednesday June, 28, 2023 (morning)
- IA6, Analysis of histopathology images with QuPath: Wednesday June, 28, 2023 (afternoon)
- IA7, Bioimage analysis with Python: Thursday June, 29, 2023 (all day)
A detailed description of the next Common Core day is available here. No registration is required. 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 or download the flyer below.
[gview file=”https://research.pasteur.fr/wp-content/uploads/2022/07/research_pasteur-bioinformatics-program-for-phd-students-2022-2023-flyer2022-2023.pdf”] 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 enrol. Once done, you should receive a confirmation by e-mail. Registration to the modules will open on the 21st of October 2022, 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.
| Session | Course | Course Dates | Room | Enrolment Link |
|---|---|---|---|---|
| Common core | ||||
| Session 1 | CC – Mandatory common core | October 21, 2022 | Retrovirus Lwoff | No need for registration |
| Session 2 | CC – Mandatory common core | February 17, 2023 | Retrovirus Lwoff | Enroll |
| Bioinformatics track | ||||
| Session 1 | B1 – Unix basic commands | March 20-21, 2023 | Room 6 | Enroll |
| Session 1 | B2 – Introdcution to sequence analysis | March 22-23, 2023 | Room 6 | Enroll |
| Session 1 | B3 – Refresher on utilities for HTS data analysis | March 24, 2023 | Room 6 | Enroll |
| Session 1 | B4 – Basic concepts in HTS data analysis | March 27, 2023 | Room 6 | Enroll |
| Session 1 | B5 – Expression, quantification, differential analysis | March 28, 2023 | Room 6 | Enroll |
| Session 1 | B6 – Variant calling | March 29, 2023 | Room 6 | Enroll |
| Session 1 | B7 – Genotype data and association studies | March 30, 2023 | Room 6 | Enroll |
| Session 1 | B8 – ChiP-seq data analysis | March 31, 2023 | Room 6 | Enroll |
| Session 1 | B9 – Single-cell analysis | April 17-18, 2023 | Room 6 | Enroll |
| Session 1 | B10 – Functional analysis | April 19-20, 2023 | Room 6 | Enroll |
| Session 1 | B11 – Advanced Unix Commands | May 11-12, 2023 | Room 6 | Enroll |
| Image analysis track | ||||
| Session 5 | IA1 – Getting started in BioImage Analysis with Fiji | January 10, 2023 | Room 5 | Enroll |
| Session 5 | IA5 – Using Machine Learning for BioImage Analysis | January 11, 2023 | Room 5 | Enroll |
| Session 5 | IA6 – Analysis of histopathology images with QuPath | January 11, 2023 | Room 5 | Enroll |
| Session 5 | IA7 – Bioimage analysis with Python | January 12, 2023 | Room 5 | Enroll |
| Session 6 | IA1 – Getting started in BioImage Analysis with Fiji | June 27, 2023 | Room 5 | Enroll |
| Session 6 | IA5 – Using Machine Learning for BioImage Analysis | June 28, 2023 | Room 5 | Enroll |
| Session 6 | IA6 – Analysis of histopathology images with QuPath | June 28, 2023 | Room 5 | Enroll |
| Session 6 | IA7 – Bioimage analysis with Python | June 29, 2023 | Room 5 | Enroll |
| Statistics track | ||||
| Session 1 | RS1 – Introduction to R and Statistics | November 7-10, 2022 | Teams | Enroll |
| Session 1 | RS2 – Hypothesis testing | November 14-15 and 17-18, 2022 | Teams | Enroll |
| Session 1 | RS3 – Linear Models | November 28-29 and December 1-2, 2022 | Teams | Enroll |
| Session 1 | RS4 – Multivariate Analysis | December 5-6 and 8-9, 2022 | Teams | Enroll |
| Session 2 | RS1 – Introduction to R and Statistics | April 3-5, 2023 | Rooms 2&3 | Enroll |
| Session 2 | RS2 – Hypothesis testing | April 6-7, 2023 | Rooms 2&3 | Enroll |
| Session 2 | RS3 – Linear Models | April 11-12, 2023 | Rooms 2&3 | Enroll |
| Session 2 | RS4 – Multivariate Analysis | April 13-14, 2023 | Rooms 2&3 | Enroll |