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Scientific Fields
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Starting Date
01
Oct 2024
Ending Date
30
Jun 2025
Time
09:00:00
Address
2024-10-01 09:00:00 2025-06-30 17:00:00 Europe/Paris Bioinformatics program for PhD students 2024 2025 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, […] Emeline Perthame emeline.perthame@pasteur.fr

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, from 9:30 AM to 16:00 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
    • 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 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 (January 6-10, 2025)- 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.

Hub Moodle login page with Pasteur ID circled in red

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 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
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
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
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
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