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Scientific Fields
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Technique
Starting Date
21
Oct 2022
Ending Date
30
Jun 2023
Time
09:30:00
Address
2022-10-21 09:30:00 2023-06-30 18:00:00 Europe/Paris Bioinformatics program for PhD students 2022-2023 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 […] Emmanuelle Permal emmanuelle.permal@pasteur.fr

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.

Download (PDF, 405KB)

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 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

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