Computational Cytometry Summer School

Computational Cytometry Summer School

29 April 2024 - 01 May 2024

Ghent - VIB/UGent FSVM II

live training

Computational Cytometry Summer School

Target Audience:
VIB PhD Student
VIB Postdoc
VIB Staff Scientist
VIB Group leader & Expert
VIB Technical support
Flemish Academics & Reseachers
Non-Flemish Academics & Researchers
Industry professionals
Location:

Ghent - VIB/UGent FSVM II

Duration:

29/04/2024

30/04/2024

01/05/2024

General context

The amount of data collected with cytometers keeps increasing. With studies measuring up to 40 markers, millions of cells per sample and up to thousands of samples, manual gating of all this data becomes infeasible. In this summer school, we will have workshops on all steps of a computational cytometry pipeline in R.

On Monday morning, we offer two tracks, one for people with a cytometry background and one for people with a computational background.

From Monday afternoon onwards, we will dive into the computational cytometry specifics. We will cover data cleaning, cell population identification and downstream statistics.  In addition, we will also have some sessions where these concepts are demonstrated on commercial platforms, such as FlowJo, FCSExpress and OMIQ. 

Objectives

By the end of the summer school, researchers will better understand the dos and don'ts of many different algorithms and feel comfortable to start exploring cytometry data in R. While an example dataset will be provided, participants are encouraged to bring their own FCS files to explore.

This ISAC Live Education workshop is sponsored by FlowJo and Dotmatics.

Required skills

None.

The training is targeted both at cytometrists with an interest in computational tools and bioinformaticians with an interest in cytometry. On the morning of the first day 2 parallel tracks will be offered to get everyone on the same page.

Registration procedure
This form is intended for scientists who want to join the Summer School. Registration will remain open until November 30th. Registration fee is 90€ (excl. VAT).
Participants will be selected based on their motivation and CV. Selected participants will receive confirmation by December 10th.
On the morning of the first day, we offer two tracks:
- people with a cytometry background choose the R intro track
- people with a computational background choose the cytometry intro track
One file only.
20 MB limit.
Allowed types: txt, rtf, pdf, doc, docx, odt, ppt, pptx, odp, xls, xlsx, ods.

Trainers

Gert Van Isterdael
VIB Flow Core, Ghent

As head of the VIB Flow Core,  Gert provides flow cytometry expertise to the users of the core facility by giving technical help to the scientists, maintaining the machines, implicating high quality SOPs as well as providing both experimental setup and data analysis consultations. The Flow Core develops novel automated analysis techniques for multi-parameter flow cytometry data to remove user bias in close collaboration with the on-site Bioinformatics team headed by Prof. Yvan Saeys. 

Contact Gert Van Isterdael :
Sofie Van Gassen
SaeysLab, VIB-UGent Center for Inflammation Research

Sofie is Postdoc at Ghent University working on optimization of the analysis of flow cytometry data by developing suitable machine learning algorithms. She's the creator of the FlowSOM algorithm. 

Contact Sofie Van Gassen :
Yvan Saeys
SaeysLab, VIB-UGent Center for Inflammation Research

Yvan Saeys is associate professor at Ghent University and principal investigator at VIB, where he is heading an interdisciplinary research team of 25 people.

The Saeys lab studies the design and application of novel data mining and machine learning techniques, motivated by specific questions in biology and medicine. The group develops new computational approaches to unravel the regulatory landscape of immune cell differentiation and functioning.

Contact Yvan Saeys :

Program

8:00-9:00 : Help with installation of software if needed

9:15-10:00 : Parallel track biologists: Guided tour of the flow core

10:00-10:30 : Parallel track biologist: Intro R part1 (Sofie Van Gassen)

9:15-10:30 : Parallel track bioinformaticians: Intro cytometry part1 (Gert Van Isterdael, Julie Van Duyse)

10:30-11:00 : Coffee break

11:00-12:30 ; Parallel track biologists: Intro R part2 (Sofie Van Gassen)

11:00-11:45 : Parallel track bioinformaticians: Intro cytometry part2 (Gert Van Isterdael, Julie Van Duyse)

11:45-12:30 : Parallel track bioinformaticians: Guided tour of the flow core

12:30-13:30 : Lunch

13:30-14:00 : Welcome + overview of a typical computational cytometry pipeline(Sofie Van Gassen)

14:00-15:30 : Basic cytometry data handling in R (Sarah Bonte)

15:30-16:00 : Coffee break

16:00-17:30 : Commercial tutorial - FlowJo

17:30-20:00 : Dinner

9:00-10:30 : Quality control of individual files in R (Annelies Emmaneel)

10:30-11:00 : Coffee break

11:00-12:30 : Normalization in R (Katrien Quintelier)

12:30-13:30 : Lunch

13:30-15:30 : Clustering tools in R (Yvan Saeys)

15:30-16:00 : Coffee break

16:00-17:30 : Commercial tutorials – FCSExpress (Dotmatics) and OMIQ (Dotmatics)

17:30-20:00 : Transport to the city center + dinner

9:00-10:00 : Downstream analysis use cases

10:00-11:00 : Downstream analysis and statistics in R (David Novak)

11:00-11:30 : Coffee break

11:30-12:30 : Publication ready figures in R (Artuur Couckuyt)

12:30-13:30 : Lunch

13:30-15:30 : Work on your own data - Part1

15:30-16:00 : Coffee break

16:00-17:30 : Work on your own data - Part2

Practical info

Location & Venue

29 April 2024 - 01 May 2024

Ghent - VIB/UGent FSVM II

Technologiepark 75
9052 Zwijnaarde
Belgium

Public transport

29 April 2024 - 01 May 2024

Ghent - VIB/UGent FSVM II
Public transport

From Ghent Sint-Pieters station, you can take bus 49, 50 or 70 to Technologiepark. Please check Routeplanner De Lijn for schedules.

Route description

29 April 2024 - 01 May 2024

Ghent - VIB/UGent FSVM II
Parking

Route description

There is only one entrance to Technologiepark. At the entrance, please take a ticket and have it validated at the reception desk of the FSVM building. Parking will only be allowed in regular parking spots (for instance in front of the building) and in the new parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited and after initial warnings, fines will be issued (€ 50).

Venue contact

29 April 2024 - 01 May 2024

Ghent - VIB/UGent FSVM II
Extra information

Room L5 of the FSVM2 building, Technologiepark, Gent

https://cmb.sites.vib.be/en/contact