Computational Cytometry Summer School
Computational Cytometry Summer School
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.
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.
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.
Trainers
Gert Van Isterdael
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.
Sofie Van Gassen
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.
Yvan Saeys
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.
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
29 April 2024 - 01 May 2024
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
29 April 2024 - 01 May 2024
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take bus 49, 50 or 70 to Technologiepark. Please check Routeplanner De Lijn for schedules.
29 April 2024 - 01 May 2024
Ghent - VIB/UGent FSVM II
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).
29 April 2024 - 01 May 2024
Ghent - VIB/UGent FSVM II
Room L5 of the FSVM2 building, Technologiepark, Gent
https://cmb.sites.vib.be/en/contact