Functional Plant Bioinformatics (PLAZA)

Functional Plant Bioinformatics (PLAZA)

Target Audience:
21 October 2019

General context

Using PLAZA to get more out of your plant omics data.

This two-day workshop (21-22 October 2019) will introduce the basic concepts of comparative and functional -omics data analysis in plants through lectures and practical hands-on sessions. Plant biologists and geneticists with an interest in bioinformatics and data analysis are encouraged to attend this training.  After this workshop, you will have a good understanding of the organization of plant genomes, the evolution of plant gene families and the different systems used to describe gene functions. In addition, you will know how to extract relevant biological information from -omics gene sets.

There will be a dinner in the historic centre of Ghent on the first day where you will have the possibility to network. Registrations are free but required by sending an e-mail to tuur.muyldermans@vib.be. 

Objectives
  • Introduction plant comparative genomics (genes and gene families) + introduction PLAZA platform
  • Functional characterization of plant genes (Gene families, GO, InterPro)
  • Synteny analysis in polyploid cereals
  • Gene set analysis for different plant -omics data sets:
    • Functional interpretation of RNA-Seq and ChIP-Seq genes using the PLAZA Workbench
    • Comparing gene sets between different di/polyploidy crop species
Required skills

Basic knowledge of genes, genomes, transcript profiling, BLAST and homology (no programming skills are required).

Trainers

Klaas Vandepoele

Klaas Vandepoele is VIB Group leader (Center for Plant Systems Biology) and Associate Professor of Ghent University (Department of Plant Biotechnology and Bioinformatics). He (co-)authored more than 100 international peer-reviewed publications and is a Highly Cited Researcher (H-index: 45). He is an expert in bioinformatics, tool development and genomics data analysis in plants. Lab website: http://bioinformatics.psb.ugent.be/cnb/.

Michiel Van Bel

Michiel Van Bel is a postdoctoral researcher at the VIB Center for Plant Systems Biology. Aside from being the main developer of the PLAZA platform, he has actively collaborated with many research groups resulting in over 20 publications. Highly experienced in both bioinformatics and software development, he is constantly improving the PLAZA platform. Orcid website

Program

Welcome: general information
-
PLAZA introduction
-
Coffee break
-
Theory I: genes, gene families and genome organization
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Exercises I: genes, gene families and genome organization
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Lunch
-
Theory II: Orthologs, paralogs and phylogenetic trees
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Exercises II: orthologs, paralogs and phylogenetic trees
-
Coffee break
-
Theory III: Functional annotation & functional enrichments
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Exercises III: Functional annotation & functional enrichments
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Diner at Café des Arts
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Theory IV: PLAZA workbench
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Exercises IV: PLAZA workbench registration + upload gene set(s)
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Coffee break
-
Exercises IV: PLAZA workbench functional data analysis
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Lunch
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Theory V: Advanced orthology, synteny and expression analysis in cereals
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Exercises V: Advanced orthology, synteny and expression analysis in cereals
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Coffee break
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Exercises V: Advanced orthology/synteny using PLAZA workbench
-
Feedback + closing workshop
-

Practical info

21 October 2019 - 22 October 2019

UGent-VIB Research Building FSVM

Technologiepark 71
9052 Zwijnaarde
Belgium

21 October 2019 - 22 October 2019

UGent-VIB Research Building FSVM
Public transport

Itineraries:

At Gent St Pieters station you can take the following city buses: Buses 70, 71 and 72 ("Tramstraat"). You get off at the stop marked "Bollebergen" (on the Grote Steenweg Noord). The Technology Park is straight in front of you on the other side of the soft verge. Walk into the park to the roundabout and then straight on. The UGent-VIB research building is the first building on the left.

There is also a shuttle bus between Gent-Sint-Pieters and Technologiepark, more information can be found here.

 

21 October 2019 - 22 October 2019

UGent-VIB Research Building FSVM
Parking

Route description

There is free parking available in front of the building.

21 October 2019 - 22 October 2019

UGent-VIB Research Building FSVM
Location contact

+32 9 331 36 00

Contact

VIB training
Tel: +32 9 244 66 11
Mail: training@vib.be