Training resources

transPLANT is running a series of training courses across Europe. The next one will be held at EMBL-EBI, Hinton, UK, 1st-3rd July, 2015. When registration is opened, details will be posted here. Meanwhile, you can access material from the previous transPLANT training courses here, including presentations, tutorials and worked examples for transPLANT tools, services and standards. Materials are grouped by (currently 6) transPLANT user training workshops and related events.

Mining Plant Variation Data

Attachment	Size
Workshop announcement	204.1 KB
The European Variation Archive at EMBL-EBI: a home for plant variation data - G. Saunders, EBI	4.6 MB
Plant Variation Data: what's available, what new projects are expected - M. Mascher, IPK	7.55 MB
Hands-on Tutorial on SNP Calling - G. Haberer, PGSB	4.17 MB
Introduction to the transPLANT Consortium - M. Spannagl, PGSB	2.71 MB
Variation data in Ensembl Plants - D Bolser, EBI	5.32 MB
Variation data in Ensembl Plants - Course booklet - D. Bolser, EBI	3.16 MB
iBrowser Tutorial - JP Nap, KeyGene	334.67 KB
iBrowser Tutorial Quiz Answers - JP Nap, KeyGene	114.08 KB
PolyMarker: Genome Specific Primer Design - R. Ramirez-Gonzalez, TGAC	3.1 MB
Resequencing Approaches - S. Ayling, TGAC	2.76 MB
TILLING at TGAC - S. Ayling, TGAC	6.27 MB
Hands-on Tutorial to Genome-Wide Association Studies (GWAS), GMI	9.52 MB

Exploiting and understanding Solanaceous genomes

Attachment	Size
Introduction and Program	156.23 KB
Overview of program and Introduction to the status of solanaceous genomes - Gabino Sanchez Perez, WUR	3.11 MB
Mining solanaceous data with GnpIS - Cyril Pommier, URGI	2.19 MB
An overview of Ensembl Plants, including the 150 tomato genomes variation data - Dan Bolser, EBI	12.11 MB
Fast and easy variation querying in tomato genomes - Antoine Janssen & Lorena da Ponte, KeyGene	2.19 MB
Protein function prediction with BMRF - Sven Warris & Aalt-Jan van Dijk - WUR	1.53 MB
Mining integrated data sources using LAILAPS - Matthias Lange, IPK	4.52 MB
Advanced breeding of solanaceous crops using BreedDB - Richard Finkers, WUR	5.44 MB

transPLANT workshop on resources for Triticeae genomics and phenotyping standards

Attachment	Size
Announcement, Application form, and Programme.	94.72 KB
An overview of Ensembl Plants.	2.12 MB
The Triticiae genomes in Ensembl Plants.	1.2 MB
A walk-through tutorial of Ensembl Plants functionality.	6.42 MB
Sample solutions to the tutorial.	140 KB
Genomic, genetic and phenomic plant data at INRA, URGI. Introduction to GnpIS. BioMart tutorial and answers.	1.27 MB
Methods of standardisation and annotation for plant phenotypic data. Tutorial on the annotation of an example experiment.	1009.97 KB
Introduction and tutorial for the MIPS PlantsDB barley & wheat databases	1.28 MB
Analysis of the bread wheat genome using whole-genome shotgun sequencing	4.29 MB
Introduction to the analysis and data generation concepts for complex triticeae genomes – barley & wheat	3.82 MB
Tutorial for the MIPS PlantsDB barley & wheat databases	608.84 KB
Exercise: ELF3 – Use case for accessing barley genome data	285.68 KB
Tutorial answers	131 KB

Crop Plant Trait Ontology Workshop, Oregon State University

Attachment	Size
Short news item about the Crop Plant Trait Ontology Workshop	15.7 KB
Short news item about the Crop Plant Trait Ontology Workshop (PDF)	74.09 KB

transPLANT user training workshop

Attachment	Size
Agenda	137.86 KB
Introduction to transPLANT, Paul Kersey, EMBL-EBI	3.35 MB
Introduction to the transPLANT portal and distributed search, Dan Bolser, EMBL-EBI	1.9 MB
Tutorial, LAILAPS - An Integrated Search Engine for Life Science Data, Uwe Scholz and Jinbo Chen, IPK	4.69 MB
Overview of Ensembl Genomes, Paul Kersey and Dan Bolser, EMBL-EBI	2.89 MB
An Introduction into Triticeae genome analysis concepts and data generation, Klaus Mayer MIPS	6.74 MB
Workshop, Browsing Genomic Information with Ensembl Plants, Paul Kersey, Bert Overduin and Dan Bolser, EMBL-EBI	6.42 MB
Workshop answers, Browsing Genomic Information with Ensembl Plants, Paul Kersey, Bert Overduin and Dan Bolser, EMBL-EBI	138.5 KB
Tutorial, Triticeae data in Ensembl Plants, Paul Kersey and Dan Bolser, EMBL-EBI	1.11 MB
Workshop, Triticeae genome resources in PlantsDB, Manuel Spannagl, MIPS	1.44 MB
Tutorial on GnpIS, Delphine Steinbach, INRA URGI	14.92 MB
Workshop, GnpIS training session, Michael Alaux, INRA URGI	3.37 MB
Tutorial, Annotating Triticeae sequences: the TriAnnot pipeline, Phillipe Leroy, INRA Clermont-Ferrand	4.09 MB

Crop Ontologies for Agronomic Traits

Attachment	Size
The workshop programme	20.42 KB
Plant and Trait Ontology: Current Status	1.73 MB
Community Ontology Development: Lessons from the Gene Ontology	643.36 KB
Other standardisation initiatives for plant genomics: transPLANT and EU-US Biotechnology Task Force	398.68 KB
Ontologies for Genotype, Phenotype and Environment interaction studies at the INRA	692.7 KB
An Online GCP Crop Ontology (CO) for Annotating Trait Data Useful for Plant Breeders	964.76 KB
Solanaceae Phenotype Ontology (SPO)	713.57 KB
Legumes: From Beans To Trees	51.34 KB
Ontology - Crop Breeding Perspective	72.24 KB
Traits Related to Photosynthesis	941.57 KB
Field-based phenotyping of agronomic traits	790.48 KB
NUE and wheat ontology	516.17 KB
Examples of Trait Descriptions	298.88 KB
Useful links	47.61 KB

The transPLANT logo with link to the homepage

transPLANT

trans-national infrastructure for plant genomic science