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Scientific topics: Plant biology 

Plant Phenotyping Data managment Webinar (MIAPPE)

The Minimal Information About Plant Phenotyping Experiment, MIAPPE (www.miappe.org), has been designed by ELIXIR, EMPHASIS and Bioversity international, to guide plant scientist in the management of experimental data. Furthermore, since genetic studies relies on the integration and the linking...

Scientific topics: Data submission, annotation, and curation, Data quality management, Phenomics, Plant biology

Operations: Standardisation and normalisation

Resource type: Video, Slides

Plant Phenotyping Data managment Webinar (MIAPPE) http://tess.elixir-uk.org/materials/plant-phenotyping-data-managment-webinar-miappe The Minimal Information About Plant Phenotyping Experiment, MIAPPE (www.miappe.org), has been designed by ELIXIR, EMPHASIS and Bioversity international, to guide plant scientist in the management of experimental data. Furthermore, since genetic studies relies on the integration and the linking between phenotype and genotype datasets, relevant section of MIAPPE are beginning to be used for genotyping standards. This Webinar will give an overview of the current practices and methods for plant phenotyping data standardization, and how to deal with the variability and heterogeneity inherent to research and breeding data sets. Data management approaches at some of the major research organizations will be given as examples. The recording is available [here](https://youtu.be/4FOQPAWl6_M) and the slides are [here](https://drive.google.com/file/d/1FORlCX662T9dxiG4uzQwVXDXnq-sP0FP/view?usp=sharing) Cyril Pommier Anne-Françoise Adam-Blondon Célia Michotey Data submission, annotation, and curation Data quality management Phenomics Plant biology Researchers Biologists, Genomicists, Computer Scientists Biologists software developers, bioinformaticians
Plant Phenotyping Data managment (MIAPPE)

This material is first targetting plant biologist willing to describe and annotate their phenotyping experiments before publication. Database managers and software developpers will also receive an introduction of the current plant phenotyping standards (MIAPPE, BrAPI, Crop ontology). Learners...

Scientific topics: Data management, Plant biology, Phenomics

Operations: Formatting, Annotation

Keywords: Plant Phenotyping, Data-format, data sharing

Resource type: Training materials

Plant Phenotyping Data managment (MIAPPE) http://tess.elixir-uk.org/materials/plant-phenotyping-data-managment-miappe This material is first targetting plant biologist willing to describe and annotate their phenotyping experiments before publication. Database managers and software developpers will also receive an introduction of the current plant phenotyping standards (MIAPPE, BrAPI, Crop ontology). Learners will know how to use standards and ontologies, how to describe their measurment protocole and practices how to fill a template with their data and how to apply the standards concept in some data managment tools. Data management Plant biology Phenomics Plant Phenotyping, Data-format, data sharing Biologists geneticists plant researchers software engineers database managers
PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics

PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics. [Materials](ftp://ftp.psb.ugent.be/pub/plaza/workshop/ELIXIR/)

Scientific topics: Plant biology, Functional genomics, Comparative genomics, Evolutionary biology, Phylogenomics, Genotype and phenotype

Operations: Annotation, Visualisation, Comparison

Keywords: plants, Plants bioinformatics, genomics, Visualisation, Annotation

Resource type: Training materials

PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics http://tess.elixir-uk.org/materials/plaza-is-a-plant-oriented-online-resource-for-comparative-evolutionary-and-functional-genomics PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics. [Materials](ftp://ftp.psb.ugent.be/pub/plaza/workshop/ELIXIR/) Plant biology Functional genomics Comparative genomics Evolutionary biology Phylogenomics Genotype and phenotype plants, Plants bioinformatics, genomics, Visualisation, Annotation Life Science Researchers plant researchers experimeintal biologist researchers postdoctoral researchers Research Assistants and Research Associates PhD
TGAC_SeqAhead: NGS current challenges and data analysis for plant researchers

Hands on course held at TGAC (http://www.tgac.ac.uk/) on Monday 19 to Friday 23 May 2014 What is this workshop about? The course will combine lectures and led discussions to identify key challenges, opportunities and bottlenecks, with practical session on: Automated and standardized data...

Scientific topics: Sequence analysis, Plant biology, Database management, Bioinformatics

Keywords: Ngs, Ngs bioinformatics, Plants bioinformatics

TGAC_SeqAhead: NGS current challenges and data analysis for plant researchers http://tess.elixir-uk.org/materials/tgac_seqahead-ngs-current-challenges-and-data-analysis-for-plant-researchers Hands on course held at TGAC (http://www.tgac.ac.uk/) on Monday 19 to Friday 23 May 2014 What is this workshop about? The course will combine lectures and led discussions to identify key challenges, opportunities and bottlenecks, with practical session on: Automated and standardized data analysis for plant species data Data quality checks Estimation of reproducibility Batch effects Statistical concepts Importance of standards Data formats Data integration What will I learn? To discuss and reflect on best practice of experimental design and control for using NGS technologies in their context of addressing biological questions Identify key challenges, opportunities and bottlenecks Offering a platform for discussion and exploration of the challenges in plant research with a particular emphasis for agri-bioinformatics Sequence analysis Plant biology Database management Bioinformatics Ngs, Ngs bioinformatics, Plants bioinformatics PhD students plant researchers post-docs 2015-06-22 2017-10-09