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PLS0077
Phenotyping Technologies in Plant-environment Interactions - Common Data Standards and Omics Technologies in Phenotyping
The course is part of a NOVA course series of four courses. This course introduces the emerging technologies related to i) automated and image based plant phenotyping technologies that are intended to remove bottlenecks between genotype and phenotype screens, ii) high throughput field phenotyping technologies and iii) use of analysis tools including R to analyze plant phenotype and -omics data iv) use of common standards for data handling, metadata generation using ontologies and data storage.
Pedagogical form:
Student activation by access to pre-course literature, in depth scientific lectures, hands-on experience during workshops and post-course assignment in the form of a research plan that allows for application of the gained knowledge.
Learning outcomes:
Participation in lectures and daily learning diaries (1.5 ECTS)
- knowledge about the whole range of analysis sensors available for plant phenotyping
- gaining understanding of the opportunities and challenges in experimental design in plant phenotyping
- using R and similar tools for analysis of plant phenotyping data
- using common standards for data handling, metadata generation using ontologies and data storage
Participation in the workshops (0.5 ECTS)
- gaining hands on experience of image-based data acquisition, and handling and processing of –omics and phenotype data.
Literature study, presentation and a research plan as post assignments (1 ECTS)
- gaining deeper understanding of the chosen biological process and chosen technology through own study
- making a presentation introducing the chosen biological process or technology and describing the goal of the research plan
- application of gained knowledge in the research plan
Pedagogical form:
Student activation by access to pre-course literature, in depth scientific lectures, hands-on experience during workshops and post-course assignment in the form of a research plan that allows for application of the gained knowledge.
Learning outcomes:
Participation in lectures and daily learning diaries (1.5 ECTS)
- knowledge about the whole range of analysis sensors available for plant phenotyping
- gaining understanding of the opportunities and challenges in experimental design in plant phenotyping
- using R and similar tools for analysis of plant phenotyping data
- using common standards for data handling, metadata generation using ontologies and data storage
Participation in the workshops (0.5 ECTS)
- gaining hands on experience of image-based data acquisition, and handling and processing of –omics and phenotype data.
Literature study, presentation and a research plan as post assignments (1 ECTS)
- gaining deeper understanding of the chosen biological process and chosen technology through own study
- making a presentation introducing the chosen biological process or technology and describing the goal of the research plan
- application of gained knowledge in the research plan
Syllabus and other information
Syllabus
PLS0077 Phenotyping Technologies in Plant-environment Interactions - Common Data Standards and Omics Technologies in Phenotyping, 3.0 Credits
Subjects
BiologyEducation cycle
Postgraduate levelGrading scale
Pass / Failed
Prior knowledge
MSc degree in a relevant field is required. Relevant fields: agriculture, biological and environmental sciences.Objectives
The changing climate demands the development of faster breeding methods to provide effective solutions for the future agriculture. Plant phenotyping is used for plant-environment interactions in a number of settings, from highly controlled environments to field conditions. This course series aims to introduce the emerging research fields of high throughput plant phenotyping and omics technologies (including bioinformatics). This core focus of the course is on computational solutions for handling and analyzing plant phenotyping data. The objective of the course series is to provide the participating students with the basic knowledge and understanding of the emerging fields of plant phenomics and data processing that can serve breeding efforts as well as precision agriculture for current and future climate conditions.Content
The course is part of a NOVA course series of four courses. This course introduces the emerging technologies related to i) automated and image based plant phenotyping technologies that are intended to remove bottlenecks between genotype and phenotype screens, ii) high throughput field phenotyping technologies and iii) use of analysis tools including R to analyze plant phenotype and -omics data iv) use of common standards for data handling, metadata generation using ontologies and data storage. Pedagogical form: Student activation by access to pre-course literature, in depth scientific lectures, hands-on experience during workshops and post-course assignment in the form of a research plan that allows for application of the gained knowledge. Learning outcomes: Participation in lectures and daily learning diaries (1.5 ECTS) - knowledge about the whole range of analysis sensors available for plant phenotyping - gaining understanding of the opportunities and challenges in experimental design in plant phenotyping - using R and similar tools for analysis of plant phenotyping data - using common standards for data handling, metadata generation using ontologies and data storage Participation in the workshops (0.5 ECTS) - gaining hands on experience of image-based data acquisition, and handling and processing of –omics and phenotype data. Literature study, presentation and a research plan as post assignments (1 ECTS) - gaining deeper understanding of the chosen biological process and chosen technology through own study - making a presentation introducing the chosen biological process or technology and describing the goal of the research plan - application of gained knowledge in the research planAdditional information
Technical requirements: Own laptop.Responsible department
Department of Plant Protection Biology