Events And Training activities

Events

RESIST Kick-off meeting is scheduled for 11-12 April 2019 at Hotel Ramada, Plovdiv, Bulgaria


Training activities

A series of training events (courses and workshops) will be organized in order to enhance the transfer of knowledge between the partners and improve the qualifications of the committed scientists in specific fields such as plant -omics analyses, bioinformatics and mathematical modeling, soft skills acquisition etc.

  1. Workshop RNA-Seq analysis (UCT). The workshop will cover pre-processing of RNA-Seq reads through to identification of differentially expressed genes using the Trinity package, giving participants hands on experience in some of the key processes. Topics to be included:
    • Quality control/pre-processing, in-silico normalisation;
    • Read mapping, differential gene expression (EdgeR and DeSeq2);
    • Principle component analysis.
  2. Plant metabolomics workshop (MPG). The workshop will introduce the basic requirements to understand plant metabolism and present the techniques used to study plant metabolic processes. The lectures will provide a wide overview of different metabolomics concepts and the common work flows used in plant metabolomics as well as aspects and techniques used for data analysis. The focus will be on gas- and liquid chromatography- mass spectrometry (GC/LC-MS) as the most frequently used in plant metabolomics, but nuclear magnetic resonance (NMR) spectroscopy as a means of elucidating metabolite structures will also be reviewed. The workshop will be divided into the following parts:
    • General introduction about metabolomics. Principal and basics of GC-MS and LC-MS analysis;
    • Practice and chromatogram evaluation for GC/LC-MS;
    • NMR-based metabolomics for elucidation of metabolite structures.
  3. Workshop NGS analysis and applications (UCT). The next-generation sequencing (NGS) has become an indispensable tool for genomics and plant systems biology, as this is the basis of whole genome sequencing and analysis, evaluation of genetic and epigenetic changes including chromatin remodeling, transcriptome analysis, medical diagnostics etc. The workshop will provide an overview of the new sequencing technologies available nowadays and the computational analysis that may be required when dealing with the resulting biological data. Next to that, it reviews the major applications of NGS in plant systems biology. Topics include:
    • Overview of the sequencing technologies (Illumina NGS, Pacific Bioscienes, Oxford Nanopore);
    • NGS Applications: De novo genome sequencing, metagenomics, ChIP-Seq, Methyl-Seq, SNP/variant identification, Gene expression analysis (RNA-seq);
    • Common downstream computational tasks (e.g. quality control, genome assembly, mapping, differential gene expression analysis, variant effect prediction, annotation, co-expression analysis).
  4. Course Plant stress physiology (CPSBB). The course will introduce the concepts of biotic, abiotic, and oxidative stress signalling in plants and will cover the genetic, epigenetic, and molecular mechanisms of regulation of stress tolerance. Topics include:
    • Introduction to abiotic and oxidative stresses. Plant abiotic and biotic stress tolerance;
    • Genetic and epigenetic regulations of stress tolerance in plants;
    • Plant hormones and stress signaling.
  5. Workshop on Plant lipidomics (BGU). The workshop will consist of a theoretical part presenting the methods of sample preparation, data analysis, and biostatistics, as well as hands-on training with the available machines. Topics include:
    • Sample preparation and untargeted lipid profiling using LC-MS;
    • Data analysis: normalization, clustering, principle component analysis (PCA);
    • Statistical analysis and biological interpretation.
  6. Workshop Bioinformatics and mathematical modelling (UP). Such skills are needed to prepare ESRs for tasks such as comparative genomics, analysis of large transcriptome and metabolome datasets, integration of complex data into systems biology models. Topics include:
    • Introduction to bioinformatics and sequence analysis: Sequence alignment, sequence comparison using similarity based approaches (eg. BLAST, CLUSTAL-W), sequence annotation, phylogenetic analysis;
    • R for Bioinformatics. What are the basic commands and packages for integration of large-scale –omics data for learning gene function;
    • Comparative & evolutionary genomics: Clustering gene families. Phylogenetics. Genome evolution;
    • Data access, mining and curation: data management, biological resources (eg. KEGG, GEO, Uniprot, NCBI, ArrayExpress). Biostatistics. Introduction to R/Bioconductor and/or Python.
  7. Course Project writing and management (CPSBB). The course will introduce the EU research landscape and focus on the basic principles of project writing and management. Topics include:
    • Introduction to the EU research landscape. Funding opportunities within H2020 (the main pillars) and other European funding instruments for groups, postdocs, and ESRs;
    • How to write project proposals: basics learned from successful candidates and from evaluators;
    • Profession project manager: insights from the scientific managers.
  8. Workshop Plant genetics and crop health (BioAtlantis). The course will be divided into two modules, the first of which will be focused on basics of plant genetics and genomics, while the second one will be dedicated to biostimulant-based technologies for crop protection. The event will also involve a guided tour to present the largest fully automated seaweed extraction facility in Britain and Ireland, which uses technologies for separation, purification and spray drying. Topics of the workshop include:
    • Basics of quantitative genetics (module 1);
    • Plant translational research in the genomics era (module 1);
    • Development of innovative products for crop protection (module 2);
    • Molecular approaches to assess the mechanism of biostimulant – plant interactions (module 2).
  9. Workshop Plant genetics and crop health (BioAtlantis). The course will be divided into two modules, the first of which will be focused on basics of plant genetics and genomics, while the second one will be dedicated to biostimulant-based technologies for crop protection. The event will also involve a guided tour to present the largest fully automated seaweed extraction facility in Britain and Ireland, which uses technologies for separation, purification and spray drying. Topics of the workshop include:
    • Basics of quantitative genetics (module 1);
    • Plant translational research in the genomics era (module 1);
    • Development of innovative products for crop protection (module 2);
    • Molecular approaches to assess the mechanism of biostimulant – plant interactions (module 2).
  10. Course Entrepreneurship and transferrable skills (Bioatlantis). The course will be organized in BioAtlantis with the purpose to throw light on different aspects of the process of establishment, organization and management of new enterprises. Moreover, the set of transferrable skills, which are not directly related to a particular work position, but can be applied to a wide range of different jobs and industries, will also be discussed. Topics include:
    • Identification of opportunities to establish new enterprises; market analyses and preparation of business plans
    • Role of research and innovation (R&I) for the profitability and growth of business entities
    • Development of transferrable skills like leadership, motivation, communication and adequate time management