Events and training activities

The course will be organized with the main purposes to throw light on different aspects of the organization, performance and analyses of field trials as well as to improve 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. Topics include:

• Provision of solutions to a Global market using natural bioactives;
• Challenges and approaches to implementing statistically robust commercial field trials;
• Trial design and statistics.

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The workshop will include the following parts:

• A lecture on biostimulants and their role in agriculture;
• A lecture on molecular priming with focus on discovery of new priming molecules;
• Discussion of the mechanisms of seaweed based biostimulants as crop priming technologies (including field and in-house trials).

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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.

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The workshop provided an introduction of supervised machine learning approaches for reconstruction of gene regulatory networks (GRNs) using large-scale transcriptomics data. In the first part of the event, we provided an overview of supervised machine learning approaches, namely support vector machines and random forests. We then summarised how these approaches are used in addressing the problem of GRN reconstruction when transcriptomics data are available. We also covered aspects related to assessing the performance of reconstructions. The second part of the workshop was dedicated to showcasing the applications of these approaches to reconstructing GRNs in model plants and crops, with emphasis on Arabidopsis thaliana and maize. We also presented packages and tools developed in house that can be used in addressing this problem in future applications.

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The workshop was consisted 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 included:

• Sample preparation and untargeted lipid profiling using LC-MS;
• Data analysis: normalization, clustering, principle component analysis (PCA);
• Statistical analysis and biological interpretation.

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The course introduced the concepts of biotic, abiotic, and oxidative stress signalling in plants and cover the genetic, epigenetic, and molecular mechanisms of regulation of stress tolerance. Topics included:

• 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.

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The workshop introduced the basic requirements to understand plant metabolism and present the techniques used to study plant metabolic processes. The lectures provided a wide overview of different metabolomics concepts and the common workflows used in plant metabolomics as well as aspects and techniques used for data analysis. The focus was 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 also were reviewed. The workshop was 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.

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This workshop focused on NGS and the analysis of NGS-derived (short read) data. After introducing the different NGS technologies and applications, participants ran through a sample NGS analysis pipeline including quality assessment and preprocessing of NGS data, mapping sequencing reads, identification of differentially expressed transcripts, clustering and GO enrichment. It is assumed that those participating are familiar with working on the command line (or have already attended the first workshop), but do not need to be familiar with NGS analysis specifically.

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The first stumbling block for many experimental biologists when faced with a bioinformatics project is the need to work on a command line terminal in a Linux/UNIX environment. This skill is a prerequisite for any scientist wishing to analyze their NGS datasets (and many others). The primary focus of the first workshop was to build familiarity with working on the command line. The workshop was suitable for those with absolutely no experience with Linux/UNIX systems (covering the basics such as file system navigation and viewing and manipulating files) and progresses to more advanced topics (grep, sed and awk, package installation and scripting). These topics were covered in the context of the biological sciences and was also included an introduction to the analysis of file types one might commonly find when analyzing NGS data (e.g. FASTA/FASTQ/BED/GFF formats).

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