BIOTECH-GO O3 BIOTECH-GO Joint Study Education Programme (JSЕP)

2016-1-BG01-KA202-023686 O3 BIOTECH-GO Joint Study Education Programme (JSTP)

This Intellectual output is dedicated on preparation and offer of multilingual blended modes of education and training in the field of . The JSТ programme will be realized through Innovative VET training content in the following main topics:

I. Introduction to Bioinformatics - Biology, biological databases, and high-throughput data sources - Alignments and phylogenetic trees - and system biology II. Bioinformatics/ in Biotechnology - Health Bioinformatics - Bioinformatics in food production and engineering - The role of bioinformatics in agriculture - Application of system biology in bioremediation

Part I Detailed Content

Biology, biological databases, and high-throughput data sources

• Introduction and application of modern bioinformatics in molecular biology. Components of bioinformatics. Basic concepts of molecular biology and computer abstractions. Information growth: sequences, genomes, macromolecular structures. Searching biological databases. Introduction to NCBI Entrez.

• Databases - definition, nature, attributes and examples. Basic models database. Keys. Indices. Normalization. Programming languages to define a database. Program strategies. Interface database. HTML. WWW servers. CGI. Part I Detailed Content

Alignments and phylogenetic trees

• Genomic database. Sequence formats. Sequences align. Global and local alignment. Approaches to search genomic database. Download of DNA and protein sequences from public databases. Features of BLAST. Multiple DNA and protein sequence alignment. Working with ClustalW and ClustalX. Online for multiple DNA and protein sequence alignment.

• Software for phylogenetic analysis, development of phylogenetic trees or phylogenetic networks through alignment of DNA or protein sequences, distance matrix. Features and applications of SplitsTree, Dendroscope and Njplot. Part I Detailed Content

Proteomics and system biology

• Visualizing protein structures and computing structural properties. The chemistry of proteins. Web-based protein structure tools. Structure visualization. Structure classification. Structural alignment. Protein databases: prosite. prints. pfam. blocks.

• Predicting protein structure and function from sequence. Secondary structure prediction. Predicting 3D structure. Proteomics. Biochemical pathway databases. Part II Bioinformatics/genomics in Biotechnology

Health Bioinformatics • Introduction To Health Bioinformatics - definition and overview of health informatics

• Medical And Health Informatics - content is dedicated on presentation of Clinical Big Data, Electronic health records (EHRs), social health and Lifestyle environmental factors and public health

• Healthcare Informatics - information is provided for clinical informatics, integrated data repository and clinical research informatics

• Human Bioinformatics - Stress is made on Translational bioinformatics comprising information for Genomics in clinical care (Translational Genomics), , for drugs discovery and repurposing and Personalized genomic testing. Data is provided for Computational health informatics. Sensor and Imaging Informatics are described. 50 Part II Bioinformatics/genomics in Biotechnology

Health Bioinformatics • Bioinformatics Data Repositories – this chapter includes information for public databases and search functions, genome mapping and Expressed Sequence Tag (EST), as well as for comparative genome analysis

• Bioinformatics Analysis Tools – describing the biological sequences analyses and microarray tools

• Search Algorithms for Sequence Alignment, E.G. BLAST and FASTA, Introduction, Application of Proteomics and Web Servers are also described

• Attention is made on different Special Topics in Health Sciences like Bioinformatics in cancer biology, Computational radiobiology, Cancer biomarker discovery, Clinical decision support using bioinformatics and Genetic engineering: gene modifications and manipulations Part II Bioinformatics/genomics in Biotechnology

Bioinformatics in food production and engineering

• Food production benefits from bioinformatics Food and nutrition has an important role in regulation of human body processes. The introduction of advanced techniques like “omics” in food science and practice causes serious difficulties in interpretation of accumulated great biological data sources. A decision of this problem is implementation of bioinformatics approach giving an excellent ground for successful development of food production and engineering.

• Microbial bioinformatics for food production and safety Bioinformatics plays an increasing role in predicting and assessing the desired and undesired effects of microorganisms on food. A combination of bioinformatics with laboratory verification of selected findings is outlined with the following methods: genomics-based functional predictions; genomic scale metabolic models, design of complex food properties and engineering . Part II Bioinformatics/genomics in Biotechnology

The role of bioinformatics in agriculture

• Bioinformatics for agriculture. Genomics, and interactomics for sustainable agricultural development. Impact of genome sequencing in agriculture. Applications of agricultural bioinformatics. Agriculturally important biological database.

• Plant genomics. The role of model organisms. Managing and distributing plant genome data. Molecular plant breeding. Rational plant improvement. Genotype building experiments. QTLs (Quantitative Trait Locus) analysis and mapping.

Part II Bioinformatics/genomics in Biotechnology

Application of system biology in bioremediation

• Introduction to Bioremediation - Types of organisms used in bioremediation are described. Brief overview on bioremediation strategies and existing in situ and ex situ methods is given. Advantages and disadvantages of bioremediation techniques are provided. Influence of environmental factors on biodegradation process is denoted.

• Application of , and Metatranscriptomics – metaproteomics - metabolomics in environmental remediation is outlined.

• Several specific Case Studies are also provided.