Biological and biomedical databases

Timetable

Timetable will be included before the beginning of the semester.

Laboratories - 20h (hands-on in the computer room)

Lectures - 10h

Planned number of groups: 2

Module aim (aims)

Main aims of this module are:
1. To get familiar with the most commonly used types and formats of biological data, as well as different types and structures of databases and the systems that manage them.
2. To be able to describe and use systems for storing and searching scientific literature data, as well as databases of nucleotide and amino acid sequences and other related
resources.
3. To acquire skills in using genomic browsers and tools for filtering and downloading biological data, including Next Generation Sequencing resources.
4. To get familiar with specialized databases related to polymorphisms, mutations and human diseases.
5. To be able to search within resources of the World Health Organization (WHO) and other databases related to human health.
6. To expand your knowledge but most of all to practice all these databases by your own.

Pre-requisites in terms of knowledge, skills and social competences (where relevant)

Basic knowledge from molecular biology and human genetics.

Syllabus

1. Most commonly used types and formats of biological data. (Lectures and Laboratories)
2. Types and structure of databases and systems that manage them. (Lectures and Laboratories)
3. Systems for storing and searching literature data. (Lectures and Laboratories)
4. Databases of nucleotide and amino acid sequences and related resources. (Lectures and Laboratories)
5. Genome browsers (NCBI, Ensembl, UCSC). (Lectures and Laboratories)
6. Useful tools for filtering and downloading biological data. (Lectures and Laboratories)
7. Specialized databases related to polymorphisms, mutations and human diseases. (Lectures and Laboratories)
8. Next Generation Sequencing data - where to find it? (Lectures and Laboratories)
9. Resources of the World Health Organization (WHO) and other databases related to human health. (Lectures and Laboratories)

Reading list

1. Zou, D., Ma, L., Yu, J., & Zhang, Z. (2015). Biological databases for human research. Genomics, proteomics & bioinformatics, 13(1), 55–63, doi.org/10.1016/j.gpb.2015.01.006
2. Nishant  T,  Arun  Kumar,  Sathish  Kumar  D,  Vijaya  Shanti  B  (2011) Biological Databases-  Integration of  Life Science Data J Comput  Sci Syst  Biol 4: 087-092. doi:10.4172/jcsb.1000081

More materials will be provided during classess.