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Control of Biosystems

Course developer

Course abstract

The aim of the study course is to introduce students to the management of biosystems, which has become one of the branches of computer science and computer management application with great potential for development in biotechnology, medicine, ecology and energy. The subject is intended to provide information technology specialists in a form suitable for information about the basics of biological systems and the connection of computer technology with various branches of science and the latest technological achievements. Concepts of cybernetics and systems theory that link biological systems to technical systems in a unified formal analysis are reviewed.

Learning outcomes and their assessment

• students know about the main common features of biological and technical processes, the basic principles of biological system operation down to the cellular level - practical work, theory test
• students know how to analyze genetic information, compare gene sequences of different organisms, trace the potential consequences of genetic changes in the biological control system, interpret the results of dynamic model simulations - practical work, independent work
• students are able to use open-access biological information analysis tools in modeling and forecasting biological management processes, to be able to analyze and plan bioprocess modeling and optimization processes - practical work.

Course Content(Calendar)

1. Tools, methods and assessment of climate change modeling and forecasting in Latvia and the world - 2 h
2. Working with GHG (greenhouse gas) emission databases and calculations in the agricultural sector for climate change modeling tasks – 2 h
3. Tools for forecasting climate models on the global web - 2 h
4. Use of satellite data in GIS systems – 2 h
5. Definition of the precise agricultural sector and review of basic sub-sectors – 2 h
6. Subsectors of precision agriculture Precision beekeeping determination and modeling of computer technology tasks. Investment payback calculations for the implementation of the precision beekeeping IS system - 2 h
7. Subsectors of precision agriculture Precision animal husbandry determination and modeling of computer technology tasks – 2 h
8. Graph theory. Basic concepts of graph theory. Applications of graph theory in computer technology biosystems analysis and modeling tasks - 3 h
9. Fundamentals of genetics. Types of mutation. Analysis of the structure of biochemical networks and evolutionary modeling – 2 h
10. Gene homology analysis with the help of free access tools – 3 h
11. Navigation in genetic information databases. Different gene regions – 2 h
12. Search for homologous sequences. Interpretation of BLAST analysis results – 2 h
13. Analysis of the degree of homology of related organisms – 2 h
14. Copasi tool for modeling and optimization of bioprocesses – 3 h
15. Theory test – 1 h

Requirements for awarding credit points

To award credit points for Computer Technologies in the Management of Biosystems with a grade:
• it is necessary to complete all practical tasks;
• it is necessary to pass the theory test;
• it is necessary to develop and defend independent work.
The grade is formed as an accumulative grade, taking into account the practical tasks, theoretical test and independent work.

Description of the organization and tasks of students’ independent work

The organization of independent work during the semester takes place by studying literature independently, using academic staff member consultations.
Independent work: Analysis of gene homology with the help of an open access tool, search for homologous sequences, interpretation of BLAST analysis results and analysis of the degree of homology of related organisms (volume at least 3 pages, submitted in electronic form).

Criteria for Evaluating Learning Outcomes

The mark of the course depends on the cumulative evaluation of the semester: 1. Evaluation of the theoretical test (40%), 2. Developed and defended independent work (30%), 3. Completed practicals (30%). The maximum number of % is 100%, which corresponds to 10 points for the passing grade.

Compulsory reading

1. Ratledge C., Kristiansen B. Basic Biotechnology. 3rd edition. Cambridge: Cambridge University Press, 2006.
2. Dochain D. Bioprocess control. Wiley and Sons, 2001.
3. Klipp E., Herwig R., Kowald A., Wierling C., Lehrach H. Systems Biology in Practice. Concepts, Inplementation and Application. WILEY-VCH Verlag GmbH&Co KgaA. 2006.
4. Jones D.S. Sleeman B.D. Differential Equations and Mathematical Biology. Chapman &Hall/CRC, 2003.

Further reading

1. Szallasi Z., Stelling J., Periwal V. System Modelling in Cell Biology from concepts to nuts and bolts. MIT Press, 2006.
2. Davidson E.H. The regulatory Genome. Gene regulatory networks in development and evolution. Academic Press, Elsevier, 2006. Pieejama tiešsaistē:
http://ezproxy.llu.lv:2108/ehost/ebookviewer/ebook?sid=10915a09-2d02-4e95-8231-33df5cb67bab%40pdc-v-sessmgr02&ppid=pp_C1&vid=0&format=EB
3. Palsson B.O. Systems Biology: Properties of Reconstructed networks. Cambridge University Press, 2006.

Notes

Study course for students of the ITF academic study program "Computer Control and Computer Science".