Informatics and Bioinformatics I

Data

Official data in SubjectManager for the following academic year: 2024-2025

Topic

Students will learn the process of research planning towards conducting research effectively together practical tips and resources for successful research planning. Topics overwieved: Application of Statistics: Choosing tests and analyzing graphs. Understanding of the methodology for selecting the appropriate statistical test based on research questions and data characteristics. Molecular modelling, supercomputing, molecular symmetries, QSAR properties. Bibliographic and Chemical databases, the SciFinder and its applications.

Lectures

Practices

• 1. Overview of key concepts and applications in bioinformatics. - Ádám Zoltán Mihály
• 2. Overview of key concepts and applications in bioinformatics. - Ádám Zoltán Mihály
• 3. Process of research planning towards conducting research effectively. Practical tips and resources for successful research planning. - Ádám Zoltán Mihály
• 4. Process of research planning towards conducting research effectively. Practical tips and resources for successful research planning. - Ádám Zoltán Mihály
• 5. Prerequisites and assumptions for different statistical tests. Introduce students to the analysis and interpretation of common graph types in statistical data representation. - Ádám Zoltán Mihály
• 6. Prerequisites and assumptions for different statistical tests. Introduce students to the analysis and interpretation of common graph types in statistical data representation. - Ádám Zoltán Mihály
• 7. How to select appropriate chemical databases. Providing experience about selecting, downloading and visualization of chemical compounds and chemical reactions - Kálai Tamás
• 8. How to select appropriate chemical databases. Providing experience about selecting, downloading and visualization of chemical compounds and chemical reactions - Kálai Tamás
• 9. How to provide information about: Complex ("non-redundant") protein sequence databases. Sequence database formats. Secondary, derivative protein sequence databases. - Domián Bálint Márk
• ...

  10. How to provide information about: Complex ("non-redundant") protein sequence databases. Sequence database formats. Secondary, derivative protein sequence databases. - Domián Bálint Márk

  11. How to provide information about: Complex ("non-redundant") protein sequence databases. Sequence database formats. Secondary, derivative protein sequence databases. - Domián Bálint Márk
• 12. How to provide information about: Complex ("non-redundant") protein sequence databases. Sequence database formats. Secondary, derivative protein sequence databases. - Domián Bálint Márk
• 13. Tests - Ádám Zoltán Mihály, Kunsági-Máté Sándor, Papp Alexandra, Kálai Tamás, Domián Bálint Márk
• 14. Tests - Ádám Zoltán Mihály, Kunsági-Máté Sándor, Papp Alexandra, Kálai Tamás, Domián Bálint Márk
• 15. Data processing. Statistical analysis, selecting the relevant information. - Papp Alexandra
• ...

  16. Data processing. Statistical analysis, selecting the relevant information. - Papp Alexandra

  17. Data processing. Statistical analysis, selecting the relevant information. - Papp Alexandra

  18. Data processing. Statistical analysis, selecting the relevant information. - Papp Alexandra

  19. Data processing. Statistical analysis, selecting the relevant information. - Papp Alexandra
• 20. Data processing. Statistical analysis, selecting the relevant information. - Papp Alexandra
• 21. Vectorized calculations, supercomputers, rates, multiprocessor-computers, history. Operating systems, languages, batch-computing, partitions. Accessibilities, codes, translators, runs, architecture in Hungary - Kunsági-Máté Sándor
• 22. Vectorized calculations, supercomputers, rates, multiprocessor-computers, history. Operating systems, languages, batch-computing, partitions. Accessibilities, codes, translators, runs, architecture in Hungary - Kunsági-Máté Sándor
• 23. Geometry optimization, solvent models. Application examples: Amino acid, Nucleic acid databases, sequence editor - Kunsági-Máté Sándor
• 24. Geometry optimization, solvent models. Application examples: Amino acid, Nucleic acid databases, sequence editor - Kunsági-Máté Sándor
• 25. Molecular dynamics, molecular vibrations, entropy calculus. Chemical reactions, examples: surface properties, crystal growth, spectral properties, QSAR properties, Crystals, Saccharides, polymers - Kunsági-Máté Sándor
• 26. Molecular dynamics, molecular vibrations, entropy calculus. Chemical reactions, examples: surface properties, crystal growth, spectral properties, QSAR properties, Crystals, Saccharides, polymers - Kunsági-Máté Sándor
• 27. Tests - Ádám Zoltán Mihály, Kunsági-Máté Sándor, Papp Alexandra, Kálai Tamás, Domián Bálint Márk
• 28. Tests - Ádám Zoltán Mihály, Kunsági-Máté Sándor, Papp Alexandra, Kálai Tamás, Domián Bálint Márk

Seminars

• 1. Introduction to Bioinformatics. Highlight the importance of bioinformatics in modern biology and biomedicine. - Ádám Zoltán Mihály
• 2. Introduction to Bioinformatics. Highlight the importance of bioinformatics in modern biology and biomedicine. - Ádám Zoltán Mihály
• 3. Scientific Research Planning. Importance of scientific research in academia and beyond. - Ádám Zoltán Mihály
• 4. Scientific Research Planning. Importance of scientific research in academia and beyond. - Ádám Zoltán Mihály
• 5. Application of Statistics: Choosing tests and analyzing graphs. Understanding of the methodology for selecting the appropriate statistical test based on research questions and data characteristics. - Ádám Zoltán Mihály
• 6. Application of Statistics: Choosing tests and analyzing graphs. Understanding of the methodology for selecting the appropriate statistical test based on research questions and data characteristics. - Ádám Zoltán Mihály
• 7. Bibliographic and Chemical databases, the SciFinder and its applications. - Kálai Tamás
• 8. Bibliographic and Chemical databases, the SciFinder and its applications. - Kálai Tamás
• 9. Bioinformatics databases. Provide information about: Molecular biology databases. Primary sequence databases. - Domián Bálint Márk
• 10. Bioinformatics databases. Provide information about: Molecular biology databases. Primary sequence databases. - Domián Bálint Márk
• 11. Bioinformatics databases. Providing information about: Nucleotide sequence databases: EMBL, GenBank, DDBJ. Protein sequence database: PIR, SWISS-PROT, TrEMBL. - Domián Bálint Márk
• 12. Bioinformatics databases. Providing information about: Nucleotide sequence databases: EMBL, GenBank, DDBJ. Protein sequence database: PIR, SWISS-PROT, TrEMBL. - Domián Bálint Márk
• 13. Summary and discussions, group-projects. - Ádám Zoltán Mihály, Kunsági-Máté Sándor, Papp Alexandra, Kálai Tamás, Domián Bálint Márk
• 14. Summary and discussions, group-projects. - Ádám Zoltán Mihály, Kunsági-Máté Sándor, Papp Alexandra, Kálai Tamás, Domián Bálint Márk
• 15. From the data to the scientific information: Dental composites - Papp Alexandra
• 16. From the data to the scientific information: Dental composites - Papp Alexandra
• 17. From the data to the scientific information: PCR - Papp Alexandra
• 18. From the data to the scientific information: PCR - Papp Alexandra
• 19. From the data to the scientific information: NanoString - Papp Alexandra
• 20. From the data to the scientific information: NanoString - Papp Alexandra
• 21. High-performance computing - Kunsági-Máté Sándor
• 22. High-performance computing - Kunsági-Máté Sándor
• 23. Molecular modelling basics - Kunsági-Máté Sándor
• ...

  24. Molecular modelling basics - Kunsági-Máté Sándor

  25. Molecular modelling basics - Kunsági-Máté Sándor
• 26. Molecular modelling basics - Kunsági-Máté Sándor
• 27. Summary and discussions, group-projects. - Ádám Zoltán Mihály, Kunsági-Máté Sándor, Papp Alexandra, Kálai Tamás, Domián Bálint Márk
• 28. Summary and discussions, group-projects. - Ádám Zoltán Mihály, Kunsági-Máté Sándor, Papp Alexandra, Kálai Tamás, Domián Bálint Márk

Reading material

Obligatory literature

Micheal J. Crawley: The R Book 2007

Peter Dalgaard: Introductory statistics with R 2002

Literature developed by the Department

Slides and notes of all lectures are available electronically.

Notes

Slides and notes of all lectures are available electronically.

Recommended literature

T. K. Attwood, D. Parry-Smith: Introduction to bioinformatics; Longman, 2001, ISBN 978-0582327887

Conditions for acceptance of the semester

No additional requirements.

Mid-term exams

Two tests written on the 7th and 14th weeks.

Making up for missed classes

Electronic materials provided.

Exam topics/questions

What is bioinformatics? What are the branches, scope and aim of bioinformatics?

Classify biological databases based on data type, maintainer status, data access, data source, database design and Organism. Explain and give examples.

Selection of the appropriate equipment: Sensitivity, selectivity and data collecting. Data processing. Statistical analysis, selecting the relevant information. Conclusions.

Bibliographic and Chemical databases, the SciFinder and its applications.

How to select appropriate chemical databases. Providing experience about selecting, downloading and visualization of chemical compounds and chemical reactions

Give the applications of bioinformatics in drug discovery, QSAR, microbial genome and crop improvement.

Bioinformatics databases. The three primary database web access. Comparison of field structures.

Protein databases, comparisons. The most significant domain database. Examples for complex databases.

The use of UNIX/Linux operational system. Remote access: ssh, telnet. File handling, file movement among computers: scp, sftp, ftp, email.

Program execution: redirection of programme out- inputs. Computer networking basics.

Molecular symmetries, applications in computing. Workstations, common softwares. HyperChem and Gaussian protocols, input – output formats, visualization

Examiners

Instructor / tutor of practices and seminars

• Ádám Zoltán Mihály
• Domián Bálint Márk
• Kálai Tamás
• Kunsági-Máté Sándor
• Papp Alexandra