Introduction to Computational Molecular Biology-E2
| Numbering Code | U-LAS14 20061 SE68 | Year/Term | 2022 ・ Second semester | |
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| Number of Credits | 2 | Course Type | Seminar | |
| Target Year | All students | Target Student | For science students | |
| Language | English | Day/Period | Wed.4 | |
| Instructor name | Martin Robert (Graduate School of Pharmaceutical Sciences Program-Specific Associate Professor) | |||
| Outline and Purpose of the Course |
The last two decades have seen the rapid expansion of quantitative data in biology. Large-scale experimental approaches now provide quantitative information about biomolecules at an unprecedented pace and scale. Along with these advances, computational tools have become essential to deal with the huge amount of data and to better understand complex and dynamical living systems. The main objective of the course is to learn some of the basic principles of computational biology and bioinformatics, from the molecular perspective. |
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| Course Goals |
At the end of this course students should: - Appreciate and be able to describe different types of molecular cellular components - Understand and solve sequence matching problems and perform sequence analysis and interpretation - Use and understand computational tools widely used by research scientists - Understand and be able to analyze basic molecular network structures and their properties - Solve problems of molecular analysis using computational tools - Appreciate and utilize the power of computational modeling to study and better understand complex biological systems |
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| Schedule and Contents |
The following topics will be covered over the course of 14 classes, not necessarily in that order: Week 1 Guidance Week 2 Basic concepts in computational molecular biology Week 3 Review of biomolecule structure and properties Week 4 Introduction to biological databases Week 5-6 DNA and protein sequence analysis Week 7-8 Protein analysis (structure and biochemical properties) Week 9 Sequence alignment Week 10 Patterns in data Week 11-12 Molecular networks: principles and analysis Week 13 Reaction-diffusion systems and spatiotemporal patterns Week 14 Computational metabolic models of cells or organisms Week 15 Final examination Week 16 Feedback |
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| Evaluation Methods and Policy |
20% Class attendance/participation 40% In-class exercises and homework assignments 20% Project and presentation 20% Final examination |
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| Course Requirements |
Students will need a computer to complete in-class exercises and homework assignments. The course is meant for beginners, but students are expected to have a basic familiarity with biomolecules, cell biology, and the use of computers. |
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| Study outside of Class (preparation and review) | Mainly in the form of assigned reading and homework assignments. Students should expect to spend about 1-2 hours per week preparing for the class and completing assignments. | |||
| Textbooks | Textbooks/References | Computational biology: a hypertextbook , Kelley, Scott T. and Didulo, Dennis, (ASM Press, Wiley 2018) | ||
| References, etc. | Additional material and articles will be provided in class. | |||
