| ARCHITECTURE | |||||
| Bachelor | TR-NQF-HE: Level 6 | QF-EHEA: First Cycle | EQF-LLL: Level 6 | ||
| Course Code | Course Name | Semester | Theoretical | Practical | Credit | ECTS |
| MBG2004 | Computation for Biological Sciences II | Spring | 2 | 2 | 3 | 7 |
| This catalog is for information purposes. Course status is determined by the relevant department at the beginning of semester. |
| Language of instruction: | English |
| Type of course: | Non-Departmental Elective |
| Course Level: | Bachelor’s Degree (First Cycle) |
| Mode of Delivery: | Face to face |
| Course Coordinator : | Assist. Prof. CEMALETTİN BEKPEN |
| Course Lecturer(s): |
Prof. Dr. SÜREYYA AKYÜZ |
| Course Objectives: | This class intended to provide advanced information to computational tools for biology. This course covers the methods and tools for learning foundations of computational biology combining theory with practice. We cover both foundational topics in computational biology, and current research frontiers. We study fundamental techniques, recent advances in the field, and work directly with current large-scale biological datasets. |
|
The students who have succeeded in this course; • Genomes: Biological sequence analysis, comparative genomics, RNA structure, sequence alignment, • Pathways and Network analysis: Gene expression, clustering / classification, motifs, Bayesian networks, microRNAs, regulatory genomics, epigenomics • Molecular Evolution: Gene / species trees, phylogenomics, coalescent, personal genomics, population genomics, human ancestry, recent selection, disease mapping • Comparative Genomics/Transcriptomics: Compare current NGS mapping methodologies and genomes both theoretically and practically, • Genome Assembly: With the advances in sequencing technologies it has become much more feasible, and affordable, to assemble and annotate the genomic sequence of most organisms, including large eukaryote genomes. However, high quality genome assembly and annotation still represent a major challenge. In this class, we will discuss current methods and technologies to perform best assembly. • Current advances in systems and integrative biology (Review) |
| Advanced level sequence data, searching and alignment, structural data, genome sequencing, genome analysis, genetic variation, gene and protein expression, and biological networks and pathways. We will evaluate the results of these analyzes by using advances functional genomics, transcriptomics, enrichment methods |
| Week | Subject | Related Preparation |
| 1) | Introduction | Read the Syllabus and Describe Project Details |
| 2) | Advanced Comparative Genomics | |
| 3) | Human Genomic Variations (Population Genetics approach) | Practical Lab Assignment 1 by using https://usegalaxy.org/ |
| 4) | Variant Detection and Methods Single Nucleotide Variations (SNPs) Annotation | |
| 5) | SNP Genotyping Methods and Micro Array Analyses | Practical Lab Assignment 2 by using https://usegalaxy.org |
| 6) | Advanced Variant Detection and Methods Structural Variations (SVs) Copy Number Variation (CNVs) | |
| 7) | Gene Ontology and Gene Annotation | Practical Lab Assignment 3 by using https://usegalaxy.org/ |
| 8) | Advance Transcriptomics (RNA-Seq) Gene set enrichment analysis | |
| 9) | Midterm Review | Midterm Sınavı |
| 10) | Genome/Transcriptomics Assembly and Annotation | Practical Lab Assignment 4 by using https://usegalaxy.org/ |
| 11) | Advance Molecular Phylogenetics/Phylogenomics | |
| 12) | Molecular Evolution/PaleoGenomics | Final Project by using https://usegalaxy.org/ |
| 13) | MetaGenomics | |
| 14) | Review “Current advances in systems and integrative biology? ” | Final Project submission and Final Project Exam |
| Course Notes / Textbooks: | Ders notları haftalık olarak verilecektir. Course material will be provided weekly. |
| References: | 1) Durbin, Richard, Sean R. Eddy, Anders Krogh, et al. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, 1998. 2) Jones, Neil C., and Pavel Pevzner. An Introduction to Bioinformatics Algorithms. MIT Press, 2004. ISBN: 9780262101066. |
| Semester Requirements | Number of Activities | Level of Contribution |
| Project | 1 | % 40 |
| Midterms | 1 | % 20 |
| Final | 1 | % 40 |
| Total | % 100 | |
| PERCENTAGE OF SEMESTER WORK | % 20 | |
| PERCENTAGE OF FINAL WORK | % 80 | |
| Total | % 100 | |
| Activities | Number of Activities | Duration (Hours) | Workload |
| Course Hours | 14 | 4 | 56 |
| Study Hours Out of Class | 14 | 7 | 98 |
| Project | 5 | 4 | 20 |
| Midterms | 1 | 2 | 2 |
| Final | 1 | 2 | 2 |
| Total Workload | 178 | ||
| No Effect | 1 Lowest | 2 Low | 3 Average | 4 High | 5 Highest |
| Program Outcomes | Level of Contribution | |
| 1) | Using the theoretical/conceptual and practical knowledge acquired for architectural design, design activities and research. | 3 |
| 2) | Identifying, defining and effectively discussing aesthetic, functional and structural requirements for solving design problems using critical thinking methods. | 3 |
| 3) | Being aware of the diversity of social patterns and user needs, values and behavioral norms, which are important inputs in the formation of the built environment, at local, regional, national and international scales. | |
| 4) | Gaining knowledge and skills about architectural design methods that are focused on people and society, sensitive to natural and built environment in the field of architecture. | 3 |
| 5) | Gaining skills to understand the relationship between architecture and other disciplines, to be able to cooperate, to develop comprehensive projects; to take responsibility in independent studies and group work. | |
| 6) | Giving importance to the protection of natural and cultural values in the design of the built environment by being aware of the responsibilities in terms of human rights and social interests. | |
| 7) | Giving importance to sustainability in the solution of design problems and the use of natural and artificial resources by considering the social, cultural and environmental issues of architecture. | |
| 8) | Being able to convey and communicate all kinds of conceptual and practical thoughts related to the field of architecture by using written, verbal and visual media and information technologies. | 3 |
| 9) | Gaining the ability to understand and use technical information about building technology such as structural systems, building materials, building service systems, construction systems, life safety. | |
| 10) | Being aware of legal and ethical responsibilities in design and application processes. |