|
|
| MBG3034 | Web Applications in Molecular Biology | 2+2+0 | ECTS:4 | | Year / Semester | Spring Semester | | Level of Course | First Cycle | | Status | Compulsory | | Department | DEPARTMENT of MOLECULAR BIOLOGY and GENETICS | | Prerequisites and co-requisites | None | | Mode of Delivery | Face to face, Practical | | Contact Hours | 14 weeks - 2 hours of lectures and 2 hours of practicals per week | | Lecturer | Doç. Dr. Halil İbrahim GÜLER | | Co-Lecturer | No | | Language of instruction | Turkish | | Professional practise ( internship ) | None | | | | The aim of the course: | | It is aimed that these students learn the processing of biological data, the use of web based applications and algorithms in molecular biology. Applications for determination of three-dimensional structure of proteins, protein-ligand interactions, processing and understanding of genomic sequences are also among the objectives of this course. |
| Learning Outcomes | CTPO | TOA | | Upon successful completion of the course, the students will be able to : | | | | LO - 1 : | Biological databases can be used to access protein and genome sequence information. | 5,8 | 1,4, | | LO - 2 : | They can recognize the FASTA file format, edit and sort sequences using the BLAST algorithm. | 5,8 | 1,4, | | LO - 3 : | They can investigate 3D protein structures stored on the Protein Data Bank and can make protein sequence comparisons to estimate 3D structure. | 5,8 | 1,4, | | LO - 4 : | They can know homology modeling methods and their applications and can make 3D structure estimation for this purpose. | 5,8 | 1,4, | | LO - 5 : | They can search experimental data on ligand databases to investigate protein-ligand interactions. | 5,8 | 1,4, | | LO - 6 : | They can develop a project on the Benchling website. | 5,8 | 1,4, | | LO - 7 : | They can organize using complex genomic data. | 5,8 | 1,4, | | LO - 8 : | They can determine the physico-chemical properties and post-translational modifications of proteins. | 5,8 | 1,4, | | CTPO : Contribution to programme outcomes, TOA :Type of assessment (1: written exam, 2: Oral exam, 3: Homework assignment, 4: Laboratory exercise/exam, 5: Seminar / presentation, 6: Term paper), LO : Learning Outcome | | |
| Learning web applications that can be used for simulation of molecular biology experiments, making 3D image and prediction of protein, conducting further analysis using genomic sequence data. |
| |
| Course Syllabus | | Week | Subject | Related Notes / Files | | Week 1 | Biological sequences and file formats | | | Week 2 | Access to Biological Databases and Sequences | | | Week 3 | Protein Data Bank and Experimental determination of Protein 3-D structure | | | Week 4 | BLAST Algorithm and Applications | | | Week 5 | BLAST Algorithm and Applications | | | Week 6 | Protein 3D structure estimation methods and applications | | | Week 7 | Protein-ligand interaction and applications | | | Week 8 | Protein-ligand interaction and applications | | | Week 9 | Mid-term exam | | | Week 10 | Docking applications | | | Week 11 | Docking applications | | | Week 12 | Benchling website and applications | | | Week 13 | Genome analysis using Benchling | | | Week 14 | CRISPR exercises and Usage of web applications | | | Week 15 | Overall assessment | | | Week 16 | End-of-term exam | | | |
| 1 | Bioinformatics For Dummies, 2nd EditionBy Jean-Michel Claverie, Ph. D., Cedric Notredame, Ph.D. December 2006, 436pp, ISBN: 978-0-470-08985-9, JOHN WILEY. | | | |
| 1 | Biyoenformatik 1 dizi kIyaslamalarI, Jens Allmer, Eylül 2012, Nobel Akademik YayIncIlIk | | | |
| Method of Assessment | | Type of assessment | Week No | Date | Duration (hours) | Weight (%) | | Mid-term exam | 9 | | 1 | 35 | | Homework/Assignment/Term-paper | 15 | | 1 | 15 | | End-of-term exam | 16 | | 1 | 50 | | |
| Student Work Load and its Distribution | | Type of work | Duration (hours pw) | No of weeks / Number of activity | Hours in total per term | | Yüz yüze eğitim | 3 | 15 | 45 | | Sınıf dışı çalışma | 1 | 16 | 16 | | Laboratuar çalışması | 1 | 8 | 8 | | Arasınav için hazırlık | 2 | 1 | 2 | | Arasınav | 1 | 12 | 12 | | Dönem sonu sınavı için hazırlık | 2 | 16 | 32 | | Dönem sonu sınavı | 2 | 1 | 2 | | Total work load | | | 117 |
|