Nevşehir Hacı Bektaş Veli University Course Catalogue
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| Year/Semester of Study | 1 / Fall Semester | ||||
| Level of Course | 2nd Cycle Degree Programme | ||||
| Type of Course | Optional | ||||
| Department | BİYOLOJİ(DOKTORA) | ||||
| Pre-requisities and Co-requisites | None | ||||
| Mode of Delivery | Face to Face | ||||
| Teaching Period | 14 Weeks | ||||
| Name of Lecturer | NAŞİT İĞCİ (nasitigci@nevsehir.edu.tr) | ||||
| Name of Lecturer(s) | |||||
| Language of Instruction | Turkish | ||||
| Work Placement(s) | None | ||||
| Objectives of the Course | |||||
| To give a practical knowledge about the aims of bioinformatics approaches in the field of proteomics studies. | |||||
| Learning Outcomes | PO | MME | |
| The students who succeeded in this course: | |||
| LO-1 | can explain current bioinformatics strategies used in proteomics. |
PO-1 Have an advanced level of knowledge about the recent and best practices in Biology, deepen and expand their knowledge on the expert level, conduct and assess the analyses by employing statistical methods PO-2 Plan experiments and carry out original researches in the field by making use of the theoretical and practical knowledge at the expert level that they have obtained in their field PO-3 Make use of the knowledge they have in order to find a solution to problems by analyzing, comparing and questioning them and can carry out original research in the related field on their own PO-4 Have the qualification and capability to gain admission to doctoral programs, R&D units or occupations related to the field with the knowledge they have gathered in the field PO-7 Are able to make use of computer software as well as communication and information technology required by the field of Biology at an advanced level |
Examination Performance Project |
| LO-2 | can perform some bioinformatic analyses in proteomics. |
PO-1 Have an advanced level of knowledge about the recent and best practices in Biology, deepen and expand their knowledge on the expert level, conduct and assess the analyses by employing statistical methods PO-2 Plan experiments and carry out original researches in the field by making use of the theoretical and practical knowledge at the expert level that they have obtained in their field PO-3 Make use of the knowledge they have in order to find a solution to problems by analyzing, comparing and questioning them and can carry out original research in the related field on their own PO-4 Have the qualification and capability to gain admission to doctoral programs, R&D units or occupations related to the field with the knowledge they have gathered in the field PO-7 Are able to make use of computer software as well as communication and information technology required by the field of Biology at an advanced level |
Examination Performance Project |
| PO: Programme Outcomes MME:Method of measurement & Evaluation |
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| Course Contents | ||
| Current proteomics strategies, use of proteomics bioinformatics, analysis in gel-based expression studies, use of protein databases, mass spectrometry based proteomics experimental approaches and protein identification with bioinformatics tools, bioinformatics approaches in protein 3 dimensional structure model | ||
| Weekly Course Content | ||
| Week | Subject | Learning Activities and Teaching Methods |
| 1 | Current strategies and data sources of proteomics. | Lecture, Discussion, Question Answer, Literature Search |
| 2 | The place of bioinformatics in proteomics and their applications. | Lecture, Discussion, Question Answer, Literature Search |
| 3 | Expression analysis with gel-based methods and evaluation and presentation of the results using softwares. | Lecture, Discussion, Question Answer, Literature Search |
| 4 | Introduction of protein databases and methods of obtaining amino acid sequences in databases. | Lecture, Discussion, Question Answer, Literature Search |
| 5 | The use of protein databases to achieve the desired knowledge and their use for specific purposes. | Lecture, Discussion, Question Answer, Literature Search |
| 6 | Mass spectrometers and their use in proteomics. | Lecture, Discussion, Question Answer, Literature Search |
| 7 | Structure and information of the spectrum obtained by mass spectrometry. | Lecture, Discussion, Question Answer, Literature Search |
| 8 | mid-term exam | |
| 9 | Protein identification by mass spectrometry I: Peptide Mass Fingerprint Analysis (Applied). | Lecture, Discussion, Question Answer, Literature Search |
| 10 | Protein identification by mass spectrometry II: Peptide Fragment Fingerprint Analysis (Applied). | Lecture, Discussion, Question Answer, Literature Search |
| 11 | Mass spectrometry based de novo amino acid sequencing and software that can be used for this purpose (Applied). | Lecture, Discussion, Question Answer, Literature Search |
| 12 | Uses and applications of Protein BLAST. | Lecture, Discussion, Question Answer, Literature Search |
| 13 | Methods used in quantitative proteomics. | Lecture, Discussion, Question Answer, Literature Search |
| 14 | Use of bioinformatic analyses in quantitative proteomics. | Lecture, Discussion, Question Answer, Literature Search |
| 15 | Determining of protein 3 dimensional structures, software used in modeling and homology based structure modeling. | Lecture, Discussion, Question Answer, Literature Search |
| 16 | final exam | |
| Recommend Course Book / Supplementary Book/Reading | ||
| 1 | Özel Demiralp F, İğci N, Peker S, Ayhan B. 2014. Temel Proteomik Stratejiler. Ankara Üniversitesi Yayınevi, Ankara. | |
| 2 | Hamdan M, Righetti PG. 2005. Proteomics Today. John Wiley & Sons, New Jersey. | |
| 3 | Hubbard SJ, Jones AR. 2010. Proteome Bioinformatics. Springer. | |
| 4 | Campbell AM, Heyer LJ. 2006. Discovering Genomics, Proteomics and Bioinformatics. Benjamin Cummings. | |
| 5 | Eidhammer I, Flikka K, Martens L, Mikalsen S-O. 2007. Computational Methods for Mass Spectrometry Proteomics. Wiley. | |
| 6 | Eyers CE, Gaskell S (Eds). 2014. Quantitative Proteomics. RSC Publishing. | |
| Required Course instruments and materials | ||
| Lecture notes, books, related articles, computer | ||
| Assessment Methods | |||
| Type of Assessment | Week | Hours | Weight(%) |
| mid-term exam | 8 | 2 | 20 |
| Other assessment methods | |||
| 1.Oral Examination | |||
| 2.Quiz | |||
| 3.Laboratory exam | |||
| 4.Presentation | |||
| 5.Report | |||
| 6.Workshop | |||
| 7.Performance Project | 15 | 2 | 40 |
| 8.Term Paper | |||
| 9.Project | |||
| final exam | 16 | 3 | 40 |
| Student Work Load | |||
| Type of Work | Weekly Hours | Number of Weeks | Work Load |
| Weekly Course Hours (Theoretical+Practice) | 3 | 14 | 42 |
| Outside Class | |||
| a) Reading | 3 | 14 | 42 |
| b) Search in internet/Library | 3 | 14 | 42 |
| c) Performance Project | 2 | 14 | 28 |
| d) Prepare a workshop/Presentation/Report | 0 | ||
| e) Term paper/Project | 0 | ||
| Oral Examination | 0 | ||
| Quiz | 0 | ||
| Laboratory exam | 0 | ||
| Own study for mid-term exam | 1 | 7 | 7 |
| mid-term exam | 2 | 1 | 2 |
| Own study for final exam | 2 | 7 | 14 |
| final exam | 3 | 1 | 3 |
| 0 | |||
| 0 | |||
| Total work load; | 180 | ||