Repository for the BIO230 web site at https://vprobon.github.io. Schedule, assessment, teaching material etc.
| Date | Content | Lecture | Reading material | |
|---|---|---|---|---|
| Week 1 | Introduction | |||
| Monday, 04/09 | Course Introduction | This website site, MS TEAMS environment | ||
| Wednesday, 06/09 | No class | |||
| Thursday, 07/09 | Concepts in (Molecular/Cell) Biology | Lectures/01.Fundamentals (slides 1-23) | Understanding Bioinformatics p. 3-44 | |
| Week 2 | Introduction cont’d and Literature resources | |||
| Monday, 11/09 | An Overview of Bioinformatics | Lectures/01.Fundamentals (slides 24-35) | Understanding Bioinformatics p. 3-44 | |
| Wednesday, 13/09 | Tutorial/Q&A session | |||
| Thursday, 14/09 | Online Literature Resources for (Molecular) Biology, Part I: Information Retrieval Basics | Lectures/02.InformationRetrievalBiomed_PartI | Optional: Chapter 1 from Christopher D. Manning, Prabhakar Raghavan and Hinrich Schütze, Introduction to Information Retrieval, Cambridge University Press. 2008. | |
| Week 3 | Literature resources (cont’d) | |||
| Monday, 18/09 | Online Literature Resources for (Molecular) Biology, Part II: Selected Topics | Lectures/03.InformationRetrievalBiomed_EN-PartII | Online resources: PubMed; Venn diagram online server; SCOPUS; Google Scholar | |
| Wednesday, 20/09 | Online Literature Resources for (Molecular) Biology, Part III: Pubmed | Practicals/01..Practical-ILIOPOULOS-Pubmed_cyprus_2021_EN | Online resource: PubMed | |
| Thursday, 21/09 | Online Literature Resources for (Molecular) Biology, Part IV: Pubmed (cont’d) | See above | Online resource: PubMed | |
| Week 4 | Biological Databases | |||
| Monday, 25/09 | Part I: Brief Introduction on (Biological) Databases, Primary and Secondary Databases | Lectures/04.BiologicalDatabases-PartI | Online Resources: DOE JGI- Genomes Online Database, Nucleic Acids Research Annual database issue | |
| Wednesday, 27/09 | Tutorial/Q&A session | |||
| Thursday, 28/09 | Part II: A brief history, Features of Biological DBs, Important Providers | Lectures/05.BiologicalDatabases-PartII | Online resource: NAR Database Summary Paper Category List Major Providers: NCBI, EBI, SIB, NGDC-CNCB | |
| Week 5 | Biological Databases | |||
| Monday, 02/10 | Part III: Sequence Databases | Lectures/06.BiologicalDatabases-PartIII | Online Resources: GenBank, EMBL/ENA, DDBJ | |
| Wednesday, 04/10 | Tutorial/Q&A session | |||
| Thursday, 05/10 | Part IV: UniProt | Lectures/07.BiologicalDatabases-PartIV-UniProt | Online resource: UniProt | |
| Week 6 | Biological Databases | |||
| Monday, 09/10 | Hands on Practice on UniProt database | Self assessment quizes: Quiz 1; Quiz 2 | ||
| Wednesday, 11/10 | Midterm Exam (Fixed) | Material to be covered by Thursday, 05/10 will be examined (material covered in both lectures and practical sessions/tutorials) | ||
| Thursday, 12/10 | Part V: Structural Databases (PDB, SCOP, CATH, AlphaFoldDB) | Lectures/08.BiologicalDatabases-V-Structure_and_DBs | Understanding Bioinformatics p. 25-44. Online resources: RCSB PDB, SCOP, CATH, AlphaFoldDB |
|
| Week 7 | Biomolecular Sequence Analysis | |||
| Monday, 16/10 | ||||
| Wednesday, 18/10 | ||||
| Thursday, 19/10 | ||||
| Week 8 | Biomolecular Sequence Analysis | |||
| Monday, 23/10 | ||||
| Wednesday, 25/10 | ||||
| Thursday, 26/10 | ||||
| Week 9 | Biomolecular Sequence Analysis | |||
| Monday, 30/10 | ||||
| Wednesday, 01/11 | ||||
| Thursday, 02/11 | ||||
| Week 10 | Biomolecular Structure Analysis | |||
| Monday, 06/11 | ||||
| Wednesday, 08/11 | ||||
| Thursday, 09/11 | ||||
| Week 11 | Biomolecular Structure Analysis | |||
| Monday, 13/11 | ||||
| Wednesday, 15/11 | ||||
| Thursday, 16/11 | ||||
| Week 12 | Biomolecular Structure Analysis | |||
| Monday, 20/11 | ||||
| Wednesday, 22/11 | ||||
| Thursday, 23/11 | ||||
| Week 13 | An overview of Computational Systems Biology | |||
| Monday, 27/11 | ||||
| Wednesday, 29/11 | ||||
| Thursday, 30/11 | ||||
| Final Exam (Date to be confirmed) |
Bioinformatics Research Laboratory @UCY 2005-2023.