Genomics and bioinformatics

Schedule for the course Genomics and bioinformatics 3 p


IA = Room/Computer Lab  Ivar Arosenius, Medicinareg. 5
KN = Room/Computer Lab Karl Nordström, Medicinareg. 5 

A selection of links to other sources


11/3    IA 

	9.00-12.00 Lecture and practical : Introduction to information resources  UCSC lab(TS/MDL)
        For reference a selection of databases and resources are shown here.   

	13.00-17.00 Lecture and practical : Introduction to information resources  UCSC lab(TS/MDL)

12/3    IA	

	9.00-12.00  Lecture, introduction to information resources, cont. and practicals  NCBI lab (TS/MDL) and  Galaxy lab(TS/MDL)

	13.00-17.00  Lecture, introduction to information resources, cont. and practicals NCBI lab and  Galaxy lab (TS/MDL)

13/3    KN	

	9.00-12.00 Lecture and practical : Sequence alignment methods (TS/MDL).
	Download njplot here if it is not already installed on your computer. 
	
	13.00-17.00 Lecture and practical : Sequence alignment methods (TS/MDL)
	
14/3    KN	

	9.00-12.00 Lecture and practical : Applications of multiple alignments: Patterns/Profiles/Pfam  and assigning functions to genes and proteins (TS/MDL).

	13.00-17.00 Lecture and practical : Applications of multiple alignments: Patterns/Profiles/Pfam and assigning functions to genes and proteins (TS/MDL)

15/3    IA	

	09.00-12.00 Demonstration and practical: Introduction to Unix enviroment used in bioinformatics and NGS. 
                    Find answers to the exercises here.  
                    Book chapter being a short introduction to Unix will be handed out (and is not available from this page). 
                    Download the MobaXterm SSH client here (select portable edition) (TS).

	13.00-17.00 Lecture and NGS practical: Exome sequencing 
                    and short presentation of Genomics and Bioinformatics Core Facility resources (MDL). 
                    At 14.00: Visit at Genomics Core Facility to see NGS equipment.
                   

18/3 IA 09.00-12.00 Lecture and practical: Genomes - assembly, gene finding, annotation and gene ontology. (TS) 13.00-17.00 Lecture and NGS practical ChIP-Seq (MDL/ZS) 19/3 IA 09.00-12.00 Introduction and supervised practical: NGS - RNA-Seq (EL) 13.00-17.00 Practical NGS : Exome sequencing - variant visualization - IGV (MDL) 20/3 IA 09.00-12.00 Non-supervised practicals: Gene prediction, continued from 18/3 and Gene Ontology practical. If you cannot follow the links in the pdf document, here they are: http://www.cbs.dtu.dk/chipcourse/Exercises/Ex_GO/GOexercise11.php (CBS exercises) http://www.cbs.dtu.dk/chipcourse/Exercises/Ex_GO/InstallingCytoscape.php http://bio.biomedicine.gu.se/courses/vt13/ycc.c2.txt (the cluster 2 genes) http://www.psb.ugent.be/cbd/papers/BiNGO/Home.html (BiNGO home page) http://bio.biomedicine.gu.se/courses/vt13/batch.txt (list of genes for batch analysis) http://www.psb.ugent.be/cbd/papers/BiNGO/Tutorial.html (Another BiNGO tutorial) 21/3 IA 9.00-10.00 Lecture: The human microbiome (FB) 10.15-12.00 Lecture : Methods in phylogeny (TS). Baldauf tutorial 13.00-17.00 Molecular phylogeny practical (TS) 22/3 IA 09.00-12.00 Lectures : Molecular diagnostics, resistance (ML) Viral evolution and recombination (PN) 13.00-14.00 Lecture : Phylogeny, genotypes, hepatitis (HN) 14.00-15.00 Practical
Examination Teachers Resources - software etc