Syllabus and Schedule for Fall 2017
GCBA815: Tools and Algorithms in Bioinformatics
Week | Date | Topic | Slides | Reading Material |
1 | 8/25/17 | Introduction to bioinformatics | Slides | |
2 | 9/1/17 | Data formats, Unix tools | Slides | Unix tutorial |
3 | 9/8/17 | BLAST algorithm, theory and practice | Slides | Blast explained Submatrices Youtube video |
4 | 9/15/17 | Profiles, HMMs, PHI/PSI/RPS-Blast | Slides | |
5 | 9/22/17 | CLC Genomics Workbench | Slides | CLC Genomics Workbench user's guide |
6 | 9/29/17 | (Midterm1- In-class exam) UCSC Genome Browser / IGV |
Slides | |
7 | 10/6/17 | Microarray data analysis: ExAtlas tools | Slides | Publication ExAtlas website |
8 | 10/13/17 | NextGen - Exome-RNAseq analysis | Slides | |
9 | 10/20/17 | Functional annotation of genes and gene products (DAVID, GSEA) | Slides | GSEA tutorial |
10 | 10/27/17 | Circos diagrams/Cytoscape | Slides | |
11 | 11/3/17 | Pathway analysis-IPA (Midterm2-Project due) |
Slides | Data set |
12 | 11/10/17 | TCGA data download and analysis | Slides | |
13 | 11/17/17 | Metagenomics/MG-RAST | Slides | Reading material Metadata STAMP Metadata reads 1 reads 2 profiles |
14 | 11/24/17 | Thanksgiving Holiday | ||
15 | 12/1/17 | VectorNTI Data analysis suite | Slides | VectorNTI instructions VectorNTI tutorial Final project Final project data License |
16 | 12/8/17 | PDB- Protein Structure Data Analysis (Final project due on 12/10/17) |
Slides | |
17 | 12/15/17 | No class – Grades Posted |
We thankfully acknowledge the following sources on the internet, from where some of the reading materials were collected.
- PUBMED
- YouTube
- https://www.ndsu.edu/pubweb/~mcclean/