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
7 10/6/17 Microarray data analysis: ExAtlas tools Slides Publication    ExAtlas website
8 10/13/17 NextGen - Exome-RNAseq analysis Slides

Test data   RNA-seq Best Practices

RNA-seq statistics

9 10/20/17 Functional annotation of genes and gene products (DAVID, GSEA) Slides GSEA tutorial 
10 10/27/17 Circos diagrams/Cytoscape Slides

Midterm exam      Midterm data

Cytoscape           ClicOFS

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)
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.