PSC Bioinformatics Summer Institute Workshop (NIH MARC)

Minority Access to Research Careers

PSC Bioinformatics Summer Institute Workshop

This two-week intensive training workshop provides a robust background in bioinformatics suitable for teaching and research. Every day participants complete hands-on exercises to practice the concepts learned during lectures using various of the Pittsburgh Supercomputing Center’s massively parallel computers and various software tools such as the Galaxy web-based biomedical research tool.

A Typical Summer Institute Schedule

Week 1

• Introduction to the Computing Environments at the Pittsburgh Supercomputing Center
• Bioinformatics Databases
• Models and Significance in Searching Bioinformatics Databases
• Sequence Alignment Algorithms (NW, SW, Fasta, BLAST, BW+FM, “Seeded” SW)
• Multiple Sequence Alignment & Mapping Realignment
• Computational Tools: Analyzing Data Using Relational Databases & SQL
• Next Generation Sequencing (NGS) Technologies
• Pattern Identification
• Preparing NGS Datasets for Assembly/Mapping
• Phylogenetics and Reconciliation with Notung
• DeNovo Genome Assembly
• The R System for Statistical Analysis

Week 2

Dr. Bienvenido Velez: SQL as a Tool for BioInformatics Data Analysis

• Functional Annotation for Assembled Genomes
• Predicting Genes, Identifying Functions
• Mapping Genome Assemblies
• RNAseq: DeNovo Assembly of RNA Data
• Identifying Single-nucleotide Plymorphisms (a.k.a. SNPs) and Other Variants
• RNAseq: DeNovo Functional Annotation and Other Post-Assembly Analyses
• Gene Annotation
• Ribosomal Profiling: Genome-wide Measurements of mRNA Translation Rates

Some of the Computing Tools Used at the Institute