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
Unix Command Line Programs | TCoffee |
GeneDoc | NCBI Entreez |
Notung | Velvet (NGS) |
Galaxy | Trinity (NGS) |
SQL Database Language using SQLite | BowTie and BowTie2 |
Python Language Scripting and the BioPython Library | Trinotate |
The R Statistical Analysis System | SAM Tools |
BLAST | GATK |
MEME | edgeR |
Muscle | Phylip |
Clustal | Databases incuding PubMed, GeneBank, UniProt, PFAM and others |