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PSC Bioinformatics Summer Institute Workshop
- Pittsburgh Supercomputing Center, PA
- TBA
- Workshop web site
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
- De Novo Genome Assembly
- The R System for Statistical Analysis
Week 2
- Functional Annotation for Assembled Genomes
- Predicting Genes, Identifying Functions
- Mapping Genome Assemblies
- RNAseq: De Novo Assembly of RNA Data
- Identifying Single-nucleotide Polymorphisms (a.k.a. SNPs) and Other Variants
- RNAseq: De Novo Functional Annotation and Other Post-Assembly Analyses
- Gene Annotation
- Ribosomal Profiling: Genome-wide Measurements of mRNA Translation Rates
Faculty Training Workshops in Genomics
A collection of training workshops in genomics and bioinformatics suggested by members of the Genomics Education Alliance.
Wilson Leung
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