MARC: Developing Bioinformatics Programs: Agenda
A Two-Week Workshop at Pittsburgh Supercomputing Center
July 17-28, 2006
Sponsored by: National Institute of General Medical Services and Pittsburgh Supercomputing Center's National Resource for Biomedical Supercomputing
Monday, July 17, 2006
| Time | Topic | Instructor |
| 9:00 – 9:30 | Welcome and Introduction to the Pittsburgh Supercomputing Center | HBN RR |
| 9:30 – 10:30 | What is Bioinformatics | HBN |
| 10:30 – 10:45 | Break | |
| 10:45 – 11:45 | What is Bioinformatics (cont.) | HBN |
| 11:45 – 12:45 | Lunch | |
| 12:45 – 2:45 | Overview of Protein Biology | HBN |
| 2:45 – 3:00 | Break | |
| 3:00 – 6:00 | Introduction to PSC computer systems and laboratory | AJR |
Tuesday, July 18, 2006
| Time | Topic | Instructor |
| 9:00 – 10:15 | Introduction to Sequence Analysis Software | AJR |
| 10:15 – 10:30 | Break | |
| 10:30 – 11:30 | Introduction to Sequence Analysis Software (cont.) | AJR |
| 11:30 – 12:30 | Lunch | |
| 12:30 – 2:00 | Pairwise Alignment and Sequence Database Searching - Algorithms and Similarity Tables | RGM, HBN |
| 2:00 – 2:15 | Break | |
| 2:15 – 3:30 | Pairwise Alignment and Sequence Database Searching – Significance | HBN |
| 3:30 – 6:00 | Hands-on Computer Laboratory: | |
Wednesday, July 19, 2006
| Time | Topic | Instructor |
| 9:00 – 10:15 | Applied Database Searching | HBN |
| 10:15 – 10:30 | Break | |
| 10:30 – 12:30 | Track 1: Biology for nonbiologists | AJL |
| 10:30 – 12:30 | Track 2: Concepts of Programming | AJR |
| 12:30 – 1:30 | Lunch | |
| 1:30 – 3:00 | Global Multiple Sequence Alignment | HBN |
| 3:00 – 3:15 | Break | |
| 3:15 – 4:15 | Multiple Sequence Alignment Examples | HBN |
| 4:15 – 6:00 | Hands-on Computer Laboratory: | |
Thursday, July 20, 2006
| Time | Topic | Instructor |
| 9:00 – 10:15 | Local Multiple Sequence Alignment and Pattern Identification | RGM |
| 10:15 – 10:30 | Break | |
| 10:30 – 12:30 | Track 1: Biology for nonbiologists | AJL |
| 10:30 – 12:30 | Track 2: Introduction to Perl programming for biologists | SMP |
| 12:30 – 1:30 | Lunch | |
| 1:30 – 3:00 | Phylogenetic Analysis | RGM |
| 3:00 – 3:15 | Break | |
| 3:15 – 6:00 | Hands-on Computer Laboratory: | |
Friday, July 21, 2006
| Time | Topic | Instructor |
| 9:00 – 10:15 | Review of Sequence Analysis | |
| 10:15 – 10:30 | Break | |
| 10:30 – 12:30 | Track1: Biology for non-biologists | AJL |
| 10:30 – 12:30 | Track2: Introduction to Perl programming for biologists | SMP |
| 12:30 – 1:30 | Lunch | |
| 1:30 – 3:00 | Alignments and Truth – a statistical view of sequence alignment | HBN |
| 3:00 – 3:15 | Break | |
| 3:15 – 6:00 | Hands-on Computer Laboratory: | |
Saturday, July 22, 2006
| Time | |
| 11:00 – 1:00 | Picnic at Marriot Residence Inn – Oakland |
Monday, July 24, 2006
| Time | Topic | Instructor |
| 9:00 – 9:30 | Curriculum in Bioinformatics for Biology Students | RGM |
| 9:30 – 10:00 | Curriculum in Bioinformatics for Computer Science Students | JS |
| 10:00 – 10:30 | Curriculum in Bioinformatics for Computer Science Students | BV |
| 10:30 – 10:45 | Break | |
| 10:45 – 11:15 | Curriculum in Bioinformatics for Mathematics Students | AT |
| 11:15 – 11:45 | Curriculum in Bioinformatics for Undergraduate Students | SB |
| 11:45 – 12:15 | Evaluation of Bioinformatics Courses | JT |
| 12:30 – 1:30 | Lunch | |
| 1:30 – 2:45 | Problems in Bioinformatics | DD |
| 2:45 – 3:00 | Break | |
| 3:00 – 4:15 | NOTUNG – Analysis of gene duplication events | BV |
| 4:15 – 6:00 | Computer Laboratory - NOTUNG | |
Tuesday, July 25, 2006
| Time | Topic | Instructor |
| 9:00 – 10:15 | Molecular Graphics | VMD |
| 10:15 - 10:30 | Break | |
| 10:30 – 12:00 | Comparative Protein Modeling and Tutorial Overview | |
| 12:00 – 1:00 | Lunch | |
| 1:00 – 2:00 | Case Study – a student project | JS |
| 2:00 – 3:30 | GeneDoc Demonstration – Visualizing and refining multiple sequence alignments | HBN |
| 3:30 – 3:45 | Break | |
| 3:45 – 6:00 | Hands-on Computer Laboratory: | |
Wednesday, July 26, 2006
| Time | Topic | Instructor |
| 9:00 – 11:00 | Analysis of Isozyme Specificity | HBN |
| 11:00 - 11:15 | Break | |
| 11:15 – 12:30 | Motifs – What are they and why are they important | RGM |
| 12:30 – 1:30 | Lunch | |
| 1:30 – 3:00 | Genomics – Sequencing and Annotating Genomes | HBN |
| 3:00 – 3:15 | Break | |
| 3:15 – 6:00 | Hands-on Computer Laboratory | |
Thursday, July 27, 2006
| Time | Topic | Instructor |
| 9:00 – 10:15 | Bioinformatics for Cell Biology | HBN |
| 10:15 – 10:30 | Break | |
| 10:30 – 12:30 | Cancer Proteomics | AW |
| 12:30 – 1:30 | Lunch | |
| 1:30 – 2:15 | Protein Side Chain Packing using Voronoi Polygons | DN |
| 2:15 – 3:30 | Volume Browser – Visualizing data in four dimensions | AW |
| 3:30 – 3:45 | Break | |
| 3:45 – 4:00 | Bioengineering and Bioinformatics Summer Institute | JS |
| 4:00 – 4:45 | Modeling Neuro-Muscular Junctions | JS |
Friday, July 28, 2006
| Time | Topic | Instructor |
| 9:00 – 10:00 | Supporting Local Bioinformatics Efforts | AJR |
| 10:00 – 10:30 | Applying for Computer Time at the PSC | KH |
| 10:30 – 10:45 | Break | |
| 10:45 – 12:30 | Evaluation and Discussion | HBN |
| 12:30 – 1:30 | Pizza Lunch with the PSC Staff | |
| 1:30 – 5:00 | Leave for Airport | |
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