MARC: Developing Bioinformatics Programs: Topics
A Two-Week Workshop at Pittsburgh Supercomputing Center
July 17-28, 2006
Registration Deadline: May 31, 2006
Sponsored by: National Institute of General Medical Services and Pittsburgh Supercomputing Center's National Resource for Biomedical Supercomputing
- Internet Resources and Remote Computing Facilities
The advent of the Internet and the World Wide Web has substantially increased the availability of information and computational resources available to experimental biologists. This lecture will describe a number of on-line resources available, including resources and services available at the Pittsburgh Supercomputing Center. Also discussed will be the use of the GCG Wusconsin software and how to locate and retrieving specified sequences from a sequence databases. - Introduction to PERL for non-programmers
As a proliferation of WWW based bioinformatics resources becomes availiable, the need to convert program output or other data into an appropriate format is an important skill that the bioinformaticist needs to acquire. The PERL programming language will be introduced to the participants to help them make the file conversion process easier. - Basic Cellular and Molecular Biology for Non-biologists
An introduction/review of relevant biological topics will be provided. - Biological Statistical and Mathematical Foundations of Bioinformatics
An introduction/review of relevant bioinformatics topics including what is a random sequence and commonly used statistical significance estimates based on random sequences. - Pairwise Alignments and Database Searches
This lecture presents both the mathematical and biological foundations of sequence comparison. That is, the lecture will describe in detail the various sequence alignment algorithms including the approximations made in the heuristics (e.g., FASTA and BLAST) to decrease computational time as opposed to searches with a rigorous algorithms (e.g., Needleman-Wunsch, Smith-Waterman). The lecture will also describe the underlying mathematical and biological bases for the similarity matrices in current use and how these tables should be properly used. The intended goal of this lecture is to provide a researcher with the necessary background information about the search protocols so that they are assured of making good parameter and algorithmic choices in their database searches and understand the shortcomings of naively using a database searching tool. - Multiple Sequence Alignments
This lecture covers aligning several sequences in their entirety (global alignments) and how global alignments are related to underlying biological phylogenies. During the lecture, we will describe the mathematical and biological basis for each of the multiple alignment programs and demonstrate the inherent weaknesses in each approach (e.g., PileUp, ClustalW, MSA or SAGA). - Conserved Patterns and Motifs
Participants will be introduced to motifs and patterns and the various formats in which they are commonly represented including Consensus residues, regular expressions, hidden Markov models and weight matrices. Discusses methods available to identify short, well conserved local patterns, such as promoter sequences or catalytic sites. Also discusses profile analysis and expectation maximization techniques. - Overview of structural Biology
Participants will be introduced to structural biology concepts including molecular mechanics, molecular dynamics, and homology modeling. - Inverted Structure Prediction
The alignment of a primary structure (sequence) with known three dimensional structures can provide the basis for homology modeling. This lecture presents the theory behind this technique along with practical examples. - Visualization of Macromolecules and Sequence Alignments
Combining structural, biochemical, and genetic information is difficult and laborious when the information is presented separately as text and tables. This lecture demonstrates combining diverse information into graphic images and animation. - Sustaining and Supporting Bioinformatics Training
Discusses maintaining and supporting bioinformatics training and tools on local campuses; how to incorporate bioinformatics into research programs; and how to effectively describing bioinformatics components in funding proposals.
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