CBSU Bioinformatics Workshop
August 8 – 13 2002

The Workshop was hosted by the Computational Biology Service Unit (CBSU) from the Cornell Theory Center in collaboration with:


Lecture Slides 

© Cornell Theory Center. All rights reserved.


Module 1: Introduction to Some Bioinformatics Tools
Tools for sequence data mining: BLAST (part 1) Dave Schneider (USDA)
Tools for sequence data mining: BLAST (part 2) Qi Sun (CBSU)
Tools for constructing genome contigs: an introduction to Phred/Phrap/Consed Jaroslaw Pillardy (CBSU)
Tools for genome sequence annotation: an introduction to GenScan and Glimmer Qi Sun (CBSU)
Tools for sequence data mining: HMMER (part 1) Ron Elber (RE)
Tools for sequence data mining: HMMER (part 2) Qi Sun (CBSU)
Software developed by CBSU (RepeatAnalyzer , Parallel Blast) Jaroslaw Pillardy (CBSU)
Qi Sun (CBSU)
Module 2: Genomics Databases and Data Management Techniques
Genomic Databases Qi Sun (CBSU)
Desktop molecular biology software available at Cornell James VanEe (BRC)
Crystal structure prediction using CRYSTALG program (part 1) Yelena Arnautova (HAS)
Crystal structure prediction using CRYSTALG program (part 2) Yelena Arnautova (HAS)
Module 3: Protein Structure and Function Prediction
Introduction to molecular graphics with MolMol and RasMol

Marko Nanias (HAS)
Maurizio Chinchio (HAS)

Protein structure prediction - an introduction Ron Elber (RE)
Homology modeling (MODELLER) (part 1) Jaroslaw Pillardy (CBSU)
Homology modeling (MODELLER) (part 2) Daniel Ripoll (CBSU)
Threading (LOOPP) (part 1) Tami Galor (RE)
Threading (LOOPP) (part 2) Octavian Teodorescu (RE)
Ab-initio protein structure prediction (UNRES) (part 1) Jaroslaw Pillardy (CBSU)
Ab-initio protein structure prediction (UNRES) (part 2) Cezary Czaplewski (HAS)
Using publicly available protein sequence/structure tools like secondary structure prediction, fold analysis etc. (part 1) Jaroslaw Pillardy (CBSU)
Simple modeling and analysis of proteins using ECEPPAK (ECEPP) Daniel Ripoll (CBSU)
Molecular dynamics simulations for proteins with MOIL (part 1) Ron Elber (RE)
Molecular dynamics simulations for proteins with MOIL (part 2) Alfredo Cardenas (RE)
Analyzing protein conformations and conformational ensembles (including NMR data) with ANALYZE Cezary Czaplewski (HAS)