CBSU Bioinformatics Workshop

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:

Prof. Ron Elber's group, Computer Science Department, Cornell University (RE)
USDA-ARS Center for Agricultural Bioinformatics (USDA)
Prof. Harold Scheraga's group, Chemistry Department, Cornell University (HAS)
BioResource Center, Cornell University (BRC)

Lecture Slides

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)