The Lycoming College 
Macromolecular Modeling and Bioinformatics Page

special thanks to the following software suppliers:
DNASTAR for Lasergene

MDL Information Systems for Chime
Roger A. Sayles for RasMol
Eric Martz for RasMol Associated Resources and Protein Explorer


Molecular Biology and Bioinformatics Projects for "Core" Courses

The Bioinformatics exercises below have been designed and adapted over the years to use a variety of software packages and online tools. We are currently using DNASTAR's Lasergene package, which they provide free for educational use. We have found this package to be comprehensive, easy to use, and certainly the best for our purposes. Thanks DNASTAR!
3-D protein structure tutorials require the Chime plug-in.

 

Bio 110 - Introduction to Biology - Mr. Green Genes 
Bio 222W - Genetics - Cloning the Human Clotting Factor IX Gene 
Bio 321 - Microbiology - rRNA sequencing to identify an unknown microbe

Molecular Biology and Bioinformatics Project Assessment Survey - completed April/May, 2001. 
 

This project has been/will be presented at the following conferences/workshops

 

The Advanced Assignment: Integrated Informatics Projcet

The mission: to study a single protein from several perspectives and integrate the information into a comprehensive description of its structure, function, expression pattern, processing, biological significance, phylogenetic distribution, and evolutionary conservation.

Student-made Integrated Informatics Projects (99-06) and Protein Structure/Function Projects (98-99) 

 

Bio437 - Molecular Biology - Spring 2004

Bio/Chem 444 - Biochemistry - Fall 2003

Bio/Chem 444 - Biochemistry - Fall 2002

 

Bio 437 - Molecular Biology - Spring 2002

 

Bio 435 - Cell Biology - Fall, 2001

 

 

  Independent Study Project by Kevin Frederick and Mitchell Marzo, Spring 2001

Bio437 - Molecular Biology - Spring 2001

Bio/Chem 444 - Biochemistry  - Spring, 2000

Bio 435 - Cell Biology - Fall, 1999

 Bio/Chem 444 - Biochemistry - May Term, 1999

Bio 437 - Molecular Biology  - Spring, 1999

Bio 435 - Cell Biology - Fall, 1998

 

A similar project at Davidson College - A. Malcolm Campbell - see also Genome Consortium for Active Teaching (GCAT)
Bioinformatics project list- R. Croy, Durham Univ. (UK)
HotMolecBase - a database of 'hot molecules' - from the Weizmann Institute of Science

 

Bioinformatics/Molecular Modeling Links

  • The National Center for Biotechnology Information
  • The RCSB Protein Data Bank
  • EBI - the European Bioinformatics Institute
  • DDBJ homepage - DNA Data Bank of Japan
  • Ensembl Genome Server
  • The Institute for Genomic Research (TIGR)
  • Center for Biological Modeling
  • IMB Jena Image Library of Biological Macromolecules
  • Weizmann Institute of Science Bioinformatics and Biological Computing
  • RasMol Home Page - Eric Martz, U. Mass.
  • The Online Macromolecular Museum - D. Marcey, California Lutheran University
  • Gerstein Group -- Yale Bioinformatics
  • Molecular Models for Biochemistry -W. McClure, Carnegie Mellon
  • Computer Applications in Biotechnology -C. Klevickis, James Madison Univ.
  • Medical Biochemistry at the University of Kansas Medical Center
  • Biochemistry 218 Computational Molecular Biology - D. Brutlag, Stanford U
  • BMMB 597C Computers for Biochemists & Molecular Biologists - B. Tracy Nixon, Penn State University
  • Bioc462 - Molecular Graphics Using Chime - University of Arizona
  • Biochemistry in 3D - Lehninger Principles of Biochemistry 
  • Bioinformatics Course Information Page - R. Croy, Durham Univ. (UK)
  • Biomolecular Computing Resource (BimCore) home - Emory University
  • 1998 Molecular Graphics Art Show

  • Bioinformatics/Genomics Courses for Undergraduates

    Bioinformatics/Genomics Graduate Programs (email your URL to newman@lycoming.edu to be listed)


    This page was created or last modified on 11/17/05 by Jeff Newman

    Assistant Professor Web page: http://www.lycoming.edu/~newman
    Department of Biology Email: newman@lycoming.edu
    Lycoming College Phone: 570-321-4386
    Williamsport PA 17701 Fax: 570-321-4073

    1998-2005  Jeffrey D. Newman