BEDROCK Project
BioQUEST Curriculum Consortium
                 EOT-PACI
LifeLines OnLine
National Science Foundation
Howard Hughes Medical Institute

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Projects Submitted by Workshop Participants

    1. Dinoflagellates: Acquisitions and Mergers
    2. Using Microarray Technology to Explore Problems in Systems Biology.
    3. Influenza
    4. The Phylogenetic Tree Constructor
    5. GenMAPP and MAPPFinder for Systems Biology Education
    6. Bridges to Structure
    7. New Zealand Cyatheaceae Phylogenies?
    8. Systems Approaches to Adopting, Teaching and Learning Models
    9. Simulating Gene Expression using Netlogo
    10. Prion biology problem space: Mad cows, itchy sheep and protein structure
    11. Rice Phylogeny Revisited
    12. Campus Evolution
    13.  

 
 


Resources & Tools

Fass Presentation Materials
Marion Fass, Beloit College
New Perspectives on Emerging Diseases, Biocomplexity and Teaching for Context
     4 MB Powerpoint
The Complexity of HIV/AIDS- Where Politics Meets Biology
     1 MB Powerpoint

Ovcharenko Presentation Materials
Ivan Ovcharenko, Lawrence Livermore National Laboratory
Comparative Genomics, large scale alignment and comparison tools
       Powerpoint 1 (6.1 MB)    Powerpoint 2 (4 MB)

Sayers Presentation Materials
Eric Sayers, NCBI / NLM / NIH
Exploring 3D Molecular Structures Using NCBI Tools: A Field Guide
      8 MB  Powerpoint

Weisstein Presentation Materials
Anton Weisstein, BioQUEST Curriculum Consortium
Phylogenetic.ppt

Biology Workbench
http://workbench.sdsc.edu       Getting Started with the Biology Workbench (PDF)
The Biology WorkBench is a web-based resource for analyzing and visualizing molecular data developed at NCSA (the National Center for Supercomputing Applications). Undergoing continued development at the San Diego Supercomputer Center, the innovative Biology WorkBench integrates access to many tools within a simple graphical user interfacse.Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems.

Biology Student Workbench
http://peptide.ncsa.uiuc.edu/

The Biology Student Workbench consists of curricular materials centered around molecular biological investigations, links to educational, scientific, computational, and informational resources, and communication tools to bind together a contributing community of educators. It is designed to give a transparent introduction to the use of the Biology Workbench for learning and teaching biology at all levels.

SIB Homepage (Student Interface to the Biology Workbench) and other Bioinformatics information
http://deltas.animal.uiuc.edu/sibdoc/index.html

National Center for Biotechnology Information (NCBI)
http://www.ncbi.nlm.nih.gov
Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease.

NCBI Education
http://www.ncbi.nlm.nih.gov/Education/

Cn3D -- a 3-dimensional viewing app for your browser (help menu is extensive and useful)
http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml

PDF of the NCBI Handbook chapter on structure resources
http://www.ncbi.nlm.nih.gov/books/bookres.fcgi/handbook/ch3d1.pdf

Additional exercises and resources (look under Course Materials on the left side bar)
http://www.ncbi.nlm.nih.gov/Class/Structure/course.html

John's paper for javaBenzer
http://www.beloit.edu/%7Ebiology/benzer.html

Institute for Systems Biology
http://www.systemsbiology.org/

Systems Biology Workbench
http://sbw.sourceforge.net/

Systems Biology Software
http://www.cds.caltech.edu/~hsauro/index.htm

Jarnac Metabolic Simulation Package
http://www.cds.caltech.edu/~hsauro/Jarnac.htm


JDesigner
http://www.cds.caltech.edu/~hsauro/JDesigner.htm

GenMAPP
http://www.genmapp.org/

 

 
 

References

Biosphere 2: Research Past and Present. Edited by Marion, B. D. V. and Odum H. T. Reprinted from Ecological Engineering Special Issue, Vol. 13. Elsevier Science B.V. SCI, Ireland.

Odum, H.T., and Odum E. C.. 2000. Modeling for all scales. Academic Press, San Diego, CA.

Scientific American Frontiers Explores Biosphere 2, hosted by Alan Alda. Excerpt from Scientific American Frontiers, The Wild West, broadcast on PBS-TV.
 
 

Sponsored by a grant from the National Science Foundation (DUE/CCLI-ND)
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