Systems Biology: The Annual BioQUEST Summer Workshop 2004

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Participant Projects	Resources	References	Feedback Form

	»OnLine Project Submission »Upload Project Files »Edit Project Form Projects Submitted by Workshop Participants Dinoflagellates: Acquisitions and Mergers Using Microarray Technology to Explore Problems in Systems Biology. Influenza The Phylogenetic Tree Constructor GenMAPP and MAPPFinder for Systems Biology Education Bridges to Structure New Zealand Cyatheaceae Phylogenies? Systems Approaches to Adopting, Teaching and Learning Models Simulating Gene Expression using Netlogo Prion biology problem space: Mad cows, itchy sheep and protein structure Rice Phylogeny Revisited Campus Evolution
	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) and