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Bioinformatics Problem
Solving Spaces

HIV

West Nile Virus

Prions

Citrus Canker

Presenter's Materials

Diane Baxter's presentation (13MB)

Stephen's introduction to structural visualization for MACs (17MB)

Stephen's introduction to structural visualization for PCs (15MB)

 

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If you have question email to kumezaki@sbb.uvm.edu

Projects Submitted by Workshop Participants

HTML-supplemented Project Sample
Basic Sample

    1. Molecular Evolution of Conserved Protein Domains
    2. Using BLAST to investigate genes expressed during loblolly pine embryogenesis
    3. Avian Influenza
    4. Dolphin Phylogeny
    5. HIV Envelope Mutations and Onset of AIDS
    6. HIV Strain Variation in Africa
    7. Insulin binding to the receptor
    8. Acetylcholine Receptor Binding Toxins
    9. Molecule Informatics Portfolio
    10. Seeing the Trees Through the Forest : Arthropod phylogeny based on morphology and molecular data
    11. Anthrax toxin: Examining the relationship between structure and function
    12. Escherichia coli O157:H7 Outbreak from Fresh Spinach
    13. Protein Chronometers
    14.  


Tools

National Microbial Pathogen Data Resource
http://www.nmpdr.org/
NMPDR is an environment for the comparative functional analysis of genomes and biological subsystems, with an emphasis on pathogenic species of Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio.

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

Bioinformatics Education section of the Open Directory project.
http://dmoz.org/Science/Biology/Bioinformatics/Education/
The Open Directory Project is the largest, most comprehensive human-edited directory of the Web. It is constructed and maintained by a vast, global community of volunteer editors. Instead of fighting the explosive growth of the Internet, the Open Directory provides the means for the Internet to organize itself. As the Internet
grows, so do the number of net-citizens. These citizens can each organize a small portion of the web and present it back to the rest of the population, culling out the bad and useless and keeping only the best content.

Case It!
http://www.uwrf.edu/caseit/caseit.html
Case It! is a National Science Foundation-sponsored project initiated by members of the BioQUEST Curriculum Consortium and based at the University of Wisconsin-River Falls and Michigan State University. The goal is to provide a framework for collaborative case-based learning in molecular biology using interactive computer simulations, and to have high school and university students from around the world participate via Internet conferencing.

The ConSurf Server
http://consurf.tau.ac.il
Server for identification of functional regions in proteins.

GeneDoc
http://www.psc.edu/biomed/genedoc

GeneDoc is a full featured multimple sequence alignment editor and shading utility.

The Inquiry Page
http://inquiry.uiuc.edu/
This is a dynamic virtual community where inquiry-based education can be discussed, resources and experiences shared, and innovative approaches explored in a collaborative environment. You can search a growing database of inquiry units, and you can also build your own inquiry units. You can see pictures of inquiry-based activities and learn more about some of our partners who use inquiry methods. Learn how to assess and evaluate inquiry-based education or look for more inquiry resources to support what you're doing.

John C. Herron's Evolution Simulation Software for Evolutionary Analysis
http://faculty.washington.edu/~herronjc/SoftwareFolder/software.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/

OMIM™ Online Mendelian Inheritance in Man
http://www.ncbi.nlm.nih.gov/omim/
This database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information. The database contains textual information, pictures, and reference information. It also contains copious links to NCBI's Entrez database of MEDLINE articles and sequence information. The OMIM Morbid Map, a catalog of genetic diseases and their cytogenetic map locations arranged alphabetically by disease, is now available.

Protein Data Bank
http://www.rcsb.org/pdb/
The Protein Data Bank is a worldwide archive of three dimensional structural data of biological macromolecules. The PDB collects, validates, and distributes as widely as possible the experimental models of proteins. The management of the PDB is the responsibility of the Research Collaboratory for Structural Bioinformatics (RCSB). The vision of the RCSB is to create a resource based on the most modern technology that facilitates the use and analysis of structural data and thus creates an enabling resource for biological research. The RCSB PDB is supported by funds from the National Science Foundation, the Department of Energy, and the National Institutes of Health.

Protein Explorer
http://molvis.sdsc.edu/protexpl/frntdoor.htm
(PE) version 2.0 enables visualization of macromolecular 3D structure with exceptional ease of use. Visual analysis of proteins, nucleic acids, and ligand interactions can be done largely from menus, buttons, and forms, with context-sensitive help and color keys displayed automatically. PE employs the Chime plugin that is derived from RasMol, and PE understands all RasMol commands. However, PE enables visual analysis to considerable depth without learning a single RasMol-style command, and it is much more powerful than RasMol. PE enables easy selection of portions of a molecule, to apply different rendering or coloring schemes, and to hide selected moieties. In addition it has one-click routines to map sequence to structure, show contact surfaces (overview of noncovalent bonds to any moiety), solvent-accessible surfaces, cation-pi interactions, and salt bridges. Advanced routines simplify finding noncovalent bonds, and coloring a protein by conservation/mutation from a multiple protein sequence alignment. Websites can include hyperlinks to Protein Explorer that prespecify molecule(s). Adopted by the Protein Data Bank as a 3D structure viewer. Authored by Eric Martz, using MDL Information Systems' Chemscape Chime freeware. PE is freeware for Windows or Macintosh.

SeqPup
http://iubio.bio.indiana.edu/soft/molbio/seqpup/About-seqpup.text
SeqPup is a biological sequence editor and analysis program. It includes links to network services and external analysis programs. It is usable on common computer systems, including Macintosh, MS-Windows and X-Windows.

SWISS-PROT
http://www.expasy.ch/sprot/
SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases

Tree Finder
http://www.treefinder.de/
TREEFINDER computes phylogenetic trees from nucleotide sequences. Using the widely accepted Maximum Likelihood method, it supports six popular models of sequence evolution up to the general time reversible model with Gamma distributed rates among sites. All model parameters including the rate heterogeneity can be estimated from the data. A genetic tree search algorithm explores tree space for the likeliest trees, having a good chance to not being trapped in local optima of the likelihood surface. Its exhaustiveness is accomodable to the users patience.


Educational Resources

Phylogenetics 1.0
phylogenetics_1.0.ppt
A presentation by Tony Weisstein.

Transferrins Page
http://www.chatham.edu/undergraduate/bio/lambert/transferrin/transferrins.htm
A Project BEDROCK exploration site managed by Lisa Lambert.

Free Human Genome Project Booklet
The Human Genome Project (HGP) has created a free, downloadable publication covering what is known so far about this subject. The publication is available at http://www.ornl.gov

Genetic Science Learning Center

http://gslc.genetics.utah.edu/

Transposon Bank
http://ctcworldsrv1.tc.cornell.edu/people/cmaher/bioquest/index.html
This site assists individuals in learning about transposable elements (TEs) and their effects on everyday lives. It features examples from the worlds of garden peas, the critically important food crop rice, and the interrelationships between a commercial crop, cotton, its pest, and current management strategies.

Bioweb - Scott Cooper
http://bioweb.uwlax.edu/GenWeb/Molecular/molecular.htm
BioWeb is a collaborative website produced by faculty members from 14 different University of Wisconsin System universities and centers. By pooling our resources we hope to improve the quality of biology education at all of the UW-System institutions.

Bioinformatics Module
http://bioquest.org/bioinformatics/module/
A number of linked investigations and tutorials that are in the developmental phase by the Biology Student WorkBench project collaborators.

Molecular Evolution - David R. Nelson
http://drnelson.utmem.edu/evolution.html
Lecture on Molecular Evolution I

David Sheppard's materials
http://www.udel.edu/Biology/sheppard/bosbu/BostonBioinformatics.html
Lessons designed for use with SeqWeb, a sequence analysis program licensed for use by GCG. Files are in PDF format and can be printed to any printer using Adobe Acrobat Reader.

Looking into Glycosidases: A Bioinformatics Resource for Biology Students
Editable Word Doc (2.3 MB)     PDF Version (1 MB)
Utilizing strategic molecular investigations, bioinformatics, and visualization tools in undergraduate biology is supported here by a number of scenarios for investigation. Several introductory molecular problem spaces are featured with appendices on the glycosidases, resources, internet tools, and selected literature. NOTE: None of these scenarios comes with a solution. We generated many supportable hypotheses while working on the problems and hope you will enjoy similar success! Written by Ethel Stanley and Keith Stanley.

The EdGrid Project
http://bioquest.org/bioinformatics/EdGrid/
The Educational Grid (EdGrid) Biology Student Workbench (BSW) project is a growing collection of enhancements to the Biology Workbench including tutorials and inquiry-based materials, all of which help students and teachers conduct meaningful investigations in molecular biology. The project specifically addresses a pre-service teacher audience, and it supports the use of the inquiry-based learning and teaching approach to science education.

Action Bioscience
http://www.actionbioscience.org/
ActionBioscience.org is a non-commercial, educational web site created to promote bioscience literacy. the web site provides articles by scientists, science educators, and science students on issues related to seven bioscience challenges: environment, biodiversity, genomics, biotechnology, evolution, new frontiers in science, and bioscience education. In addition, the web site provides educators with original lessons and resources to enhance bioscience teaching.

USGS
http://fresc.usgs.gov/index.html
The USGS Forest and Rangeland Ecosystem Science Center provides research and technical assistance in support of sound management and conservation of biological systems in the western United States.

Other Resources

Highwire Press - Stanford
http://highwire.stanford.edu/
Stanford University Libraries' HighWire Press began in early 1995 with the online production of the weekly Journal of Biological Chemistry (JBC), the most highly cited (and second largest) peer-reviewed journal. As of October 2002, HighWire now produces 342 sites online.

Net Center for Plant Genomics
http://plantgenome.sdsc.edu/
A collaborative effort between the National Science Foundation (NSF), the San Diego Supercomputer Center, and the Plant Genome Research Program has resulted in this online resource for sharing plant genome information. Users can perform a more general Web literature search, or search a group of databases for nucleotide sequences. The site provides additional information such as other related NSF projects and job openings in plant genomics. The entire site is directed toward a specific and advanced audience. Annotation from the Scout Project .

Molecular Information Agent
http://mia.sdsc.edu/
This Web search tool from the San Diego Supercomputer Center allows users to "search the internet to find all current information for a molecule of interest." Molecular Information Agent (MIA) thoroughly searches several online biological databases and removes invalid links from the search results. In order to complete a search, users must complete a brief registration. Because the search function takes a few minutes to generate results, the registration allows users to choose to either save the query and return later to view the results, or have the results emailed to them. This site may prove to be a time saving tool for those users who desire up-to-date information on molecules of interest. Annotation from the Scout Project.


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