BEDROCK Project Home

Workshop Announcement
Session 27
Session 36


Bioinformatics Problem Solving Spaces

West Nile Virus

Tracking the West Nile Virus (pdf)
Finding the likely origin of the first West Nile Virus in the US.

Centers for Disease Control and Prevention: West Nile Virus information

Campbell GL, Marfin AM, Lanciotti RS, and Gubler DG. West Nile virus. Lancet Infectious Diseases. 2002;2:519-29.


Exploring HIV change within and between patients -- an HIV laboratory

Cells Alive HIV Tutorial

Centers for Disease Control and Prevention: Divisions of HIV/AIDS Prevention information

National Institute of Allergy and Infectious Diseases: HIV Life Cycle

HIV biology

Los Alamos HIV Databases



West Nile Virus sequence data
Download txt file here.
These partial nucleic acid sequences code for a glycoprotein found in the West Nile virus. Each strain is identified by the country and year it was isolated.

HIV Data files

1) "Subject_X" files contain all sequences from each individual subject. For example, "Subject_9" contains data from Subject 9 at all visits for which we have data.

2)"Visit_X" files contain all sequences from each specific visit. For example, "Visit_3" contains data from Visit 3 for all subjects for whom we have such data. As a consequence, early visits contain data from lots of subjects, while later visits contain data from only a few (since many were lost to follow-up).

3) "First/Midpoint/Last_visit" files contain sequences from each subject's first, middle, and last visits, respectively. Thus, " First_visit" is the same as "Visit_1", because we have data from visit 1 for all subjects. By contrast, "Last_visit" includes data from Subject 1 Visit 5, Subject 2 Visit 4, Subject 3 Visit 6, etc. In each case, that's the last visit we have for that subject.

First_visit.txt Subject_1.txt
Last_visit.txt Subject_2.txt
Midpoint_visit.txt Subject_3.txt
Visit_1.txt Subject_5.txt
Visit_2.txt Subject_6.txt
Visit_3.txt Subject_7.txt
Visit_4.txt Subject_8.txt
Visit_5.txt Subject_9.txt
Visit_6.txt Subject_10.txt
Visit_7.txt Subject_11.txt
Visit_8.txt Subject_12.txt
Visit_9.txt Subject_13.txt
Summary plus refs Subject_15.txt




Biology Workbench
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

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

Bioinformatics Education section of the Open Directory project.
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.


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

The Inquiry Page
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.

National Center for Biotechnology Information (NCBI)
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

OMIM™ Online Mendelian Inheritance in Man
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 Explorer
(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 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 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
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

Transferrins Page
A Project BEDROCK exploration site managed by Lisa Lambert.

Transposon Bank
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
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
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
Lecture on Molecular Evolution I

David Sheppard's materials
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.

The EdGrid Project
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.


Other Resources

Highwire Press - Stanford
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
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
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.