Bioinformatics Education Dissemination: Reaching Out, Connecting and Knitting-together

Internet Resources for the BEDROCK Community

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.
Bioinformatics Module
A number of linked investigations and tutorials that are in the developmental phase by the Biology Student WorkBench project collaborators.
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.
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.
BioQUEST homepage
The BioQUEST Curriculum Consortium actively supports educators interested in the reform of undergraduate biology and engages in the collaborative development of curricula. We encourage the use of simulations, databases, and tools to construct learning environments where students are able to engage in activities like those of practicing scientists.
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.
BRIDD Workshop At ACUBE, October 2006
Using BIRDD to study evolution. ACUBE 50th Annual Meeting BioQUEST Workshop October 28, 2006 Millikin University
David Sheppard's materials
Lessons designed for use with SeqWeb, SeqWeb is a nucleic acid and protein sequence analysis software program licensed for use by GCG [Genetics Computer Group].
Ensembl Genome Browser
Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on metazoan genomes. Extensive links between all well known databases makes this an exceptional site!
GeneDoc is a full featured multimple sequence alignment editor and shading utility.
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.
Molecular Evolution - David R. Nelson
Lecture on Molecular Evolution I. Lecture topics include: The Three Main Branches of Life. How Do They Cluster?, The Root Of the Universal Tree of Life, Genome Fusion To Make Eukaryotes?, The RNA World, A Timeline For Major Events in the History of Life on Earth,
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.
Mouse Genome Informatics (MGI)
An integrative, curated portal providing access to data on the genetics, genomics, and biology of the laboratory mouse.
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 molecular processes affecting human health and disease.
NCBI Handbook chapter on structure resources (pdf)
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 .
OMIMô 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 Data Bank
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.
SeqPup is a biological sequence editor and analysis program. It includes links to network services and external analysis programs.
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
The Ecology and Evolution of the Galapagos Finches
Donovan, Sam (2005). The Ecology and Evolution of the Galapagos Finches. Web Resource published as part of the Tree of Life.
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.
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.
Transferrins Page
The transferrins are an extended family of bi-lobed (called the N- and C-lobes) iron binding proteins found in eukaryotes. This family includes at least five subtypes: serums transferrin, ovotransferrin, lactotransferrin, melanotransferrin, and inhibitor of carbonic anhydrase. This site explores the evolutionary, structural and functional relationship shared by these sequences.
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.


If you have identified a handy site which doesn't appear on our list, please let us know.

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