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2003 Annual Science Report

Marine Biological Laboratory Reporting  |  JUL 2002 – JUN 2003

Micro*scope ( - A Web-Based Tool for Microbial Diversity Research

Project Summary

micro*scope ( is an innovative biodiversity bioinformatics web site that greatly improves access to information about microbes

4 Institutions
3 Teams
0 Publications
0 Field Sites
Field Sites

Project Progress

micro*scope ( is an innovative biodiversity bioinformatics web site that greatly improves access to information about microbes. It makes use of uBio software (, developed at the MBL/WHOI Library, to reconcile alternative names for an organism within a flexible multi-classification system and overcome problems in using organism names to retrieve information from remote sites. This project was begun in Year 3 and has continued into Year 4 and Year 5. micro*scope now contains a complete list of all bacterial and protist genera organized into a hierarchical classification. It currently provides descriptions and pictures of all categories of microorganisms and contains approximately 5000 freely downloadable high-resolution images organized in over 40 different collections, along with descriptions of 3500 protists. Habitats that have been surveyed include marine, saltwater marshes, fresh water ponds, and other environments, including Yellowstone National Park, Rio Tinto (Spain), Ross Sea (Antarctica) and Lake Toolik in Arctic Alaska. Laboratory culture collections (e.g. American Type Culture Collection) have also been surveyed.

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micro*scope makes use of a number of generic and custom software tools. It has expanded to include a novel system of dynamic, customizable outlinks which link locally held data to information on a specific taxon held at remote sites. We have developed ‘Link-in’ software that reads html and text documents and attaches hyperlinks for information held in micro*scope to the names of organisms in the document. This allows extremely rapid integration of information held within micro*scope into any document.

micro*scope is a flexible, continuously expanding resource and development is on-going. In addition to containing expert information about microbes, the generic structure of micro*scope can be adapted to the needs of both researchers and educators to organize any type of information in a hierarchical classification.

We are actively seeking continuing funding for the further growth of micro*scope.

    Mitchell Sogin Mitchell Sogin
    Project Investigator
    David Patterson David Patterson
    Lorraine Olendzenski
    Education and Public Outreach Staff

    Objective 4.1
    Earth's early biosphere

    Objective 4.2
    Foundations of complex life

    Objective 5.2
    Co-evolution of microbial communities

    Objective 6.1
    Environmental changes and the cycling of elements by the biota, communities, and ecosystems

    Objective 6.2
    Adaptation and evolution of life beyond Earth