Herbarium Management

UNIVERSITY OF FLORIDA HERBARIUM
HERBARIUM MANAGEMENT

[University of Florida Herbarium]

  Computers, Databases and the Web

Computers and the web are responsible for a paradigm shift in the way we we work in plant systematics.

  1. Computers
    • Choose operating systems based on the task you need to accomplish. You will likely need to know more than one system.
      • MS-Windows
      • Mac
      • Linux
    • Learn more than the basics about the operating systems you use.
  2. How are Computers Used in the Herbarium?
    • Form letters
    • Collection databases (specimens and libraries)
    • Collection management (loan, exchange and accession records)
    • Biodiversity data sharing and visualization
    • Public outreach
  3. Database Standards
  4. Database Programs
    • What is the difference between a spreadsheet and a database development program?
    • Develop fluency in SEVERAL database applications. Don't put data in without knowing how to get data out.
    • Don't use Microsoft Word or other word processors for preparing labels and storing structured data.
    • MS-Excel (Windows, Mac) - a spreadsheet program that is very basic and easy to use. It is useful for simple data handling. It is an excellent import/export tool.
    • MS-Access (Windows, Mac) - a fairly easy to learn program in which you may develop robust databases.
    • MS-Foxpro (Windows) - a little-known program that is actually widely-used by many corporations for robust, fast databases.
    • MS-SQL Server (Windows) - corporate-level database server, may become expensive to use.
    • MySQL (Windows, Mac, Linux) - open source, free database program.
    • PostgreSQL (Windows, Mac, Linux) - open source, free database program.
    • OpenOffice (Windows, Mac, Linux) - open-source software for word processing, spreadsheets and database development.
  5. Database Applications for Herbarium Collections
    • Biota 2: The Biodiversity Database Manager
    • Brahms: Botanical Research and Management System - widely used, especially in Europe, Africa and Latin America for cataloguing herbaria.
    • KE EMu - electronic museum management system, providing solutions for: museums, art galleries, historical societies, herbaria and botanic gardens. Used by many major institutions (New York Botanical Garden, Field Museum, Yale University). Quite expensive!
    • Specify: "The Specify Software Project supports biological collections with data management software, data conversion services, helpdesk support and training." Development supported by NSF and used by hundreds of museums.
  6. Programming (Scripting) Languages and Frameworks
    • HTML, HyperText Markup Language, - the core programming language of the web.
    • Java
    • JavaScript
    • Active Server Pages (ASP) - server-side scripting language developed by Microsoft for web pages.
    • PHP - "general-purpose scripting language that is especially suited for Web development and can be embedded into HTML".
    • PERL - high-level programming language widely deployed for use on web sites for connecting to and searching databases.
    • Ruby - "open source programming language with a focus on simplicity and productivity."
    • Ruby on Rails - open-source web framework.
  7. Specialized Applications
    • Tolkin - The Tree of Life Knowledge and Information Network. "An information management and analytical web application to provide informatics support for phylodiversity and biodiversity research projects. As a web-based application, TOLKIN is able to support collaborative projects by providing shared access to a variety of data on voucher specimens, taxonomy, bibliography, morphology, DNA samples and sequences."
    • Lucid - interactive key software... "a flexible and powerful knowledge management tool that helps users make an identification or diagnosis."
    • Molecular Data Programs....

    • PAUP
  8. Collection Databasing and Imaging
  9. Web Sites