Computers, Databases & the Web

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

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.

Herbaria and Museums are in the “Dark Ages” as compared to libraries.
Biodiversity Information Standards (TDWG) (formerly the Taxonomic Database Working Group) – develops standards and protocols for sharing biodiversity data.
Darwin Core
Herbarium Information Standards and Protocols for Interchange of Data Version 5 (HISPID 5)
Schemas and Protocols
Access to Biological Collections Data (ABCD) – schema/protocol.
Biological Collection Access Services (BIOCASE) – schema/protocol.
Distributed Generic Information Retrieval (DiGIR) – schema/protocol.

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-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.

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.

HTML, HyperText Markup Language, – the core programming language of the web.
Java
JavaScript
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.

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

Global Biodiversity Information Facility
JStor – literature and now JStor PLant Science (includes the content of Aluka)