Ensembl is a freely available software system for genomic analysis. The documentation page at Ensembl is the best place to get information on the Ensembl application programming interface (API). In particular, the tutorial document includes lots of examples of scripts and exercises for you to try.
SeqHound is a bioinformatics application programming platform that provides access to biological sequence, structure and functional annotation data. An application programming interface (API) is available to programmers using C, C++, Java and PERL.
The Entrez Programming Utilities provide a method of linking to Entrez and querying the Entrez database outside of the regular web interface. Users can access the utilities via a web address, or via a Simple Object Access Protocol (SOAP) interface.
BIND SOAP is a web service providing end users with the ability to access functionality offered by the BIND Search Service through a remote Application Programming Interface (API).
SOAP interfaces used to access the cancer Bioinformatics Infrastructure Objects(caBIO) funtionality.
Chinook is a peer-to-peer (P2P) service for the discovery, use and assessment of bioinformatics programs. Chinook Online allows researchers to connect and run distributed bioinformatics programs using a web application.
EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.
Taverna is a tool for creating and running bioinformatics workflows.
The PathPort project at the Virginia Bioinformatics Institute (VBI) has implemented a number of web-services that provide the core data access and analysis tools capabilities for the system.
XML Central of the DNA Data Bank of Japan (DDBJ) provides SOAP (Simple Object Access Protocol) server and web services for various databases and bioinformatics programs.
BioMOBY is an international research project involving biological data hosts, biological data service providers, and coders whose aim is to explore various methodologies for biological data representation, distribution, and discovery.