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November 20, 2018


Bioinformatics in the Cloud


Harrington, JL (2000) Object-Oriented Database Design Clearly Explained. Morgan Kaufmann Publishers.

Simon, AR (1995) Strategic Database Technology. Morgan Kaufmann Publishers.

Achard F, Vaysseix G, Barillot E (2001) XML, bioinformatics and data integration. Bioinformatics 17: 115-125.

Official XML website:

Initially the evolution of the Web was primarily oriented toward producing human-readable web pages, in which HTML is rendered by a web browser as text, images, and hypertext links. A higher-level restructuring of the web is taking place, in which a greater emphasis is placed on making data machine-readable, and creating web services that are accessed through programs, allowing an almost unlimited degree of flexibility for how web services are used. All of this evolution is possible due to the culture of 'open computing', which is essential for the creation of international standards and interoperability of software.

The most succinct way of summarizing these evolutionary processes is to restate the Sun Microsystems motto the early 1980's, "the network is the computer".

1. Open Computing

2. Client/Server interfaces

a. Web interfaces 
b. Java Clients

3. Turning web data into objects

a. XML: a standard for defining web objects
b. Ontologies: relations between objects

4. Web services: Methods for web objects

a. Most web services are implemented as Application Program Interfaces (API)

5. High Performance Computing (HPC)

1. Open Computing

The concept of Open Computing developed from the custom in the academic world of open sharing of research methods and data.  The vast majority of developments in software and computational methods have occurred in this open culture. The history of bioinformatics has taken place almost entirely within the Open Source model.

Why open source software?

Important Open Computing organizations

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