Biomedical Engineering Reference
In-Depth Information
re-sequencing projects such as The 1000 Genomes and The Cancer
Genome Atlas. These tools include tools for depth of coverage analysis,
a quality score re-calibration, a SNP and indel calling and a local
sequence re-alignment.
10.7.7 Development tools
An integrated development environment (IDE) is a software application
that provides comprehensive facilities for programmers to develop
software. An IDE normally consists of a source code editor, a compiler, a
debugger and tools to build the application. At OGT several different
IDEs are currently in use; this is partly due to personal preferences as well
as variations in functionality.
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NetBeans [27] - the NetBeans IDE enables developers to rapidly create
web, enterprise, desktop and mobile applications using the Java
platform. Additional plug-ins extend NetBeans enabling the
development in PHP, Javascript and Ajax, Groovy and Grails, and C/
C++;
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Eclipse [28] - Eclipse was originally created by IBM and, like NetBeans,
provides an IDE that allows development in multiple languages. One
advantage Eclipse has over other development platforms is its support
of a wide variety of plug-ins that allow the same editing environment
to be used with multiple languages including Perl and XML;
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R Studio [29] - R Studio is an IDE purely for R. (R is a statistics
processing environment, see Chapter 4 by Earll, for example.)
10.7.8 Web services
Ubiquitous within any IT offering, data must be presented to consumers
and web-based systems offer much in terms of fl exibility and speed of
development. Currently, OGT uses packages that will be familiar to
many readers of this topic, namely:
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Apache [30] - the Apache HTTP Server Project is an effort to develop
and maintain an open source HTTP server for modern operating
systems including UNIX and Windows NT. It ships with most Linux
distributions and it is our default web server;
■
Tomcat [31] - like Apache, Tomcat is an open source web server but it
is also a servlet container, which enables it to deploy Java Servlet and
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