324
V. Mittard-Runte et al.
retention time for the data. It is crucial to determine how long the storage of the
data will be required and what will happen once that period expires. The possible
options range from deletion of the data to the transfer to another medium for long
term archiving.
9.2.2 Data Access
Access to stored data can happen by various means. The data might only be processed by locally installed applications, or it could be made available to non-local
users through a web site or some kind of application programming interface (API)
such as Web Services.
Typically, data access is provided by standalone applications installed on computer systems that process or extract the desired information using locally stored
data such as sequence databases or other data sources like microarray data.
While straightforward, this approach has several disadvantages: both the software itself and the associated data impose a certain maintenance cost on the user,
e.g. when newer versions of the software become available and updates need
to be deployed, or with software relying on frequently changing databases. This
maintenance imposes an increasing problem when such tools have to be used in
environments involving different system architectures and operating systems.
In such a typical environment with different operating systems and software
being used web-based applications allow for platform-independent collaboration
among researchers. This allows them to work on common projects with the data
being stored in a centralized location. Furthermore, web interfaces are commonly
used to make newly developed tools available to the public in situations where publishing the tool itself is not desirable (e.g. due to license restrictions) or impractical
(tools operating on large or frequently updated data).
Web Services provide a standardized method to access information or perform
computations over a network via the exchange of XML-based messages. As a simple means of accessing remote resources, Web Services are becoming increasingly
popular in the bioinformatics field, allowing computationally expensive calculations
to be executed without having to provide the necessary hardware infrastructure,
or providing access to e.g. large sequence databases without the necessity of having to store the data locally (Fig. 9.1). In contrast to web-based interfaces, Web
Services can easily be integrated into other applications, thus extending their functionality. Since Web Services can be accessed from almost any system with a
network connection, they combine the advantages of web-based applications with
a lower maintenance cost in comparison with locally installed tools. The large
amount of different publicly offered Web Services gives researchers easy access
to a wide range of tools and information, helping them to analyse and evaluate their
data. The BioMOBY system (Wilkinson and Links 2002) for example, integrates
a wide range of data sources and data analysis tools that can be accessed as web
services.
V. Mittard-Runte et al.
retention time for the data. It is crucial to determine how long the storage of the
data will be required and what will happen once that period expires. The possible
options range from deletion of the data to the transfer to another medium for long
term archiving.
9.2.2 Data Access
Access to stored data can happen by various means. The data might only be processed by locally installed applications, or it could be made available to non-local
users through a web site or some kind of application programming interface (API)
such as Web Services.
Typically, data access is provided by standalone applications installed on computer systems that process or extract the desired information using locally stored
data such as sequence databases or other data sources like microarray data.
While straightforward, this approach has several disadvantages: both the software itself and the associated data impose a certain maintenance cost on the user,
e.g. when newer versions of the software become available and updates need
to be deployed, or with software relying on frequently changing databases. This
maintenance imposes an increasing problem when such tools have to be used in
environments involving different system architectures and operating systems.
In such a typical environment with different operating systems and software
being used web-based applications allow for platform-independent collaboration
among researchers. This allows them to work on common projects with the data
being stored in a centralized location. Furthermore, web interfaces are commonly
used to make newly developed tools available to the public in situations where publishing the tool itself is not desirable (e.g. due to license restrictions) or impractical
(tools operating on large or frequently updated data).
Web Services provide a standardized method to access information or perform
computations over a network via the exchange of XML-based messages. As a simple means of accessing remote resources, Web Services are becoming increasingly
popular in the bioinformatics field, allowing computationally expensive calculations
to be executed without having to provide the necessary hardware infrastructure,
or providing access to e.g. large sequence databases without the necessity of having to store the data locally (Fig. 9.1). In contrast to web-based interfaces, Web
Services can easily be integrated into other applications, thus extending their functionality. Since Web Services can be accessed from almost any system with a
network connection, they combine the advantages of web-based applications with
a lower maintenance cost in comparison with locally installed tools. The large
amount of different publicly offered Web Services gives researchers easy access
to a wide range of tools and information, helping them to analyse and evaluate their
data. The BioMOBY system (Wilkinson and Links 2002) for example, integrates
a wide range of data sources and data analysis tools that can be accessed as web
services.