Bielefeld University Center of Biotechnoloy Institute of Bioinformatics BiBiServ
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seq_nav_dist.png Databases Data Formats Genome Browser Alignments Database Search RNA Secondary Structure Webservices Literature
seq_nav_dist.png Technology A simple client Asynchronity  
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The World Wide Web is more and more used for application to application com-
munication. The programmatic inter-
faces made available are referred to as Web services.
Providing access using WebServices makes it possible to use the tools from other sites automatically and compute results remotely without detailed technical knowledge of the tool.
The underlying protocol SOAP is defined by the W3C and uses http as transport protocol. Communication to and from WebServices is performed in XML.
A WebService is described in a so called WSDL document (WebService Description Language), it includes all required information for connecting the WebService, like the location of the WebService and the interface description.
Distributing these WSDL documents makes it possible to connect WebServices using SOAP implementations, which are available for all current programming languages like Java, Perl, PHP, C and C++.
Although a lot of middleware technologies are currently available, many of them don't fit recent demands.
Some of them require commercial software (eg. TUXEDO) which is definitely an exclusion criteria. Others like J2EE are implementable with Open Source software but they are language dependant. Another issue are problems with the data format and/or the used protocols.
CORBA for example is language independant but operates with the binary IIOP protocol, which causes problems behind firewalls.
The HOBIT initiative is dedicated to form the core of a network linking bioinformatics centres together. It shall be understood as an initial organisational and technological platform for interconnection of bioinformatics activities. The aim of the network is to concatenate applications and resources in a uniform way so providing an efficient communication tier for bioinformatics resource access.
Various bioinformatics tools use a great variety of different inhomogeneous formats for reading data and storing their results. While some formats, like FASTA or CLUSTAL, are common to several programs, others are utilized by only a single tool. Even worse, prevalent formats often lack consistency, e.g. there are many different "interpretations" of the FASTA format in use. This can probably be accredited to the fact that the majority of formats are not well described - a formal definition is missing.
To adress this problem, the HOBIT project has created XML replacements for several basic biological data types and implemented BioDOM. BioDOM is a JAVA library for converting native non-XML output from various bioinformatic tools to XML formats that can be validated against XML schemas.
Different bioinformatical formats can also be converted online by using the BioDOM WebService.
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