about sitemap home home
Databases Data Formats Database Search Genome Browser RNA Secondary Structure Alignments Primer Design WebServices
Technology Simple Client Asynchronity
Demo Java Client Exercise WS choreography Exercise Combining WS
Bielefeld University Center of Biotechnoloy Institute of Bioinformatics BiBiServ
Demo1  
Simple Client in Java using Axis
The WebService call we used in a previous exercise is written in Perl using SOAP-Lite (a commonly used SOAP API for Perl). But how can a WebService be used from the Java programming language? One of the most important SOAP toolkits for Java is the OpenSource project Axis, which is supported and developed by the Apache group. Axis is more than a simple API, it is a complete toolkit supporting development of WebService Servers and Clients in many ways. It offers e.g. the following tools and features:
  • wsdl2java: generating Java source code (skeleton structure) from a given WSDL file
  • java2wsdl: generating a WSDL document from Java source code
  • tcp-monitor: a tool to have a closer look on the data which is transferred between server and client
  • exception handling: exception on server side are represented as SOAP faults
Exercise1  
WebService choreography
Real-world bioinformatics problems can usually not be solved by using just one single tool. Instead, it is often necessary to feed one tool's output as new input into another tool. This process may have to be repeated several times with different tools, each processing the data in a different way, until one gets the desired result. Therefore, it will most probably be necessary to combine several WebServices into a so-called 'WebService choreography'.
Exercise2  
Combining WebServices
Although it is possible to do this combination work manually by connecting WebService clients via the command line, it is usually more efficient and comfortable to combine the different tools directly within one program, thereby encapsulating a whole workflow into a single new tool. This program can then be used over and over again to work an different input data, taking care of all the menial tasks involved in combining the different WebServices used within.
 
HOBIT Project
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.
 
  
BioDOM
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.