Automatic running of bioinformatical tools on remote servers

Audrius Meskauskas, Frank Lehmann-Horn, Karin Jurkat Rott

Ulm university, Current Genetics group

Motivation: Bioinformatical tools on remote servers can be used more effectively by creating a group of specialized internet robots. A universal package, including specialized code generators and reusable library significantly facilitates this task.

Results: We created and tested the java-based package Sight, including code generator set and library. The code generators assist in creating new web robots that simulate filling of web forms and that analyse the received response. Sight builds the entire application without programming, realizing requested data flow diagram. The generated web robots can also work as parts of the user-written program. The library provides date-sensitive databases of the previously received responses and strategies of connecting the remote server. Integration of the locally installed executables is not much different from the integration of the web services. Also, Sight provides interfacing with the Weka classifiers system.

The most recent release Sight 2.1.0 has much more developed system of code generators. These generators produce complete, working java classes that can be without problems integrated into your own applications. It can also create the complete applications for integrated analysis  realising tree-like data flow.

Platforms: Tested under Linux (Mandrake 9.0 and Phat 4.0) and Windows (2000 Pro and NT 4.0 sp5).

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This work was supported by the Interdisciplinary Clinical Research Center (iZKF) of Ulm University funded by the General Ministry of Research (BMBF) and the GRU 460 Graduate College funded by the German Research Foundation (DFG). Logo