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ERCIM News 98
July 2014
Special theme:
Smart Cities

Guest editors:
- Ioannis Askoxylakis, ICS-FORTH, Greece
- Theo Tryfonas, Faculty of Engineering, University of Bristol, UK

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Spanish Pilot Project for Training and Development of Technology Applied to Systems Biology

The ‘KHAOS’ research group at the University of Málaga has developed several applications in a pilot project for training and development of technology applied to Systems Biology.



With the appearance of analysis tools in systems biology, sources of information have been growing exponentially, creating a necessity to approach the problem of the integration of existing information. The applications developed in the pilot project solve specific problems facing the researchers working in this area. These applications focus on data integration and Web Services by means of semantics (and the use of data available as Liked Data):

  • BioBroker - This tool integrates different biological databases using XML as a model of data interchange (Navas-Delgado et al. SPE 2006). This was the starting point for the activities of Khaos in Computational Biology.
  • SB-KOM - A mediator based on using KOMF as the framework and using optimized scheduling algorithms for the biological data bases (Navas-Delgado et al. Bioinformatics 2008). This mediator is the natural evolution of BioBroker towards the use of semantics when integrating biological data.
  • ASP 3D Model Finder (AMMO Prot) - An application that enables the user to view the three-dimensional protein structure in the metabolism of Amines, using computer generated methods. This structure is generated using existing information and it is the first tool that took advantage of SB-KOM.
  • SBMM-Assistant - This assistant allows the user to locate information about metabolic routes (including details about their components) (http://sbmm.uma.es). In addition, it allows the edition of these routes by the users. This tool allows users studying metabolic pathways to retrieve information from many databases and curate them manually.
  • Social Pathway Annotation (http://sbmm.uma.es/SPA). This extension of SBMM introduces the use of social networking tools to enable the collaborative curation of pathway models.
  • BioSStore. In this work we address the drawbacks presented by bioinformatics services and try to improve the current semantic model introducing the use of the W3C standard Semantic Annotations for WSDL and XML Schema (SAWSDL) and related proposals (WSMO Lite).
  • Scientific Mashups. The application of mashups can be useful within biology . Automatic processes are needed to develop biological components which will be applied by end-users to develop specific biological mashups using a mashup platform, ie. EzWeb Platform.


All research conducted by KHAOS is funded by several research grants.

More information: http://khaos.uma.es