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The Swiss Grid Proteomics Portal

Citation Kunszt, Peter; Espona Pernas, Lucia; Quandt, Andreas; Schmid, Emanuel; Hunt, Ela; Malmstrom, Lars; The Swiss Grid Proteomics Portal. Proceedings of the Second International Conference on Parallel, Distributed, Grid and Cloud Computing for Engineering (2011), -: 81.
Abstract Our portal provides the possibility to define simple and complex workflows, combining the available tools to improve the data analysis or to create new analysis pipelines. It serves both the end-user community who just want to ensure that their data is analyzed in the best-possible way, as well as the expert community developing new tools and methods to improve the data analysis pipelines. The expert user community can create workflows through the portal's workflow editor and link together existing tools (power-users). In addition, we also define a category of super-users who can also deploy new tools and algorithms that can be used as new building blocks by the power-users to build new workflows. They can control the software execution and parameters completely. The portal is based on the P-GRADE portal technology, giving us the ability to submit to a large number of grid systems and to different kinds of remote and local resources. We have extended the functionality of P-GRADE in the workflow system adding chaining individual workflows to larger sets of super-workflows. We have also successfully hidden the complexities of the grid secure authentication and authorization from the end-users by interfacing the portal with the Swiss national AAI infrastructure. Grid certificates for the users are obtained by making use of the delegation feature of the SAML security protocol used by the Swiss AAI service. We integrated into the portal a metadata management system, openBIS, which keeps track of all data products in a highly scalable and customizable manner. The portal queries the openBIS metadata catalog and instructs the data storage services to make the data available at the right places when the analysis takes place. The portal provides three predefined portlets to the end-users. These are a quality control workflow, a proteomics identification workflow and a proteomics quantification workflow.
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