SSDBM 2010 in Heidelberg, 30th June-2nd July

Scientific and Statistical Database Management Conference has a long tradition of over 20 years. The conference started with an excellent keynote by Daniel Abadi from Yale. He talked about HadoopDB. Hadoop is a data management and query solution for very large data sets based on the Map Reduce paradigm (MR). It is excelent in splitting a query over many processing nodes and then assembling the results. It is free and scalable. However, in comparison with relational databases, it is not as fast as the commercial products in some types of searching. HadoopDB tries to get the best of both worlds, fast storage layer with indexing and compression from relational platforms and parallelisation for free from Hadoop. The future of scientific data processing may well lie in hybrid solutions, such as HadoopDB or openBIS which is being developed by the CISD and SyBIT in Basel. MR is a paradigm that might be adapted to the type of data processing we support in our scientific workflows.

Another important development in scientific databases is the development and management of workflows. Two conference sessions were devoted to this problem, presenting both research issues and existing solutions and innovations. I particulary liked the talk about Taverna given by Paolo Missier who debunked a lot of the myths surrounding Taverna. In particular, Taverna now supports workflow provenance via its ProvenanceDB. The structure of Taverna is similar to the division of roles in the systems we are building – openBIS and iBRAIN2. One database is normally responsible for the management of experimental results data, both raw and derived databasets, and another database manages provenance, i.e. workflow history for a data set.

OME Users Meeting, Paris 15-16 June 2010

I attended the European Open Microscopy Environment (OME) User Meeting in Paris. There were around 50 attendees showcasing their tools, giving demos and gathering new user requirements. OME produce OMERO, a database and visualisation software suite for microscopy, and the new release of this software was presented in detail. OME software is being developed by a team from Dundee, led by Jason Swedlow and funded by the Wellcome Trust. Two main areas of application for OME software are high content sreening and large 3D imaging of organs, tissues and organisms. Current focus is on image storage and processing, but this is slowly shifting towards providing support for workflows which can automate data analysis, and towards results storage in OMERO. More information is available at the OME website.

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