Today we release Mayday 2.11.

During the development of version 2.11, 214 core builds (#947-#1160) were produced since April 28, 2010 (233 days). Compared to version 2.10, this release contains 40k additional lines of code. It is also the first to contain more than 250k lines of code in total (as counted by sloccount).

Some large additions mark this release:

• Roland Keller implemented a new plugin for Gene Set Enrichment (GSEA) and similar methods. It supports several methods for the standard enrichment analysis (of simple gene sets), but especially focuses on computing the enrichment of hierarchically dependent gene sets, such as Gene Ontology terms, for instance. The new plugin allowed us to remove many dependencies, making the Mayday download much smaller.
• Günter Jäger contributed a complete framework for three-dimensional plots, featuring a 3D scatter plot, a 3D profile plot, a 3D heatmap/heightmap, a 3D principal component plot, and others. These plots use OpenGL via the JOGL package and thus depend on the availability of hardware-accelerated graphics. He also implemented a multi-dimensional version of the timeseries analysis plugin.
• Tobias Ries used Mayday’s generic framework for interactive shells and implemented a shell that allows to control all aspects of Mayday via JavaScript code. The shell can be used to automate many daily tasks, such as the creation of a standard set of plots, for instance.
• The heatmap plot was reimplemented to be more flexible. It allows to add groups of columns, reorder them, add tree clustering, is more interactive and faster than the old version. Furthermore it works around a bug in Mac Java where displaying large heatmaps would take very long times.

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