Today we release Mayday 2.13.
During the development of version 2.13, 149 core builds (#1261-#1409) were produced since March 29, 2011 (323 days). Compared to version 2.12, this release contains 45k additional lines of code, with more than 369k lines of code in total (as counted by sloccount).
This release contains a large number of small improvements and bugfixes, which are not all listed here. The most exciting new features are:
- All Mayday plots can now be exported as vector PDF files which can be used in publications, sent to collaborators, and even edited further (e.g. using Inkscape).
- Mayday can now be connected to The Gaggle allowing users to exchange data and selections with other Systems Biology applications. This new feature is based on work by Claudia Broelemann during her diploma thesis.
- The Silhouette Plot was added to Mayday’s visualization framework. It can be used to inspect the results of any partitioning clustering method and interacts with all other plots.
- Mayday now offers support for visualizing arbitrary subsets of experiments, as well as for combining replicate experiments for the purpose of visualization.
- Additional columns can be added to profile plots to include numerical meta-data in the parallel coordinate plot.
- The Timeseries Statistics plugin was added to allow users to search for probes with specific patterns in time-series datasets. Supported patterns are: permanent switching, transient regulation, small-scale switching events, and generic differential expression.
- A easy-to-use method for moving probes between ProbeLists was added (Plot menu: Selection->Selection Mover).
Here’s a list of other important changes.
Visualization - MIO values in visualizations can now also be modified by Manipulation Methods - Layout of elements in plot legends is now more flexible - Colors in categorical value maps can now be configured - 3D visualizations are now supported on Windows Server 2008 - New data manipulation: Scaling - New data manipulation: Exponential mapping - All scatter plots: Display of axis titles can be configured for improved visual clarity - All scatter plots: x-axis labels are now optimized automatically like y-axis labels - All scatter plots: Font size can now be configured in Chart Settings - All scatter plots: Plot axis are now automatically titled with useful names depending on data source and manipulation - All tabular views try to maintain user defined column order during updates - GenomeBrowser: Current mouse position can be indicated with vertical line - GenomeBrowser: Wiggle tracks can now indicate missing values - GenomeBrowser: New menu item to zoom to 1bp/pixel resolution - GenomeBrowser: Export of large scale is limited to the visible area, resulting in smaller files, faster export - Graph Viewer: New edge routers - Graph Viewer: new highlighting functions for selected experiments - MultiProfilePlot: All plots can now be configured in a common setting - Profile Plot: Support break-and-shift for label connectors - Profile Logo: More binning strategies - Tree Viewer: Experiment nodes can be colored according to classes - Venn diagram: Percentages can be displayed instead of absolute numbers Meta Information - New probe statistic: Range of expression values - New probe statistic: Window-corrected probe variance - New probe statistic: Noise-corrected probe variance - New probe statistic: Fold change - Data manipulation methods can be applied to MIO values - Statistically significant probes can now be filtered directly with multiple thresholds - Direct visualizion of meta information as histogram, table is now available from MI context menu - Parser for locus data knows more strand identifier pairs (F/R,S/A,W/C,+/-,D/P) - GFF importer allows for a default species to be defined User Interface and other improvements - DataSet drag/drop support added - When importing a matrix with nonunique identifiers, these are made unique instead of being discarded - Hierarchical clustering methods now show progress and allow user to cancel - Class Selections can now be created from categorical meta information attached to experiments - FileSetting and PathSetting now remember last used paths - When tasks are still running, Mayday shows a warning message before exiting - New Dynamic ProbeList Processor: Collection mean - SQL shell uses syntax highlighting to show reserved words (SELECT, FROM, ...) - Column-wise DataSet merging can now merge more than 2 datasets Gene Mining - Quartet mining and quartet puzzling now show a progress indicator - More distance measures were added to the quartet mining and quarted puzzling methods - Genemining can now directly filter by p-value SeaSight (Mayday's raw import and normalization tool) - Parallelisation of transformations is now configurable - Support for importing ScanArray files - Read quantification method added: Geometric mean - Wiggle files can be imported and converted to expression values - New transformation to simulate read counts from expression data New features for developers - New vector functions: unique(), range(), isNA(), isFinite(), isInfinite(), is(value) - Vectors can now be constructed from files and streams - Vectors and matrices now support binning methods - MasterTableColumns can now be mutable upon request - Matrices now support mean and stddev directly - Vector.asList returns an instance of RandomAccessList for faster binary search - String Tokenizer in Universal Shell now supports reserved words Bugfixes and other important changes - Mayday's core uses more threadsafe, lock-free structures - Fixed a horrible memory leak occurring if DataSetOverview display (after DataSet loading) was switched off in the Preferences. - Genomic structures coverage iterators work better on small ranges with nonzero starting position - Dynamic Probelists referencing other dynamic Probelists no longer show up empty on dataset opening - When multiple properties of a ProbeList were changed, not all chances would be applied correctly - Drag/Drop of ProbeLists within the same folder was improved - Graph Viewer uses caching to speed up rendering - More fixes to the ever-evolving ClassSelectionModel - Several bugfixes to iterators in genomic containers, overlap arrays - Plots react to all relevant ViewModel events: GenomeBrowser. Venn Diagram, Heatmap