Run Reveal in Mayday

After starting Mayday, you can open Reveal via the “Mayday” menu.

For more information on how to use Reveal please refer to this tutorial that gives an overview over the key features and shows an exemplary analysis of the BioVis 2011 contest data set.

For information on how to use Mayday’s core features, please refer to the tutorials and how-to documents.

Example data of the BioVis 2011 contest data set can be downloaded as a single ZIP archive from here.

Further information on the data set and the different file types can be found here.

For detailed information on Reveal we recommend to read:

Jäger, G., Battke, F. & Nieselt, K. (2012), “Reveal - visual eQTL analysis.”, Bioinformatics., Sep, 2012. Vol. 28(18), pp. i542-548.

Run GenomeRing in Mayday

After starting Mayday, you can open GenomeRing with an example alignment via the “Mayday” menu.

For information on how to use Mayday’s core features, please refer to the tutorials and how-to documents.

We provide an example dataset with a step-by-step guide to recreate the Campylobacter analysis presented in our manuscript.

1. Start Mayday
2. Download one of the SuperGenome alignment files (we recommend to load the original xmfa file and to set the minimal block size in Mayday)
   • precomputed for minimal block size 10000:
     Campylobacter_jejuni_10000.blocks
   • precomputed for minimal block size 7500:
     Campylobacter_jejuni_7500.blocks
   • precomputed for minimal block size 5000:
     Campylobacter_jejuni_5000.blocks
   • original XMFA alignment file with 4 genomes (SuperGenome will be generated in Mayday):
     Cjejuni.xmfa
3. Download the additional dataset Campylobacter_jejuni.maydayz
4. Follow the steps in the step-by-step guide

For detailed information on GenomeRing we recommend to read:

Herbig, A., Jäger, G., Battke, F. & Nieselt, K. (2012), “GenomeRing: alignment visualization based on SuperGenome coordinates.”, Bioinformatics., Jun, 2012. Vol. 28(12), pp. i7-15.

Run Mayday to try Gaggle Support

For more information on Gaggle please visit the Gaggle website.

For information on how to use Mayday’s core features, please refer to the tutorials and how-to documents.

For detailed information on GaggleBridge we recommend to read:

Battke, F., Symons, S., Herbig, A. & Nieselt, K. (2011), “GaggleBridge: collaborative data analysis.”, Bioinformatics., Sep, 2011. Vol. 27(18), pp. 2612-2613.

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

The new version fixes a bug where single columns of the expression matrix could not be accessed directly.

The new version is available for download. Please read the included how-to document for a quick installation guide.

Run Mayday to try MGV

Additional Information about MGV:

• Features of MGV
• MGV Gallery
• FAQ

During the development of version 2.12, 100 core builds (#1161-#1260) were produced since December 17, 2010 (102 days). Compared to version 2.11, this release contains 65575 additional lines of code and it’s the first release to contain more than 320k lines of code in total (as counted by sloccount).

This release is mainly a maintenance and bugfix release, but we have some exciting new features as well:

• Since our group was renamed to “Integrative Transcriptomics“, we have a new splash screen and a new self-signed certificate is used to sign our webstart JAR files.
• Günter Jäger contributed a new version of the Timeseries Alignment Plugin. It allows to compare several timeseries datasets in a three-dimensional visualization embedded into the existing timeseries alignment GUI.
• Matthias Munz wrote a plugin to create an interactive HTML standalone visualization including box plot, profile plot, heatmap, as well as tabular views. The standalone is a single HTML file that can be displayed using any modern web browser. Standalones can also be sent to collaborators by email or placed on a web server to facilitate scientific discussions.
• As a major addition, Stephan Symons introduces MGV, a generic graph viewer for Mayday. It can display graphs enriched with probe and meta information. Graphs can be created from many sources, including Mayday data, biological pathways (BioPax, KEGG), biochemical models and general-purpose graph formats (GML, DOT, GraphML). Both specialized and general graph layout algorithms can be applied. The entire display of graphs, including nodes, edges, node labels, graph title is highly customizable: For the display of data associated with nodes, more than 20 renderers are available, which can be extended by so-called decorators that add meta information. Edges can be drawn in various styles, strokes and colors. Working with graphs is made easy using more than 40 extension plugins for arranging, introducing and evaluating edges, adding nodes, filtering nodes, summarizing and merging nodes. MGV graphs can contain probes from more than one dataset. This allows, among other features, graphical clustering comparisons. For biochemical pathways, all of transcriptomics, proteomics and metabolomics data can be displayed in the same plot. Given mappings of probes and experiments, statistical measures can be applied to perform cross-study comparisons. Included is a Correlation Heatmap that displays the correlation of probes from two datasets.

Here’s a list of other important changes.

Visualization
- New heatmap column type: Expression bars (for black and white printing)
- New heatmap column type: Gene models (if exon data is available)
- Heatmap column headers are now horizontally placed if space permits it
- The "Windows" menu now directly contains the list of open windows.
- Plots can now support selections on experiments (e.g. the tree visualizer)
- Plots can now sort experiments by meta information (e.g. in the heatmap)
- The histogram now is about 100 times faster when binning data to few values
- If colors are assigned by categorical meta-data, an extra window shows the color assignment

User Interface and other improvements
- Drag support: ProbeLists can be dragged out of Mayday (e.g. into excel)
- Drop support: List of probe names can be dragged into Mayday to create ProbeLists
- MIGroup names are now shortened if too long
- Selected elements in tables are remembered after sorting
- The dataset properties dialog is now structured to give a better overview
- New plugin: Summarize experiment on display names
- The Hierarchical Clustering Plugin now supports stored and default settings
- GSEA result probelists now contain a better annotation

Meta Information
- Experiments can be annotated with meta information
- Experiments can be associated with display names for nicer plots
- Drag&Drop support: Meta Information can be dragged into Mayday

SeaSight (Mayday's raw import and normalization tool)
- Memory mapping now uses fewer, larger files
- Memory mapping footprint is reduced by compression if the data permits it
- New locus transformation: Split complex coordinates into their atoms
- Median Polish is much faster now due to synchronized name caches
- CEL import uses more aggressive caching for speed up
- Added "Locus Consistency Check" to prevent disappointment if annotation and mapped
  reads don't agree, e.g. on chromosome names
- Fixed a large bug that potentially concerned all matrix operations from the GUI
- New read summary method: Arcsin
- New read summary method: RPM (the previous version did not work correctly)
- "Naive read count" now offers an option to only use completely overlapping reads
- Great improvements in the SAM/BAM importer in terms of speed and safety
- Experiment properties now also show the initial state next to the current state
- SeaSight can now handly NaN in array expression experiments

New features for developers
- Improved vector subset creation
- DoubleVectors can now be directly created from Double[] as well as double[] arrays
- Drag&Drop support can be extended via plugins
- Memory-mapped structures for booleans
- Memory-mapped structures for genetic strands
- ProbeListManagerView is now a pluggable object, new views can be implemented in the future
- The "Plot" menu of visualizations can now be extended via plugins

Bugfixes and other important changes
- Sequence loading in Genome Browser is much faster now
- GeneMining can now be called on only 2 experiments
- Added detection for first-time use: Mayday now asks for plugin path setting.
  This should eliminate 50% of all support requests
- Removed a dangerous bug in our quantile function
- Time Point scaling and Global Min/Max scaling now work together correctly in Profile Plot
- Time-series alignment now also works with less than 4 experiments.
- FDR correction now also works if some pValues are NaN

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.

Here’s a list of other important changes.

Visualization
- New plot: Quantile-Quantile (QQ) plot allows to compare the distributions of two variables
- New plot: Star Plot (Radial view of a profile plot)
- New plot: Venn Diagram to compare probelists
- Histogram: amazing speedup in histogram creation for large datasets
- New probe lookup plugin for StrepDB
- Genome Tracks:
  * New track for wiggle data
  * New track for sequence data (fasta files)
  * New track for mapped reads imported via SeaSight
  * New track for read coverage computed from reads imported via SeaSight
  * New renderer for all-experiment heatmap track
  * Better GUI for chromosome selection
  * Disabled direct rendering, only use buffered method for more responsive gui
  * use complete chromosome length instead of only maximum of covered positions
  * Allow users to clone existing tracks
  * Add functionality to save/load track layout
  * Add option to allow free track placement
  * All tracks are now transparent to allow them to placed on top of each other
  * Many speed improvements (e.g. Scale ticks in O(1) instead of O(n))
  * Allow to zoom to more than 1px per base, adapt scale to this case
- Graph Viewer:
  * complete SBGN compliance (PD 1.1)
  * Enhancing meta information display
  * Extensive help text
  * Improved edge rendering: Added enhanced bezier curves
- Profile Plot:
  * Can now display individual centroids for each probelist
  * Allows to hide non-centroid profiles
  * Individual Profiles can now be labelled (CTRL+right click on a profile)
- New online data manipulations:
  * Logarithm
  * Derivative

User Interface and other improvements
- Probelist previews now show histograms in single-experiment datasets
- Added option to export display names from tables
- Replace "MIO" by "meta-information" in GUI elements and filters
- Mayday is now friendlier and says goodbye when started from a shell window
- Mayday now has proper parameter parsing and new parameters (run it with "-?" to learn more)
- Error information in the task manager is now clearer and more complete, showing causal exceptions
- Name clashes in dataset, probelist and mi group names are now resolved in a nice dialog
- Added a setting to automatically save every K minutes, add menu option to restore auto-saved settings
- Experiments are now explicitely modeled and can be enriched with meta-information
- Use probe display names in user defined probelist creation dialog
- Experiment Class Labellings can now be stored for later re-use.
- The Class Selection Dialog was redesigned and now offers new options: Create new named class, Create class with predefined name

Genomic Data, Meta Information
- New coordinate model:
  * All genetic coordinates in Mayday have been moved to a new framework.
  Instead of single start-end coordinates we now support multi-element
  coordinates, such as exon models, for instance. For developers this
  brings many new methods and new structures for efficient storage and
  computation.
- New plugin to merge mio groups
- New import plugin to read gene models from GFF files
- New generic GenBank importer
- New importer for EMBL files
- Empty LocusMIO groups are not attached after importing, instead a warning is issued.
- There is now a central repository structure for chromosome sequences, with its own importer plugin class.

SeaSight (Mayday's raw import and normalization tool)
- Median Polish now has the variant described in tRMA with fewer artifacts for studies with few samples
- GenePix importer is more lenient when parsing
- Mappings for feature summarization are automatically produced for Agilent, GenePix and ImaGene experiments
- Locus Data Inspector added to make SeaSight locus handling more transparent
- Expression is now computed using the newly introduced complex coordinates (e.g. exon models)
- SAM/BAM importer added
- SAM/BAM importer has special options when importing paired-end reads
- SAM/BAM importer uses first the MAPQ field, then NM and then AS for mapping quality
- SeaSight now provides information on WHY certain transforms can not be applied
- New transformation: Read per Million (RPM) to complete the set (RPKM, RPM, RPK)
- New transformation: Depth of coverage per million (DCPM)
- Memory consumption is now very very low since we switched to memory-mapped files
- Added consistent handling of meta information in SeaSight transformation pipelines
- The storage format was changed from text to binary for smaller files and faster storage

New features for developers
- A whole new package of memory-mapped large-array structures (MMStringArray, MMCharArray...)
- Memory-mapped structures can fall back to in-memory buffers in the case of problems
- The directory where memory mapped structures are stored is configurable (scratch dir)
- A memory-mapped large hashmap structure
- added GUI for ChromosomeSetContainer inspections
- MIGroupSettings can now be set to strictly filter acceptable classes, disallowing derived classes
- AbstractVector framework: Adding sum() and prod()
- Added support for tooltips in setting menu elements
- PluginManager: now contains an annotation @IGNORE_PLUGIN to disable plugins
- PluginManager: information during mayday start is now much clearer
- GenomeTracks: tracks can now have custom mouse listeners
- The Settings Implementation Checker is only run in debug mode now.
- A new structure for sparse overlap arrays which gives huge speed & memory improvements
- Experiments are now explicitely modeled and can be enriched with meta-information
- New provisions to serialize huge meta-data (e.g. mapped reads information)
- MIGroupSettings are now populated with more meaningful defaults
- PluginManager now supports native library paths
- The AbstractMatrix framework now supports R-like apply() methods
- New complex Setting types to manage sorted stacks of (potentially, but not necessarily) plugin-based elements with their own settings
- Chromosomes can now compute the coverage for each base, also for subregions of the chromosome
- New access method allows to find all elements overlapping a certain region, and all elements overlapping them, recursively.
- New access methods to distinguish overlapping and spanning coordinates

Bugfixes and other important changes
- DetachableComponent and DetachablePlot now also allow object hiding
- Removed a possible deadlock on plot export
- Fixed a axis labels in MA plots
- Rank Product is now able to deal with NAs
- The dialog to search the optimal number of clusters for k-means now allows other centroid algorithms
- Fix reentrancy issue in "Synchronize selection with Visualizer"
- Graphics and text antialiasing were swapped in rasterexport
- Plots can now be created automatically, e.g. from scripts
- Vector permutation always left the first element unpermuted
- and many more small improvements

During the development of version 2.10, 225 core builds (#722-#946) were produced since December 1, 2009. Here’s a list of the most important changes.

New Visualizations for Meta Information

Stephan Symons added three visualizations focused towards interpretation of meta information: The Tag Cloud, Term Pyramid and Chromogram plots (described below). The plots can be found in the “ProbeList” menu, under “Visualization“.

The chromogram is a method to visualize long textual sequences using color. Original publication by Wattenberg et al. We are using meta information, and create an order of the probes via sorting the genes using different criteria. This includes name, values, meta information and experiment with extremes.
The term pyramid is used to compare the abundance of meta information terms in two probe lists via bar charts (comparable to population age pyramids). Alternatively, it can visualize the average expression value of the probes associated with the terms in several ways.
A tag cloud is a clever way to display the abundance of terms (called tags) annotating a collection of objects. The height of a tag is proportional to the frequency of the tag. Mayday’s tag cloud can display tags coming from meta information, in various orderings (largest first, center largest, alphabetical) either displaying the tags as strings or displaying the associated probes. Aided by a histogram of tag frequencies, the user can also filter to concentrate on interesting tags.

Gene Mining

Günter Jäger rewrote the GeneMining plugin. It now offers a much cleaner and more intuitive user interface can quickly be extended with new feature selection methods (as plugins) and results are added as hierarchical meta information. Start GeneMining from the “ProbeList” menu, under “Data Mining“.

Mayday SeaSight

The largest addition is the new SeaSight framework for importing raw microarray data and mapped reads.

Data from different platforms can now be integrated and analyzed together using Mayday’s wealth of methods for visualization, data-mining, classification, and statistics. Mayday SeaSight offers methods for computing expression values from mapped reads, raw microarray data import, background correction, normalization and summarization and linking microarray probes to genomic coordinates. These transformations can be combined in a user-friendly graphical interface to quickly construct powerful normalization pipelines.You can start SeaSight from the “DataSet” menu, “Further import options“.

Visualizations

+ New Visualization: Chromogram block view
+ New Visualization: Term pyramid
+ New Visualization: Tag cloud
+ New Online Data Manipulations: Ranking, Threshold Binning
+ Online data manipulations can now be combined in manipulation stacks
+ Improved gui for online manipulations
+ The default probelist order can now be changed for each visualizer
+ The visualizer button bar is now sorted, with "major" plots at the beginning
+ Genome Browser rendering is now much fast (see our paper)
+ Genome Browser track labels are now fully configurable
+ Genome Browser has improved rendering of very small loci
+ Genome Browser now renders elements with "unspecified"/"both" strand distinctly
+ New menu item "Only export the visible area" helps with huge Genome Browser views
+ Color Gradient editor was rewritten from scratch to be more user-friendly
+ Tabular views now show the row number for easier navigation and better overview
+ The HeatMap is now acceptably fast even with thousands of columns
+ Graph component renderers are more configurable
+ We now only use finite values when computing mean, min, max
+ New percentile table added
+ Data underlying a histogram plot can now be exported
+ New rainbow gradient now mimics visible light spectrum
+ Profile Plot can now be scaled using global OR local minima/maxima
+ Transparency is now independent of anti-aliasing for all vis2-based plots
+ Plot window titles now indicate whether an update is in progress
+ "Brushing" selection added to: pca plot, profile plots, scatter and MA plot
+ Selection set operations intersect(ALT), subtract(CTRL-ALT), union(CTRL) for brushing selections
+ PCA plot now uses the probelist ordering as basis for its z-ordering of points
+ Relevance can be used to set transparency in Profile Plots
+ Class labels can be added to experiments in the Heatmap
+ Histogram now supports selection

Genomic Data, Meta Information
+ Parser for GFF data
+ Parser for GenBank locus data (single and multi record files)
+ Locus Data can be mapped towards other locus data
+ Subelements can be extracted from Locus MIOs
+ MIO types can now be converted
+ MIO groups can be send to other datasets
+ MIO values can now be binned
+ MIO values can now be ranked
+ p-values can now be corrected at any time

Dynamic ProbeLists
+ New processor: All mio values
+ New processor: String mio values
+ Rules now discard missing values by default
+ New processor: Case-insensitive string comparisons
+ New processor: Contained in MIO value subset defined by a probelist
+ New processor: Value contained in List MIO subset defined by a probelist
+ Processor "Similar to example probe" has a nicer, persistent GUI
+ New processor: Probe similar to probelist median
+ New processor: Absolute value of a number
+ New processor: Extract length from Locus MIO

Statistics, Mathematics
+ The "Statistical Test" plugin now offers p-value correction
+ Add the Spearman Rank correlation distance
+ "One sample t-test" plugin is now directly visible in the "Statistics" menu
+ Added Storey's FDR correction method
+ Extended the Statistics Framework to allow generic "Scoring" methods that do not produce real p-values

User Interface and other improvements
+ Completely new MIO import dialog, MIOs can now be linked via ProbeName, DisplayName or other MIOs
+ Main window status bar now shows a real progress bar if a task is active.
+ Fixed percentage display for very slow tasks
+ Density-based clustering dialog is now a lot nicer
+ Added export/import of hierarchical probelist selections
+ Improved window handling
+ Main window now has an area for pluggable GUI enhancements (accessible from the "Window" Menu)
+ Pluggable GUI elements: Window list, Dataset annotation, Quick visualization buttons
+ Pluggable GUI elements can be configured in Preferences/Plugins/Core/
+ Plot buffering code rewritten, now returns from awt thread as fast as possible
+ DataSet->Quickly visualize probes has more search options now
+ Class Selections can now contain unclassified objects
+ Class Selections can now be automatically inferred based on object names
+ Task Manager handles failed tasks better and has a cleaner look.
+ New dialog to resolve probelist name conflicts, offering suggestions
+ Buttonbars now have overflow wrapping and nicer icon handling
+ Added icons for main window actions ("Move up", "Move Down", ...)
+ ProbeLists (including Dynamic Probelists) can now be cloned.
+ New datasets can be derived from existing by applying a online data manipulation method
+ Autocomplete in Mayday's shells (R, SQL) now also works on empty input
+ CSV dataset import now automatically configures IntegerMIO and Ignored columns
+ Nicer handling of the window list, whole groups can be simultaneously brought to front/closed
+ File Menu actions are more intuitive
+ Property dialogs now show MIO Groups' paths
+ Mayday makes an effort to fit large popup menus to the user's screen size
+ Mayday now can be configured to start in full-screen mode. Default is full-screen mode.

New features for developers
+ With SeaSight, we have greatly improved and optimized data types for genetic coordinates, genomes, etc.
+ We have added efficient structures to store growable lists of native types
+ New Setting Types were added: MappingSourceSetting, PluginMultiselectListSetting, PluginInstanceListSetting
+ New Structures: Pairs and Triples
+ Finally cleared up the confusion regarding getGlobalProbeList()
+ Statistics methods now have methods to deal with NAs in min,mean,max,rank,...
+ PNorm and DNorm now behave exactly like their R counterparts
+ Vector framework additions: abs, log, exp, shallow cloning, quantiles, subsetting by row names, which(), replace(), median absolute deviation (mad),
+ Vector framework has now columns based on a MasterTable
+ MIGroupSelectionDialog/Panel can now support more than one acceptable class
+ More efficient helper functions in the graph framework
+ Mayday Webstart now writes stdout,stderr and plugin list to temp directory when the MAYDAY_DEBUG environment variable is set to TRUE
+ Mayday's normale distribution (PNorm, DNorm) is now equivalent to that of R
+ PluginManager supports "surrogate" plugins that wrap around scripting languages and the like.

Bugfixes and other important changes to core
+ GUI improvements for many Setting types, e.g. tooltips in Plugin*Setting
+ Dynamic ProbeList parsing is now more robust
+ ObjectSelectionSetting does no longer show some items twice
+ Tabular-text parser is now as memory-efficient as humanly possible, and much faster.
+ We have a new snapshot format which is even faster, more memory efficient (again!) and easier to parse by other tools.
+ Prevent taskman gui from bringing main window to front everytime it is set visible
+ Setting Implementation Checker is now run less often
+ PluginManager is now less verbose, does not cache instances any more, provides clearer error messages
+ Bugs in Java's progress bar can no longer kill Mayday's tasks
+ Complete rewrite of the code creating menus dynamically from plugins.
+ Plugins can now implement "ApplicableFunction" to check whether they like a given input
+ PluginManager can now directly clone plugins with settings
+ Task progress can now be reported to a "parent" task
+ Fixed problem with spaces in experiment names in Class Selections

Mayday - Integrative analytics for expression data

It is now available from BMC Bioinformatics.

Publishing this paper is the result of several years of hard work. We thank everyone who participated in developing Mayday or supported the team and the project!

Mayday’s development does of course not end here, stay tuned for more cool features!

If you want to cite Mayday, please now cite this article:

Florian Battke, Stephan Symons and Kay Nieselt: Mayday - Integrative analytics for expression data; BMC Bioinformatics 11 (1):121 (2010)

Or simply use this Bibtex entry:

@Article{Battke2010,
AUTHOR = {Battke, Florian and Symons, Stephan and Nieselt, Kay},
TITLE = {Mayday - Integrative analytics for expression data},
JOURNAL = {BMC Bioinformatics},
VOLUME = {11},
YEAR = {2010},
NUMBER = {1},
PAGES = {121},
URL = {http://www.biomedcentral.com/1471-2105/11/121},
DOI = {10.1186/1471-2105-11-121},
ISSN = {1471-2105},
}