Mayday


Welcome to Mayday!

Mayday is a workbench for visualization, analysis and storage of microarray data.

It features a graphical user interface and supports the development and integration of existing and new analysis methods.

Besides the infrastructural core functionality, Mayday offers a variety of plug-ins, such as various interactive viewers, a connection to the R statistical environment, a connection to SQL-based databases, and different clustering methods, including phylogenetic methods.

In addition, so-called meta information objects are provided for annotation of the microarray data allowing integration of data from different sources. This meta information can be used to enhance visualizations, such as in the enhanced heatmap visualization.

Written in the Java programming language, Mayday is extremely portable and runs on all platforms supporting the Java runtime environment 1.6.

The Mayday core is open source software distributed under the terms of the GNU General Public License. All Mayday plug-ins are free software distributed under the GNU Lesser General Public License.

Mayday is an ongoing project of the Integrative Transcriptomics research group led by Kay Nieselt.


Citation

If you use Mayday for your scientific work, please use the following citation.

Battke F, Symons S, Nieselt K.
Mayday – Integrative Analytics for Expression Data. BMC Bioinformatics 2010, 11:121 (doi:10.1186/1471-2105-11-121).

For Mayday SeaSight, please use the following citation.

Battke F, Nieselt K.
Mayday SeaSight: Combined Analysis of Deep Sequencing and Microarray Data. PLoS ONE 2011, 6(1): e16345 (doi:10.1371/journal.pone.0016345).


Webstart

You can try Mayday right now without any installation!

The only requirement is a Oracle Java 7u72 (or higher) Webstart Environment. If you want to use the Mayday-R interface, a local installation of R is, of course, required.

We offer three versions:

  • Mayday stable webstart (Release 2.14)
    … or run it with 2 GB memory*
    … or run it with 6 GB memory* (only 64 bit Java!)
    – Recommended version
  • Mayday experimental webstart (development version)
    … or run it with 2 GB memory*
    … or run it with 6 GB memory* (only 64 bit Java!) The experimental version contains new features and improvements, but not all functions have been tested as thoroughly as in the stable version.

Due to new safety regulations introduced with Java 8 you have to install a Mayday certificate in order to use Mayday in the webstart version. The Mayday Certificate can be obtained from here.

If you have used Mayday before with a Java version below Java 7u51, please make sure to clear your Java Webstart Cache before running the Mayday Webstart.

** If you need help running Mayday Webstart, please follow the installation instructions below. **


Standalone Version

  • Mayday download version (Stable Release 2.14)
  • Mayday download version (development version)
    … you can run Mayday using the executables in the ‘*platform*_executables’ subdirectory for your operating system
    … after starting Mayday make sure that you set the plugin path under Mayday/Preferences to the ‘plugins’ subdirectory

*) On some machines, you will have to start Mayday twice to get the correct amount of memory. Mayday displays available memory in the bottom left status bar.


Mayday SeaSight

We have now integrated our new extension, SeaSight, allowing users to import raw microarray data together with mapped sequencing 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.

Click here to start Mayday (including SeaSight) with 512M of memory. You can also use our versions with 2GB or 6GB of memory, depending on your operating system.

Note that for more than 2G, you will need a 64bit version of Java. On some systems, you need to start Mayday twice to use the desired amount of memory, due to a limitation of the JVM. See the lower left corner of the Mayday window for a status of memory consumption.

We also prepared a small example dataset and a tutorial.


Tutorials

Mayday’s documentation consists of two types of document: The core documentation and plugin-specific “how-to” documents.

Documentation for Mayday 2.9 (also applies to 2.12)

Older documentation

 


Mayday Webstart Installation Instructions

To run Mayday Webstart with Java 7u51 (or higher) you need to add the Mayday Certificate to your local Java installation. You can download the certificate from here.

  • Installation instructions for Linux & Mac users:
    • Open a terminal and type in the following command
      • sudo keytool -importcert -v -file “download_location/MaydayCertificate.crt” -keystore “java_jre_location/lib/security/cacerts” -storepass changeit
      • Answer with “yes” to add the certificate to the Java keystore when prompted.
      • If you have changed the default password for the Java keystore, replace the default password “changeit” with your chosen password
    • Example on Ubuntu 14.04 with Java JDK version 8u25:
      • sudo keytool -importcert -v -file “/home/users/dummy/Downloads/MaydayCertificate.crt” -keystore “/usr/lib/jvm/jdk1.8.0_25/jre/lib/security/cacerts” -storepass changeit
    • If you cannot add the certificate because an older version is already included, run the following command before installing the certificate:
      • sudo keytool -delete -alias mykey -keystore “java_jre_location/lib/security/cacerts” -storepass changeit
      • This will delete the old version and the new version can now be installed
  • Installation instructions for Windows users:
    • In the Start Search box, type cmd, and then press CTRL+SHIFT+ENTER
    • This opens a terminal with administration rights where you can add the Mayday certificate with the following command:
      • keytool -importcert -v -file “download_location/MaydayCertificate.crt” -keystore “java_jre_location/lib/security/cacerts” -storepass changeit
      • Answer with “yes” to add the certificate to the Java keystore when prompted.
      • If you have changed the default password for the Java keystore, replace the default password “changeit” with your chosen password
    • Example on Windows 8.1 with Java JRE version 8u25:
      • keytool -importcert -v -file “C:\Users\dummy\Downloads\MaydayCertificate.crt” -keystore “C:\Program Files\Java\jre1.8.0_25\lib\security\cacerts” -storepass changeit
    • If you cannot add the Mayday certificate because an older version is already included in the Java keystore, run the following command before installing the certificate:
      • keytool -delete -alias mykey -keystore “java_jre_location/lib/security/cacerts” -storepass changeit
      • This will delete the old version and the new version can now be installed
  • Please note that if you update your Java version, it will be necessary to install the Mayday certificate again for the new version!

If you have installed the Mayday certificate correctly and Mayday Webstart is still not running, please try to clear the Java Webstart cache on your computer. This can for example be done in a terminal (or cmd in Windows) with the following command:

  • javaws -uninstall

This will remove all Java Webstart files from your system and the new Mayday files will be downloaded from our server after restarting the Mayday Webstart.


Mayday Source Code

The source code of Mayday is available here. A detailed instruction for importing the code into Eclipse will be announced as soon as possible.

Contact

For further information about Mayday please contact

Günter Jäger via jaeger–$at$–informatik.uni-tuebingen.de or
André Hennig via hennig-$at$-informatik.uni-tuebingen.de.