Focus on Data Management
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White paper
data management
Managing data for:
decision support in plant breeding
marker-assisted breeding
marker-assisted breeding & QC
plant breeding
seed drying
seed quality
seed testing


Web resources

  • Collaborative website for the Molecular Breeding Platform (MBP)
    Generation Challenge Programme
    - How the MBP can support Information Management for Molecular Breeding
    - Timeline for the development of informatics tools for the MBP
  • Using plant breeding software
    Wikia Inc.
  • Wageningen UR
    Genetics and breeding related software which is available for download
  • Michigan State Statistical Analysis (MSTAT)
    Design, management and statistical research tool
  • Data Analysis for Participatory Plant Breeding
  • PBStat: A web-based statistical analysis software for participatory plant breeding
    Willy Bayuardi Suwarno, Sobir, Hajrial Aswidinnoor, and Muhamad Syukur
    The 3rd International Conference on Mathematics and Statistics (ICoMS-3)
    Bogor Agricultural University, Indonesia, August 5-6, 2008


  • International Crop Information System (ICIS)
    A database system that provides integrated management of global information on genetic resources, crop improvement and evalutation for individual crops.
  • Bioinformatics software applications from the Scottish Crop Research Institute (SCRI)
    • Flapjack
      Still in development, Flapjack is a high performance genotype visualization tool capable of handling very large datasets., where the number of lines and/or markers to be displayed may run into the many thousands - this makes it a very useful tool in genetic analysis. Flapjack allows the user to quickly navigate around a data set, instantly displaying any selected part of the data at any zoom level. The tool provides a single main view of the data, with several additional sub-views alongside, some of which provide dynamic information depending on where the mouse is over the main data area. Flapjack is fully internationalized, and we currently provide versions that run in English and German.
    • TOPALi
      TOPALi provides a graphical interface to advanced phylogenetic model selection, Bayesian analysis (BA) and Maximum Likelihood (ML) phylogenetic tree estimation, detection of sites under positive selection, and recombination breakpoint location analysis. All of TOPALi's methods can be run on remote, high-performance computing clusters, and many of them can be run in parallel to enhance performance even more. TOPALi is developed by BioSS with assistance from SBRN.
    • CurlyWhirly
      CurlyWhirly is a simple-to-use 3D graph viewer suited for viewing any kind of data in three dimensions. This includes, but is not restricted to, output from Principal Components Analysis or Principal Coordinate Analysis.
    • Comparative Map Viewer
      Still in development, this is a graphical tool for visualizing genetic and physical maps of genomes for comparative purposes. Currently in prototype form, and implemented in Java 2D and Swing, this tools aims to let the user examine their data at a variety of different levels of resolution, from entire maps to individual markers, and explore syntenic relationships between genomes.
    • TetraploidMap
      TetraploidMap is a graphical user interface for calculating linkage maps for autotetraploid populations. It is suitable for handling markers scored on two parents and the full-sib offspring of a cross between them. TetraploidMap handles both codominant and dominant molecular markers, in all possible configurations, and takes into account the presence of null alleles in the analysis. It now includes a routine for QTL mapping. TetraploidMap is developed by BioSS.
  • Phenom-Networks: software solutions for plant breeding
  • QU-GENE software (The University of Queensland)
    Developed to be a flexible platform for investigation of the characteristics of genetic systems undergoing repeated cycles of selection and marking
  • Software of Applied Genetics and Plant Breeding (Hohenheim University)
    - PLABSTAT: A concise package to analyse plant breeding experiments (lattices, unreplicated and multi-factor experiments)
    - PLABQTL: QTL analysis with composite interval mapping (regression method)





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