DArT Software

DArTsoft

DArTsoft is a data-extraction and analysis software developed to automatically discover and score DArT markers. Our technology is quite unique in its quantitative approach to evaluating marker quality and the confidence associated with each individual genotype call (score). DArTsoft computes quality and confidence estimates, and these features will be critical to improve the performance of downstream data-analysis software packages.

DArTsoft can work as a stand-alone package or integrated with DArTdb, our Laboratory Information Management System (LIMS). We are using the DArTdb-version of DArTsoft in our genotyping service to assure correct sample/data tracking throughout the entire analysis & reporting procedure.

The current version of DArTsoft has the following features:

• Microarray image analysis: fully automatic spot localisation (320 Kb) and quality evaluation, computation of several relative hybridisation-intensity parameters, generation of a report containing a range of parameters for downstream data analysis,
• Identification of polymorphic markers & scoring of markers: classification of relative hybridisation intensities for all spots on the array, scoring of markers in a dominant (bimodal distribution of intensities) or hemi-dominant manner (trimodal distribution), reporting of score confidence estimates, call rate, and PIC value.

DArTsoft will be available to members of the DArT network, and possibly outside of this framework.

DArTdb

DArTdb is a Laboratory Information Management System (LIMS) based on a relational database entirely built from Open Source components (using the so-called LAMP architecture: Linux, Apache, MySQL and Perl). It has been developed to manage resources for both technology development and the provision of genotyping service.

The current version of DArTdb has the following features:

• Management of DNA sources names (species, genotype, tissue), DNA extracts (samples). Tracking of sample plates is done using barcoding system
• Management of libraries and clone / markers within them. Tracking of library plates is also done through barcodes
• Definition of microarray design and print runs. Slides in print runs are also barcoded and tracked within a system
• Defninition of hybridisation experiments
• Fully automatic import of scanned images. Images are stored within system
• Image data extraction, using DArTsoft image module
• Many utility functions (e.g. barcode search), which produce reports helpful in everyday work

DArTdb will be available to members of the DArT network.

Breeding software

We fully recognise the importance of information technologies, and breeding software in particular, for a successful application of whole-genome profiling. We also recognise that some of our clients may not have sufficient access to software in this critical area. We have therefore established a partnership with the leading breeding software company, GeneFlow Inc., to facilitate access to their software for breeders in Australia. This software can efficiently store, process, filter and visualize both phenotypic variation and marker information, making breeding with markers more efficient.