Biogemma Selects Spotfire for Genetic Research Data Management
TIBCO Software has announced that Biogemma, a biotech company in Europe involved in genomics applied to field crops, has selected Spotfire 3.1 to move beyond transcriptomic analyses and embark on new types of integrative research based on genetic maps.
“Before, genetic analyses were mainly conducted with the help of software developed inside a laboratory, but the advantage of using Spotfire to process data positioned on genetic maps quickly became apparent. In addition, with the new version of Spotfire, certain features seemed interesting and prompted us to consider extending its use throughout the company,” said Oliver Dugas, Upstream Genomics Coordinator and Bioinformatics Manager at Biogemma.
As part of its overall plan to develop a comprehensive solution to search all the data produced by the company’s various platforms, Biogemma’s first objective is to centralize data from outside projects, projects in collaboration with public or private partners, or data available in the public domain generally published in scientific articles. This data must be integrated and formatted before it can be used; however, with Spotfire, Biogemma’s researchers get around this problem and are able to work with heterogeneous data. They quickly create links between the data produced internally and all other data from various sources and can produce an accurate and efficient analytical view of their research.
The principal users of Spotfire are the members of the GeneDiscovery team, engineers and Ph.D.s who conduct in silico analyses by integrating and comparing data from the services platforms in order to discover the most effective genes for improving plants in an agricultural context. In addition to this team, other researchers and project managers use Spotfire, for instance to visualize analyses of research into similarities between DNA sequences or when they wish to add more of a reporting dimension to the analyses.
These Biogemma researchers work in several areas of research and on four main types of crops: corn, wheat, sunflower and oilseed rape. Their approach aims to improve these species in order to better meet farmers’ requirements.
Their principal research entails identifying the elements (genes) that encourage the growth of plants adapted to the various growing locations based on the climate constraints (cold, drought), biological constraints (presence of insects, mushrooms, parasites), regulatory constraints (decrease in pesticide inputs) and environmental constraints (reduction of fertilizer and water inputs). Spotfire allows users to quickly identify favorable genes among the natural biodiversity of these plants. This identification occurs by using genetic maps, by association genetics and by using all the genomic or expressed sequences and, of course, the genomic sequence of the species of interest or of related species when they are available.
Although the process of genetic map creation has now been fully mastered, the various statistics modules available in the Spotfire software make it possible to manipulate the data positioned on the genetic maps and to add information and essential research elements.
“The analysis of the various levels of expression of tens of thousands of genes at the same time will be able to be cross-checked with genetic information to provide even more certainty that a genetic region actually contains an overexpressed gene under conditions of stress. That is where the full power of Spotfire lies,” confirms Dugas.