Fig. 1

The SECIMTools structure: The outside cloud represents the Galaxy environment. The inside circle represents the set of SECIMTools. A common data handling and input/output architecture for all the SECIMTools, enables the development of analytical workflows without continual data manipulation and reformatting. Most tools expects two files describing the data, one giving information about each sample and the experimental design (design formatted file), and one giving the estimated feature intensities for each sample (wide formatted files). Galaxy expects files in a tab separated format (tsv). Tools that convert to tsv format from other common formats exist as a part of Galaxy. The output files are result files (e.g. -values from an ANOVA) and figures (e.g. Scatterplots). The result tables are returned to the user in a Galaxy compatible tsv format. Plots have a common color scheme with a customizable color palate that will apply the same coloring scheme to all results. A detailed description of the data formats is given in the user guide