Stemformatics.org was built as a collaboration platform for Stem Cells Australia, for the analysis, visualisation and sharing of multiple omic datasets. It was designed for stem cell researchers with minimal experience in bioinformatics, so needed to provide an intuitive, gene-centric search interface, transparent access to primary references, and high-quality graphics. Analyses were implemented from the most common questions asked of the bioinformatics team. It was developed from the recognition of the value of published gene expression signatures, and acknowledged the difficulty that many stem cell researchers had to identify, search, compare, extract or analyse this data in generic array repositories.
We have over 60 public and 50 private datasets hosted and in our latest v5.0 release, we have focused on making some core changes to simplify the way our end users find and use our functionality. We provide users with easy to use functionality to answer the most commonly asked questions, use interactive graphics to show complex data in multiple ways including co-visualisation of different datasets, and identify that users want rapid return of relevant information without having to navigate through too many areas. We work closely with collaborators to tailor specific tasks to their needs, and provide options for securely sharing datasets, gene lists and analyses between linked collaborative groups.