Stemformatics is a collaboration between the stem cell and bioinformatics community. We were motivated by the plethora of exciting cell models in the public and private domains, and the realisation that for many biologists these were mostly inaccessible. We wanted a fast way to find and visualise interesting genes in these exemplar stem cell datasets. We'd like you to explore. You'll find data from leading stem cell laboratories in a format that is easy to search, easy to visualise and easy to export.
We recognised that the most commonly asked questions of a microarray dataset were: "What is the expression of my gene-of-interest in this dataset", "What else behaves like this gene", "What are the genes that best discriminate between these cell types" and "How similar are these samples". We've provided a simple-to-use gene search interface and a private workbench where you can upload your own gene lists, or run some of these questions and save your results.
Stemformatics is not a substitute for good collaboration between bioinformaticians and stem cell biologists. We think of it as a stepping stone towards that collaboration. We'd like to encourage stem cell biologists to use more genomic data, so we've also provided 'translation tools' that will let you download datasets in formats that can be used by the gold-standard analysis engines such as MeV and GenePattern . We'll also point you to the scripts that we've used for our standard statistical analyses so that you can re-run and refine those analyses externally if you wish.
All of the data on this site has been handpicked, checked for experimental reproducibility and design quality, and normalized in-house. You can find documentation on all of our data processing, QC and analysis on our help page.
Stemformatics Core Team
Stemformatics is a collaborative effort between the members of our multi-disciplinary team.
Systems Architect and Infrastructure Engineer
Developer and UX Designer
Stemformatics is a collaborative effort between leading Australian stem cell researchers
Australian Institute of Bioengineering and Nanotechnology (Wells laboratory)
Institute of Molecular Biosciences
Queensland Centre for Medical Genomics (Grimmond laboratory)
Queensland Cyber Infrastructure Foundation
Queensland Facility for Advanced Bioinformatics
Walter and Eliza Hall Institute
National Centre for Adult Stem Cell Research (Mackay-Sim Laboratory)