Stem Cell Commons

Promoting Discovery and Reproducibility in Stem Cell Research

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The Stem Cell Commons: promoting discovery and reproducibility in stem cell research

The Stem Cell Commons ( was initiated by the Harvard Stem Cell Institute to develop a community for stem cell bioinformatics. This open source environment for sharing, processing and analyzing stem cell data brings together stem cell data sets with tools for curation, dissemination and analysis. Standardization of the analytical approaches will enable researchers to directly compare and integrate their results with experiments and disease models in the Commons.


Key features of the Stem Cell Commons

  • Contains stem cell related experiments (see Statistics)

  • Includes microarray and NGS data from human, mouse, rat and zebrafish

  • Data from multiple cell types and disease models

  • Carefully curated experimental metadata using controlled vocabularies

  • Export in the Investigation-Study-Assay tabular format (ISA-Tab) that is used by over 30 organizations worldwide

  • A community oriented resource with public data sets and freely available code in public code repositories such as GitHub


Currently in development

  • Development of Refinery, a novel analysis platform that links Commons data to the Galaxy analytical engine

  • ChIP-seq analysis pipeline (additional pipelines in development)

  • Integration of experimental metadata and data files with Galaxy to guide users to choose workflows, parameters, and data sources



The Stem Cell Common is led by Winston Hide, an Associate Professor of Bioinformatics and Computational Biology in the Department of Biostatistics at Harvard School of Public Health.


All content otherwise noted is licensed under a Creative Commons Attribution 3.0 Unported License.