The goal of the modENCODE project is to provide the biological research community with a comprehensive encyclopedia of genomic functional elements in the model organisms C. elegans and D. melanogaster. modENCODE is run as a Research Network and the consortium is formed by 11 primary projects , divided between worm and fly, spanning the domains of gene structure, mRNA and ncRNA expression profiling, transcription factor binding sites, histone modifications and replacement, chromatin structure, DNA replication initiation and timing, and copy number variation. The raw and interpreted data from this project is vetted by a data coordinating center (DCC) to ensure consistency and completeness. All the data is publicly available and can be accessed on this site, using modMine or the Dataset Search Tool, on the Amazon Cloud and on the Open Science Data Cloud (OSDC). There are some restrictions on its use for 9 months following publication (see our Publication Policy ). All the software of the project is publicly available on the on-line public repository GitHub. In particular, please check the code for the integration of modENCODE data in Galaxi on the Amazon Cloud. The modENCODE project’s aims are described in Nature 2009 Jun 18;459(7249):927-30. Unlocking the Secrets of the Genome. Please use this reference to cite the project.