The Genomic Open-Source Breeding informatics initiative (GOBii) is a Bill and Melinda Gates funded project (http://gobiiproject.org). Our mission is to enable the routine implementation of genomic and marker-assisted selection in breeding programs, hence increasing the rates of genetic gains. We believe that much of the genetic gains have achieved in major ag-biotech companies can also be achieved in small under-resourced breeding programs when low cost, highly multiplexed genotyping technologies, integrated data management systems, bioinformatics pipelines, and decision support tools are routinely adopted there. Genomic selection offers great potential to transform breeding by increasing the rates of genetic gain, decreasing generation interval, and identifying the best performers for use as parents in the next generation. To bring genomic selection into routine application, we first built an open-source genomic database management system that is designed with performance in mind and can flexibly handle diverse crops and marker and sequence-based platforms. This system has built-in quality control and support flexible and efficient data querying. The source-code for this system is available at: https://github.com/gobiiproject. Using CIMMYT’s wheat and maize use cases and test datasets, we have built an integrated genomic selection analysis pipeline in Galaxy. It has the capabilities to calculate and visualize best linear unbiased estimate (BLUE), best linear unbiased prediction (BLUP), and genomic best linear unbiased prediction (GBLUP) based on well-defined training population, split and match sub-datasets across populations, years, and locations, batch process for multiple traits, and model training. These tools and workflows are free and available for the public to test at http://galaxy-demo.excellenceinbreeding.org/. We are working to connect and house open-source data management systems, analysis pipelines and application tools in a web-based portal to allow single entry point data access. Additional open source marker-assisted selection tools that this portal house include pedigree verification, forward breeding, marker-assisted back crossing modules in Flapjack tool. Partnering with Excellence in Breeding (EiB) platform, GOBii not only develops open-source databases and decision support tools but also hosts webinars, workshops, and hackathons, coordinates use cases, and builds global community for adoption of best practices and new emerging breeding technologies required to transform breeding.