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Updated: Apr 7, 2026
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Competitive Genomic Screens of Barcoded Yeast Libraries
Published on: August 11, 2011
18.9K
The NIH BD2K center for big data in translational genomics.
Benedict Paten1, Mark Diekhans2, Brian J Druker3
1UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA benedict@soe.ucsc.edu haussler@soe.ucsc.edu.
Summary
Genomics data must be shared across international repositories to understand rare diseases. The Global Alliance for Genomics and Health is developing shared APIs and open-source software (ADAM) to create a connected genome informatics ecosystem.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Genomics data is globally distributed across numerous repositories.
- No single repository holds sufficient data for comprehensive genotype-phenotype relationship analysis, especially for rare diseases.
- Data sharing is crucial for advancing genomic research and understanding complex diseases.
Purpose of the Study:
- To establish common standards and protocols for seamless data sharing and computation across distributed genomic sites.
- To develop an integrated genome informatics ecosystem that facilitates data accessibility and analysis.
- To ensure the performance and utility of developed tools through benchmarking and real-world projects.
Main Methods:
- Pioneering the development of shared application programming interfaces (APIs) to interconnect global genome repositories.
- Developing an open-source software stack (ADAM) that leverages these APIs for data analysis.
- Utilizing containerization to facilitate software deployment across diverse computing environments.
- Conducting benchmarking and big data driver projects to validate performance and utility.
Main Results:
- Development of shared APIs for connecting disparate genome repositories.
- Creation of the open-source ADAM software stack designed to work with these APIs.
- Demonstrated capability of deploying the software stack in various environments using containers.
- Validation of ADAM's performance and utility through benchmarking and big data projects.
Conclusions:
- A cohesive genome informatics ecosystem can be achieved through standardized APIs and open-source software.
- Facilitating data sharing across distributed repositories is essential for advancing genomic research, particularly for rare diseases.
- The developed tools and standards pave the way for more efficient and collaborative global genomics research.
