We propose to create IDASH, a national center for biomedical computing that will develop new algorithms, open-source tools, computational infrastructure and services that will enable biomedical and behavioral researchers nationwide to integrate Data for Analysis, Anonymization, and Sharing, IDASH will address fundamental challenges to research progress by providing a secure, privacy-preserving environment in which researchers can analyze genomic, transcriptomic and highly annotated phenotypical data. Leveraging the high performance capabilities of the San Diego Supercomputer Center (SDSC), and scalable cyberinfrastructure developed by the California Institute for Telecommunications and Information Technology, iDASH will provide synergistic application of tools and systems to advance research and improve human health. iDASH will focus on privacy protection through anonymization, data simulation, and an informed consent management system. It will focus on data analysis through the development of new tools for data annotation and integration across temporal and spatial dimensions, and develop algorithms for rare event detection and risk adjustment. To enable efficient analysis of short-reads from massively parallel sequencing, compression algorithms and a new genomic query system will be developed. Three Driving Biological Projects that span the molecular-individual-population spectrum will motivate, inform and support tool development: (1) Molecular Phenotyping of Kawasaki Disease;(2) Post-Marketing Pharmacosurveillance of Anticoagulation Agents;(3) Individualized Intervention to Enhance Physical Activity. iDASH trainees will complete core biomedical informatics courses and will have options for short- and long-term graduate training at San Diego State University and UCSD. We will collaborate with other NCBCs and disseminate tools via annual workshops for users and developers, presentations at major conferences, and scientific publications. We will develop a comprehensive web portal to download tools, upload data, and obtain documentation and user-friendly training materials. An experienced leadership team will use effective project management practices to support collaboration as well as monitor and ensure progress toward iDASH goals.
Contemporary biomedical and behavioral research requires significant computational resources. There is an increasing divide between researchers who have these resources and those who do not. iDASH will decrease this gap and accelerate discoveries by providing innovative services, algorithms, open-source software, infrastructure, and training to facilitate data analysis and sharing by biomedical researchers.
|Chen, Luyao; Aziz, Md Momin; Mohammed, Noman et al. (2018) Secure large-scale genome data storage and query. Comput Methods Programs Biomed 165:129-137|
|Groat, Danielle; Soni, Hiral; Grando, Maria Adela et al. (2018) Self-Reported Compensation Techniques for Carbohydrate, Exercise, and Alcohol Behaviors in Patients With Type 1 Diabetes on Insulin Pump Therapy. J Diabetes Sci Technol 12:412-414|
|Nguyen, Nghia H; Khera, Rohan; Ohno-Machado, Lucila et al. (2018) Annual Burden and Costs of Hospitalization for High-Need, High-Cost Patients With Chronic Gastrointestinal and Liver Diseases. Clin Gastroenterol Hepatol 16:1284-1292.e30|
|Burgoyne, Adam M; De Siena, Martina; Alkhuziem, Maha et al. (2017) Duodenal-Jejunal Flexure GI Stromal Tumor Frequently Heralds Somatic NF1 and Notch Pathway Mutations. JCO Precis Oncol 2017:|
|Chen, Feng; Wang, Shuang; Jiang, Xiaoqian et al. (2017) PRINCESS: Privacy-protecting Rare disease International Network Collaboration via Encryption through Software guard extensionS. Bioinformatics 33:871-878|
|Vaidya, Jaideep; Shafiq, Basit; Asani, Muazzam et al. (2017) A Scalable Privacy-preserving Data Generation Methodology for Exploratory Analysis. AMIA Annu Symp Proc 2017:1695-1704|
|Spahn, Philipp N; Bath, Tyler; Weiss, Ryan J et al. (2017) PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens. Sci Rep 7:15854|
|Wang, Meng; Ji, Zhanglong; Wang, Shuang et al. (2017) Mechanisms to protect the privacy of families when using the transmission disequilibrium test in genome-wide association studies. Bioinformatics 33:3716-3725|
|Groat, Danielle; Grando, Maria Adela; Soni, Hiral et al. (2017) Self-Management Behaviors in Adults on Insulin Pump Therapy. J Diabetes Sci Technol 11:233-239|
|Wang, Shuang; Jiang, Xiaoqian; Singh, Siddharth et al. (2017) Genome privacy: challenges, technical approaches to mitigate risk, and ethical considerations in the United States. Ann N Y Acad Sci 1387:73-83|
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