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Benchmarking blockchain-based gene-drug interaction data sharing methods: A case study from the iDASH 2019 secure genome analysis competition blockchain track

International Journal of Medical Informatics

Kuo, Tsung T.; Bath, Tyler; Ma, Shuaicheng; Pattengale, Nicholas D.; Yang, Meng; Cao, Yang; Hudson, Corey H.; Kim, Jihoon; Post, Kai; Xiong, Li; Ohno-Machado, Lucila

Background: Blockchain distributed ledger technology is just starting to be adopted in genomics and healthcare applications. Despite its increased prevalence in biomedical research applications, skepticism regarding the practicality of blockchain technology for real-world problems is still strong and there are few implementations beyond proof-of-concept. We focus on benchmarking blockchain strategies applied to distributed methods for sharing records of gene-drug interactions. We expect this type of sharing will expedite personalized medicine. Basic Procedures: We generated gene-drug interaction test datasets using the Clinical Pharmacogenetics Implementation Consortium (CPIC) resource. We developed three blockchain-based methods to share patient records on gene-drug interactions: Query Index, Index Everything, and Dual-Scenario Indexing. Main Findings: We achieved a runtime of about 60 s for importing 4,000 gene-drug interaction records from four sites, and about 0.5 s for a data retrieval query. Our results demonstrated that it is feasible to leverage blockchain as a new platform to share data among institutions. Principal Conclusions: We show the benchmarking results of novel blockchain-based methods for institutions to share patient outcomes related to gene-drug interactions. Our findings support blockchain utilization in healthcare, genomic and biomedical applications. The source code is publicly available at https://github.com/tsungtingkuo/genedrug.

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Prototype Distributed Ledger Technology of UF6 Cylinder Tracking in Ethereum

Pattengale, Nicholas D.; Farley, David R.

We have created a demonstration permissioned Distributed Ledger Technology (DLT) datastore for the UF6 cylinder tracking safeguards use-case utilizing the Ethereum DLT framework and using Solidity for smart contract code. Our demonstration creates a simulated dataset representing tracking of 75,000 UF6 cylinders across 11 example nuclear facilities worldwide. Our DLT system allows for easy input and reading of shipping and receiving data, including a Graphical User Interface (GUI). Sandia’s Emulytics capability was leveraged to help create the DLT node network and assess performance. We find that our DLT prototype can easily handle to ~150,000 UF6 cylinder shipments per year worldwide, without any excessive computational or storage burden on the IAEA or Member States. Next steps could include a demonstration to the IAEA and potentially demonstrating integration with TradeLens, a DLT in use by a consortium of international shipping companies representing over half of world shipping trade.

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Proteus: A DLT-agnostic emulation and analysis framework

12th USENIX Workshop on Cyber Security Experimentation and Test, CSET 2019, co-located with USENIX Security 2019

Van Dam, Russell V.; Dinh, Thien-Nam D.; Cordi, Christopher N.; Jacobus, Gregory J.; Pattengale, Nicholas D.; Elliott, Steven E.

This paper presents Proteus, a framework for conducting rapid, emulation-based analysis of distributed ledger technologies (DLTs) using FIREWHEEL, an orchestration tool that assists a user in building, controlling, observing, and analyzing realistic experiments of distributed systems. Proteus is designed to support any DLT that has some form of a “transaction” and which operates on a peer-to-peer network layer. Proteus provides a framework for an investigator to set up a network of nodes, execute rich agent-driven behaviors, and extract run-time observations. Proteus relies on common features of DLTs to define agent-driven scenarios in a DLT-agnostic way allowing for those scenarios to be executed against different DLTs. We demonstrate the utility of using Proteus by executing a 51% attack on an emulated Ethereum network containing 2000 nodes.

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Nested Narratives Final Report

Wilson, Andrew T.; Pattengale, Nicholas D.; Forsythe, James C.; Carvey, Brad

In cybersecurity forensics and incident response, the story of what has happened is the most important artifact yet the one least supported by tools and techniques. Existing tools focus on gathering and manipulating low-level data to allow an analyst to investigate exactly what happened on a host system or a network. Higher-level analysis is usually left to whatever ad hoc tools and techniques an individual may have developed. We discuss visual representations of narrative in the context of cybersecurity incidents with an eye toward multi-scale illustration of actions and actors. We envision that this representation could smoothly encompass individual packets on a wire at the lowest level and nation-state-level actors at the highest. We present progress to date, discuss the impact of technical risk on this project and highlight opportunities for future work.

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Characterization of Pathogens in Clinical Specimens via Suppression of Host Background for Efficient Second Generation Sequencing Analyses

Branda, Steven B.; Jebrail, Mais J.; Van De Vreugde, James L.; Langevin, Stanley A.; Bent, Zachary B.; Curtis, Deanna J.; Lane, Pamela L.; Carson, Bryan C.; La Bauve, Elisa L.; Patel, Kamlesh P.; Ricken, James B.; Schoeniger, Joseph S.; Solberg, Owen D.; Williams, Kelly P.; Misra, Milind; Powell, Amy J.; Pattengale, Nicholas D.; May, Elebeoba E.; Lane, Todd L.; Lindner, Duane L.; Young, Malin M.; VanderNoot, Victoria A.; Thaitrong, Numrin T.; Bartsch, Michael B.; Renzi, Ronald F.; Tran-Gyamfi, Mary B.; Meagher, Robert M.

Abstract not provided.

Copy of Automated Molecular Biology Platform Enabling Rapid & Efficient SGS Analysis of Pathogens in Clinical Samples

Branda, Steven B.; Jebrail, Mais J.; Van De Vreugde, James L.; Langevin, Stanley A.; Bent, Zachary B.; Curtis, Deanna J.; Lane, Pamela L.; Carson, Bryan C.; La Bauve, Elisa L.; Patel, Kamlesh P.; Ricken, James B.; Schoeniger, Joseph S.; Solberg, Owen D.; Williams, Kelly P.; Misra, Milind; Powell, Amy J.; Pattengale, Nicholas D.; May, Elebeoba E.; Lane, Todd L.; Lindner, Duane L.; Young, Malin M.; VanderNoot, Victoria A.; Thaitrong, Numrin T.; Bartsch, Michael B.; Renzi, Ronald F.; Tran-Gyamfi, Mary B.; Meagher, Robert M.

Abstract not provided.

Automated Molecular Biology Platform Enabling Rapid & Efficient SGS Analysis of Pathogens in Clinical Samples

Branda, Steven B.; Jebrail, Mais J.; Van De Vreugde, James L.; Langevin, Stanley A.; Bent, Zachary B.; Curtis, Deanna J.; Lane, Pamela L.; Carson, Bryan C.; La Bauve, Elisa L.; Patel, Kamlesh P.; Ricken, James B.; Schoeniger, Joseph S.; Solberg, Owen D.; Williams, Kelly P.; Misra, Milind; Powell, Amy J.; Pattengale, Nicholas D.; May, Elebeoba E.; Lane, Todd L.; Lindner, Duane L.; Young, Malin M.; VanderNoot, Victoria A.; Thaitrong, Numrin T.; Bartsch, Michael B.; Renzi, Ronald F.; Tran-Gyamfi, Mary B.; Meagher, Robert M.

Abstract not provided.

Modeling and simulation for cyber-physical system security research, development and applications

McDonald, Michael J.; Atkins, William D.; Mulder, John M.; Richardson, Bryan T.; Cassidy, Regis H.; Chavez, Adrian R.; Pattengale, Nicholas D.; Pollock, Guylaine M.; Urrea, Jorge M.; Schwartz, Moses D.

This paper describes a new hybrid modeling and simulation architecture developed at Sandia for understanding and developing protections against and mitigations for cyber threats upon control systems. It first outlines the challenges to PCS security that can be addressed using these technologies. The paper then describes Virtual Control System Environments (VCSE) that use this approach and briefly discusses security research that Sandia has performed using VCSE. It closes with recommendations to the control systems security community for applying this valuable technology.

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32 Results
32 Results