Sciunits: Reusable Research Objects

Science is conducted collaboratively, often requiring knowledge sharing about computational experiments. When experiments include only datasets, they can be shared using Uniform Resource Identifiers (URIs) or Digital Object Identifiers (DOIs). An experiment, however, seldom includes only datasets, but more often includes software, its past execution, provenance, and associated documentation. The Research Object has recently emerged as a comprehensive and systematic method for aggregation and identification of diverse elements of computational experiments. While a necessary method, mere aggregation is not sufficient for the sharing of computational experiments. Other users must be able to easily recompute on these shared research objects. In this paper, we present the sciunit, a reusable research object in which aggregated content is recomputable. We describe a Git-like client that efficiently creates, stores, and repeats sciunits. We show through analysis that sciunits repeat computational experiments with minimal storage and processing overhead. Finally, we provide an overview of sharing and reproducible cyberinfrastructure based on sciunits gaining adoption in the domain of geosciences

Efficient, Dependable Storage of Human Genome Sequencing Data

A compreensão do genoma humano impacta várias áreas da vida. Os dados oriundos do genoma humano são enormes pois existem milhões de amostras a espera de serem sequenciadas e cada genoma humano sequenciado pode ocupar centenas de gigabytes de espaço de armazenamento. Os genomas humanos são críticos porque são extremamente valiosos para a investigação e porque podem fornecer informações delicadas sobre o estado de saúde dos indivíduos, identificar os seus dadores ou até mesmo revelar informações sobre os parentes destes. O tamanho e a criticidade destes genomas, para além da quantidade de dados produzidos por instituições médicas e de ciências da vida, exigem que os sistemas informáticos sejam escaláveis, ao mesmo tempo que sejam seguros, confiáveis, auditáveis e com custos acessíveis. As infraestruturas de armazenamento existentes são tão caras que não nos permitem ignorar a eficiência de custos no armazenamento de genomas humanos, assim como em geral estas não possuem o conhecimento e os mecanismos adequados para proteger a privacidade dos dadores de amostras biológicas. Esta tese propõe um sistema de armazenamento de genomas humanos eficiente, seguro e auditável para instituições médicas e de ciências da vida. Ele aprimora os ecossistemas de armazenamento tradicionais com técnicas de privacidade, redução do tamanho dos dados e auditabilidade a fim de permitir o uso eficiente e confiável de infraestruturas públicas de computação em nuvem para armazenar genomas humanos. As contribuições desta tese incluem (1) um estudo sobre a sensibilidade à privacidade dos genomas humanos; (2) um método para detetar sistematicamente as porções dos genomas que são sensíveis à privacidade; (3) algoritmos de redução do tamanho de dados, especializados para dados de genomas sequenciados; (4) um esquema de auditoria independente para armazenamento disperso e seguro de dados; e (5) um fluxo de armazenamento completo que obtém garantias razoáveis de proteção, segurança e confiabilidade a custos modestos (por exemplo, menos de $1/Genoma/Ano), integrando os mecanismos propostos a configurações de armazenamento apropriadasThe understanding of human genome impacts several areas of human life. Data from human genomes is massive because there are millions of samples to be sequenced, and each sequenced human genome may size hundreds of gigabytes. Human genomes are critical because they are extremely valuable to research and may provide hints on individuals’ health status, identify their donors, or reveal information about donors’ relatives. Their size and criticality, plus the amount of data being produced by medical and life-sciences institutions, require systems to scale while being secure, dependable, auditable, and affordable. Current storage infrastructures are too expensive to ignore cost efficiency in storing human genomes, and they lack the proper knowledge and mechanisms to protect the privacy of sample donors. This thesis proposes an efficient storage system for human genomes that medical and lifesciences institutions may trust and afford. It enhances traditional storage ecosystems with privacy-aware, data-reduction, and auditability techniques to enable the efficient, dependable use of multi-tenant infrastructures to store human genomes. Contributions from this thesis include (1) a study on the privacy-sensitivity of human genomes; (2) to detect genomes’ privacy-sensitive portions systematically; (3) specialised data reduction algorithms for sequencing data; (4) an independent auditability scheme for secure dispersed storage; and (5) a complete storage pipeline that obtains reasonable privacy protection, security, and dependability guarantees at modest costs (e.g., less than$1/Genome/Year) by integrating the proposed mechanisms with appropriate storage configurations

Deduplicated Disk Image Evidence Acquisition and Forensically-Sound Reconstruction

The 17th IEEE International Conference on Trust, Security and Privacy in Computing and Communication (TustCom), New York, United States of America, 1-3 August 2018The ever-growing backlog of digital evidence waiting for analysis has become a significant issue for law enforcement agencies throughout the world. This is due to an increase in the number of cases requiring digital forensic analysis coupled with the increasing volume of data to process per case. This has created a demand for a paradigm shift in the method that evidence is acquired, stored, and analyzed. The ultimate goal of the research presented in this paper is to revolutionize the current digital forensic process through the leveraging of centralized deduplicated acquisition and processing approach. Focusing on this first step in digital evidence processing, acquisition, a system is presented enabling deduplicated evidence acquisition with the capability of automated, forensically-sound complete disk image reconstruction. As the number of cases acquired by the proposed system increases, the more duplicate artifacts will be encountered, and the more efficient the processing of each new case will become. This results in a time saving for digital investigators, and provides a platform to enable non-expert evidence processing, alongside the benefits of reduced storage and bandwidth requirements

Making Data Storage Efficient in the Era of Cloud Computing

We enter the era of cloud computing in the last decade, as many paradigm shifts are happening on how people write and deploy applications. Despite the advancement of cloud computing, data storage abstractions have not evolved much, causing inefficiencies in performance, cost, and security. This dissertation proposes a novel approach to make data storage efficient in the era of cloud computing by building new storage abstractions and systems that bridge the gap between cloud computing and data storage and simplify development. We build four systems to address four data inefficiencies in cloud computing. The first system, Grandet, solves the data storage inefficiency caused by the paradigm shift from upfront provisioning to a variety of pay-as-you-go cloud services. Grandet is an extensible storage system that significantly reduces storage costs for web applications deployed in the cloud. Under the hood, it supports multiple heterogeneous stores and unifies them by placing each data object at the store deemed most economical. Our results show that Grandet reduces their costs by an average of 42.4%, and it is fast, scalable, and easy to use. The second system, Unic, solves the data inefficiency caused by the paradigm shift from single-tenancy to multi-tenancy. Unic securely deduplicates general computations. It exports a cache service that allows cloud applications running on behalf of mutually distrusting users to memoize and reuse computation results, thereby improving performance. Unic achieves both integrity and secrecy through a novel use of code attestation, and it provides a simple yet expressive API that enables applications to deduplicate their own rich computations. Our results show that Unic is easy to use, speeds up applications by an average of 7.58x, and with little storage overhead. The third system, Lambdata, solves the data inefficiency caused by the paradigm shift to serverless computing, where developers only write core business logic, and cloud service providers maintain all the infrastructure. Lambdata is a novel serverless computing system that enables developers to declare a cloud function's data intents, including both data read and data written. Once data intents are made explicit, Lambdata performs a variety of optimizations to improve speed, including caching data locally and scheduling functions based on code and data locality. Our results show that Lambdata achieves an average speedup of 1.51x on the turnaround time of practical workloads and reduces monetary cost by 16.5%. The fourth system, CleanOS, solves the data inefficiency caused by the paradigm shift from desktop computers to smartphones always connected to the cloud. CleanOS is a new Android-based operating system that manages sensitive data rigorously and maintains a clean environment at all times. It identifies and tracks sensitive data, encrypts it with a key, and evicts that key to the cloud when the data is not in active use on the device. Our results show that CleanOS limits sensitive-data exposure drastically while incurring acceptable overheads on mobile networks

Solving the Secure Storage Dilemma: An Efficient Scheme for Secure Deduplication with Privacy-Preserving Public Auditing

Existing cloud storage systems obtain the data in its plaintext form and perform conventional (server-side) deduplication mechanisms. However, disclosing the data to the cloud can potentially threaten the security and privacy of users, which is of utmost importance for a real-world cloud storage. This can be solved by secure deduplication mechanisms which enables the user to encrypt the data on the client-side (or via an encryption-as-a-service module) before uploading it to the cloud storage. Conventional client-side encryption solutions unfortunately make the deduplication more challenging. Privacy-preserving public auditing schemes, on the other hand, is also crucial because the clients outsource their data to the cloud providers and then permanently deletes the data from their local storages. In this paper, we consider the problem of secure deduplication over encrypted data stored in the cloud while supporting a privacy-preserving public auditing mechanism.We show that existing solutions cannot support both goals simultaneously due to the conflict of their security and efficiency requirements. In this respect, we present an efficient and secure deduplication scheme that supports client-side encryption and privacy-preserving public auditing. We finally show that our scheme provides better security and efficiency with respect to the very recently proposed existing schemes

Enabling Program Analysis Through Deterministic Replay and Optimistic Hybrid Analysis

As software continues to evolve, software systems increase in complexity. With software systems composed of many distinct but interacting components, today’s system programmers, users, and administrators find themselves requiring automated ways to find, understand, and handle system mis-behavior. Recent information breaches such as the Equifax breach of 2017, and the Heartbleed vulnerability of 2014 show the need to understand and debug prior states of computer systems. In this thesis I focus on enabling practical entire-system retroactive analysis, allowing programmers, users, and system administrators to diagnose and understand the impact of these devastating mishaps. I focus primarly on two techniques. First, I discuss a novel deterministic record and replay system which enables fast, practical recollection of entire systems of computer state. Second, I discuss optimistic hybrid analysis, a novel optimization method capable of dramatically accelerating retroactive program analysis. Record and replay systems greatly aid in solving a variety of problems, such as fault tolerance, forensic analysis, and information providence. These solutions, however, assume ubiquitous recording of any application which may have a problem. Current record and replay systems are forced to trade-off between disk space and replay speed. This trade-off has historically made it impractical to both record and replay large histories of system level computation. I present Arnold, a novel record and replay system which efficiently records years of computation on a commodity hard-drive, and can efficiently replay any recorded information. Arnold combines caching with a unique process-group granularity of recording to produce both small, and quickly recalled recordings. My experiments show that under a desktop workload, Arnold could store 4 years of computation on a commodity 4TB hard drive. Dynamic analysis is used to retroactively identify and address many forms of system mis-behaviors including: programming errors, data-races, private information leakage, and memory errors. Unfortunately, the runtime overhead of dynamic analysis has precluded its adoption in many instances. I present a new dynamic analysis methodology called optimistic hybrid analysis (OHA). OHA uses knowledge of the past to predict program behaviors in the future. These predictions, or likely invariants are speculatively assumed true by a static analysis. This creates a static analysis which can be far more accurate than its traditional counterpart. Once this predicated static analysis is created, it is speculatively used to optimize a final dynamic analysis, creating a far more efficient dynamic analysis than otherwise possible. I demonstrate the effectiveness of OHA by creating an optimistic hybrid backward slicer, OptSlice, and optimistic data-race detector OptFT. OptSlice and OptFT are just as accurate as their traditional hybrid counterparts, but run on average 8.3x and 1.6x faster respectively. In this thesis I demonstrate that Arnold’s ability to record and replay entire computer systems, combined with optimistic hybrid analysis’s ability to quickly analyze prior computation, enable a practical and useful entire system retroactive analysis that has been previously unrealized.PHDComputer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/144052/1/ddevec_1.pd

Proceedings of the 12th International Conference on Digital Preservation

The 12th International Conference on Digital Preservation (iPRES) was held on November 2-6, 2015 in Chapel Hill, North Carolina, USA. There were 327 delegates from 22 countries. The program included 12 long papers, 15 short papers, 33 posters, 3 demos, 6 workshops, 3 tutorials and 5 panels, as well as several interactive sessions and a Digital Preservation Showcase