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Today's datacenter applications rely on datastores that are required to provide high availability, consistency, and performance. To achieve high availability, these datastores replicate data across several nodes. Such replication is managed…
(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…
Organizations increasingly need to collaborate by performing a computation on their combined dataset, while keeping their data hidden from each other. Certain kinds of collaboration, such as collaborative data analytics and AI, require a…
Multi-socket machines with 1-100 TBs of physical memory are becoming prevalent. Applications running on multi-socket machines suffer non-uniform bandwidth and latency when accessing physical memory. Decades of research have focused on data…
Workflow and serverless frameworks have empowered new approaches to distributed application design by abstracting compute resources. However, their typically limited or one-size-fits-all support for advanced data flow patterns leaves…
As database deployments shift toward cloud platforms and edge devices, thin clients need to securely retrieve sensitive records without leaking their query intent or metadata to the proxies that mediate access. Oblivious Transfer (OT) is a…
Scientific computing applications usually need huge amounts of computational power. The cloud provides interesting high-performance computing solutions, with its promise of virtually infinite resources on demand. However, migrating…
A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly-used CrossMap tool.…
Serverless platforms essentially face a tradeoff between container startup time and provisioned concurrency (i.e., cached instances), which is further exaggerated by the frequent need for remote container initialization. This paper presents…
Cheap high-throughput DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food…
Scientists rely on simulations to study natural phenomena. Trusting the simulation results is vital to develop sciences in any field. One approach to build trust is to ensure the reproducibility and traceability of the simulations through…
We present SSS, a scalable transactional key-value store deploying a novel distributed concurrency control that provides external consistency for all transactions, never aborts read-only transactions due to concurrency, all without…
Process migration refers to the act of transferring a process in the middle of its execution from one machine to another in a network. In this paper, we proposed a process migration framework for Linux OS. It is a multilayer architecture to…
Modern imaging instruments can produce terabytes to petabytes of data for a single experiment. The biggest barrier to processing big image datasets has been computational, where image analysis algorithms often lack the efficiency needed to…
Background: Genomic data have been collected by different institutions and companies and need to be shared for broader use. In a cross-site genomic data sharing system, a secure and transparent access control audit module plays an essential…
We introduce NebulOS, a Big Data platform that allows a cluster of Linux machines to be treated as a single computer. With NebulOS, the process of writing a massively parallel program for a datacenter is no more complicated than writing a…
In recent IoT (Internet of Things) and Web 2.0 technologies, a critical problem arises with respect to storing and processing the large amount of collected data. In this paper we develop and evaluate distributed infrastructures for storing…
Millions of sensors, mobile applications and machines now generate billions of events. Specialized many-core key-value stores (KVSs) can ingest and index these events at high rates (over 100 Mops/s on one machine) if events are generated on…
This paper presents a portable, privacy-preserving, in-browser platform for the reproducible assessment of mutational signature detection methods from sparse sequencing data generated by targeted gene panels. The platform aims to address…
The search for similar genetic sequences is one of the main bioinformatics tasks. The genetic sequences data banks are growing exponentially and the searching techniques that use linear time are not capable to do the search in the required…