The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process. Here we introduce EAGER, a time-efficient pipeline, which greatly simplifies the analysis of large-scale genomic data sets. EAGER provides features to preprocess, map, authenticate, and assess the quality of ancient DNA samples. Additionally, EAGER comprises tools to genotype samples to discover, filter, and analyze variants. EAGER encompasses both state-of-the-art tools for each step as well as new complementary tools tailored for ancient DNA data within a single integrated solution in an easily accessible format.

/pdf/eager-efficient-ancient-genome-reconstruction-3vka35o1ve.pdf

EAGER: efficient ancient genome reconstruction

Programs that take highly-structured files as inputs normally process inputs in stages: syntax parsing, semantic checking, and application execution. Deep bugs are often hidden in the application execution stage, and it is non-trivial to automatically generate test inputs to trigger them. Mutation-based fuzzing generates test inputs by modifying well-formed seed inputs randomly or heuristically. Most inputs are rejected at the early syntax parsing stage. Differently, generation-based fuzzing generates inputs from a specification (e.g., grammar). They can quickly carry the fuzzing beyond the syntax parsing stage. However, most inputs fail to pass the semantic checking (e.g., violating semantic rules), which restricts their capability of discovering deep bugs. In this paper, we propose a novel data-driven seed generation approach, named Skyfire, which leverages the knowledge in the vast amount of existing samples to generate well-distributed seed inputs for fuzzing programs that process highly-structured inputs. Skyfire takes as inputs a corpus and a grammar, and consists of two steps. The first step of Skyfire learns a probabilistic context-sensitive grammar (PCSG) to specify both syntax features and semantic rules, and then the second step leverages the learned PCSG to generate seed inputs. We fed the collected samples and the inputs generated by Skyfire as seeds of AFL to fuzz several open-source XSLT and XML engines (i.e., Sablotron, libxslt, and libxml2). The results have demonstrated that Skyfire can generate well-distributed inputs and thus significantly improve the code coverage (i.e., 20% for line coverage and 15% for function coverage on average) and the bug-finding capability of fuzzers. We also used the inputs generated by Skyfire to fuzz the closed-source JavaScript and rendering engine of Internet Explorer 11. Altogether, we discovered 19 new memory corruption bugs (among which there are 16 new vulnerabilities and received 33.5k USD bug bounty rewards) and 32 denial-of-service bugs.

Skyfire: Data-Driven Seed Generation for Fuzzing

Virtual machine monitors are becoming popular tools for the deployment of database management systems and other enterprise software applications. In this paper, we consider a common resource consolidation scenario, in which several database management system instances, each running in a virtual machine, are sharing a common pool of physical computing resources. We address the problem of optimizing the performance of these database management systems by controlling the configurations of the virtual machines in which they run. These virtual machine configurations determine how the shared physical resources will be allocated to the different database instances. We introduce a virtualization design advisor that uses information about the anticipated workloads of each of the database systems to recommend workload-specific configurations offine. Furthermore, runtime information collected after the deployment of the recommended configurations can be used to refine the recommendation. To estimate the effect of a particular resource allocation on workload performance, we use the query optimizer in a new what-if mode. We have implemented our approach using both PostgreSQL and DB2, and we have experimentally evaluated its effectiveness using DSS and OLTP workloads.

Automatic virtual machine configuration for database workloads

Energy efficiency is a primary constraint in modern systems. Approximate computing is a promising approach that trades quality of result for gains in efficiency and performance. State- of-the-art approximate programming models require extensive manual annotations on program data and operations to guarantee safe execution of approximate programs. The need for extensive manual annotations hinders the practical use of approximation techniques. This paper describes FlexJava, a small set of language extensions, that significantly reduces the annotation effort, paving the way for practical approximate programming. These extensions enable programmers to annotate approximation-tolerant method outputs. The FlexJava compiler, which is equipped with an approximation safety analysis, automatically infers the operations and data that affect these outputs and selectively marks them approximable while giving safety guarantees. The automation and the language–compiler codesign relieve programmers from manually and explicitly an- notating data declarations or operations as safe to approximate. FlexJava is designed to support safety, modularity, generality, and scalability in software development. We have implemented FlexJava annotations as a Java library and we demonstrate its practicality using a wide range of Java applications and by con- ducting a user study. Compared to EnerJ, a recent approximate programming system, FlexJava provides the same energy savings with significant reduction (from 2× to 17×) in the number of annotations. In our user study, programmers spend 6× to 12× less time annotating programs using FlexJava than when using EnerJ.

FlexJava: language support for safe and modular approximate programming

This book focuses on the core question of the necessary architectural support provided by hardware to efficiently run virtual machines, and of the corresponding design of the hypervisors that run them. Virtualization is still possible when the instruction set architecture lacks such support, but the hypervisor remains more complex and must rely on additional techniques. Despite the focus on architectural support in current architectures, some historical perspective is necessary to appropriately frame the problem. The first half of the book provides the historical perspective of the theoretical framework developed four decades ago by Popek and Goldberg. It also describes earlier systems that enabled virtualization despite the lack of architectural support in hardware. As is often the case, theory defines a necessary-but not sufficient-set of features, and modern architectures are the result of the combination of the theoretical framework with insights derived from practical systems. The second half of the book describes state-of-the-art support for virtualization in both x86-64 and ARM processors. This book includes an in-depth description of the CPU, memory, and I/O virtualization of these two processor architectures, as well as case studies on the Linux/KVM, VMware, and Xen hypervisors. It concludes with a performance comparison of virtualization on current-generation x86- and ARM-based systems across multiple hypervisors.

Hardware and Software Support for Virtualization

Reconfiguring your existing system to do something new is painful. Using VirtualBox is not.

VirtualBox: bits and bytes masquerading as machines

Podcasting for the penguin

Handle everyday research tasks with reliable, citation-backed results

Your personal Research Agent to handle research tasks with citation-backed results

Popular Tasks used by Researchers

How can I help with your research?

Meet SciSpace

Get more enhanced response by uploading the PDFs you want me to reference.

No relevant PDFs in your library

SciSpace is the AI research assistant for academics. Run systematic literature reviews on 280M+ papers, and write papers with cited sources. Trusted by 1M+ students, PhDs & researchers.

SciSpace | AI for Research

Analyze PDFs

Code & Manuscripts

Funding & Grants

Literature & Patents

Medical & Clinical Data

Systematic Review

Visualize & Present

Web & Data

Build a Google Scholar-like website for your research.

Build a website

Create charts and images for your research

Create a Chart

Write a paper for submission to a journal

Draft a manuscript

Patent Search

Design eye-catching scientific posters in minutes.

Scientific Poster Generation

Systematic Literature Review

One task is running at the moment. Your messages will be shown right after.

Drag and drop or click here to browse

Loved by <highlight>1 million+</highlight> researchers

Extract a list of specific topics and their sources from unstructured text

Topics

Compare and analyze relevant papers that matches with your search

Papers

Get insights from PDFs and bookmarked papers from your library

My library

Recent searches

Try searching for:

Catch AI-generated content in scholarly and non-scholarly content

{ai} Detector

Ai Writer

Get PDF Summaries, highlighted text explanations 

Chat with PDF

Effortlessly create in-text citations and bibliographies in APA and 2,500 other formats

Citation generator

Get explanations, summaries, and answers on academic papers

Ease up your research workflow with {scispace}'s cohort of exciting AI tools

Elevate your academic writing skills and convey your ideas the way you want

Paraphraser

Explore our range of reading and writing tools

Your file is being prepared and should be ready in a few minutes. If it's a large file, it might take a bit longer. You can close this window, and we'll email you the file when it's done.

You have reached a maximum limit of <strong>{limit}</strong> columns in the table. Remove at least <strong>1</strong> column to add or create another one.

Jon Watson

Author Tools

Chat about Author

Papers

VirtualBox: bits and bytes masquerading as machines

Podcasting for the penguin