2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador

Background: Rhodnius ecuadoriensis is the main triatomine vector of Chagas disease, American trypanosomiasis, in Southern Ecuador and Northern Peru. Genomic approaches and next generation sequencing technologies have become powerful tools for investigating population diversity and structure which is a key consideration for vector control. Here we assess the effectiveness of three different 2b restriction site-associated DNA (2b-RAD) genotyping strategies in R. ecuadoriensis to provide sufficient genomic resolution to tease apart microevolutionary processes and undertake some pilot population genomic analyses. Methodology/Principal findings: The 2b-RAD protocol was carried out in-house at a non-specialized laboratory using 20 R. ecuadoriensis adults collected from the central coast and southern Andean region of Ecuador, from June 2006 to July 2013. 2b-RAD sequencing data was performed on an Illumina MiSeq instrument and analyzed with the STACKS de novo pipeline for loci assembly and Single Nucleotide Polymorphism (SNP) discovery. Preliminary population genomic analyses (global AMOVA and Bayesian clustering) were implemented. Our results showed that the 2b-RAD genotyping protocol is effective for R. ecuadoriensis and likely for other triatomine species. However, only BcgI and CspCI restriction enzymes provided a number of markers suitable for population genomic analysis at the read depth we generated. Our preliminary genomic analyses detected a signal of genetic structuring across the study area. Conclusions/Significance: Our findings suggest that 2b-RAD genotyping is both a cost effective and methodologically simple approach for generating high resolution genomic data for Chagas disease vectors with the power to distinguish between different vector populations at epidemiologically relevant scales. As such, 2b-RAD represents a powerful tool in the hands of medical entomologists with limited access to specialized molecular biological equipment. Author summary: Understanding Chagas disease vector (triatomine) population dispersal is key for the design of control measures tailored for the epidemiological situation of a particular region. In Ecuador, Rhodnius ecuadoriensis is a cause of concern for Chagas disease transmission, since it is widely distributed from the central coast to southern Ecuador. Here, a genome-wide sequencing (2b-RAD) approach was performed in 20 specimens from four communities from Manabí (central coast) and Loja (southern) provinces of Ecuador, and the effectiveness of three type IIB restriction enzymes was assessed. The findings of this study show that this genotyping methodology is cost effective in R. ecuadoriensis and likely in other triatomine species. In addition, preliminary population genomic analysis results detected a signal of population structure among geographically distinct communities and genetic variability within communities. As such, 2b-RAD shows significant promise as a relatively low-tech solution for determination of vector population genomics, dynamics, and spread

Timing Aware Information Flow Security for a JavaCard-like Bytecode

AbstractCommon protection mechanisms fail to provide end-to-end security; programs with legitimate access to secret information are not prevented from leaking this to the world. Information-flow aware analyses track the flow of information through the program to prevent such leakages, but often ignore information flows through covert channels even though they pose a serious threat. A typical covert channel is to use the timing of certain events to carry information. We present a timing-aware information-flow type system for a low-level language similar to a non-trivial subset of a sequential Java bytecode. The type system is parameterized over the time model of the instructions of the language and over the algorithm enforcing low-observational equivalence, used in the prevention of implicit and timing flows

Mechanising and verifying the WebAssembly specification

WebAssembly is a new low-level language currently being implemented in all major web browsers. It is designed to become the universal compilation target for the web, obsoleting existing solutions in this area, such as asm.js and Native Client. The WebAssembly working group has incorporated formal techniques into the development of the language, but their efforts so far have focussed on pen and paper formal specification. We present a mechanised Isabelle specification for the WebAssembly language, together with a verified executable interpreter and type checker. Moreover, we present a fully mechanised proof of the soundness of the WebAssembly type system, and detail how our work on this proof has exposed several issues with the official WebAssembly specification, influencing its development. Finally, we give a brief account of our efforts in performing differential fuzzing of our interpreter against industry implementations

A formally verified compiler back-end

This article describes the development and formal verification (proof of semantic preservation) of a compiler back-end from Cminor (a simple imperative intermediate language) to PowerPC assembly code, using the Coq proof assistant both for programming the compiler and for proving its correctness. Such a verified compiler is useful in the context of formal methods applied to the certification of critical software: the verification of the compiler guarantees that the safety properties proved on the source code hold for the executable compiled code as well

Particpants' Proceedings on the Workshop: Types for Program Analysis

As a satellite meeting of the TAPSOFT'95 conference we organized a small workshop on program analysis. The title of the workshop, ``Types for Program Analysis´´, was motivated by the recent trend of letting the presentation and development of program analyses be influenced by annotated type systems, effect systems, and more general logical systems. The contents of the workshop was intended to be somewhat broader; consequently the call for participation listed the following areas of interest:- specification of specific analyses for programming languages,- the role of effects, polymorphism, conjunction/disjunction types, dependent types etc.in specification of analyses,- algorithmic tools and methods for solving general classes of type-based analyses,- the role of unification, semi-unification etc. in implementations of analyses,- proof techniques for establishing the safety of analyses,- relationship to other approaches to program analysis, including abstract interpretation and constraint-based methods,- exploitation of analysis results in program optimization and implementation.The submissions were not formally refereed; however each submission was read by several members of the program committee and received detailed comments and suggestions for improvement. We expect that several of the papers, in slightly revised forms, will show up at future conferences. The workshop took place at Aarhus University on May 26 and May 27 and lasted two half days

Continuing WebAssembly with Effect Handlers

WebAssembly (Wasm) is a low-level portable code format offering near native performance. It is intended as a compilation target for a wide variety of source languages. However, Wasm provides no direct support for non-local control flow features such as async/await, generators/iterators, lightweight threads, first-class continuations, etc. This means that compilers for source languages with such features must ceremoniously transform whole source programs in order to target Wasm. We present WasmFX an extension to Wasm which provides a universal target for non-local control features via effect handlers, enabling compilers to translate such features directly into Wasm. Our extension is minimal and only adds three main instructions for creating, suspending, and resuming continuations. Moreover, our primitive instructions are type-safe providing typed continuations which are well-aligned with the design principles of Wasm whose stacks are typed. We present a formal specification of WasmFX and show that the extension is sound. We have implemented WasmFX as an extension to the Wasm reference interpreter and also built a prototype WasmFX extension for Wasmtime, a production-grade Wasm engine, piggybacking on Wasmtime's existing fibers API. The preliminary performance results for our prototype are encouraging, and we outline future plans to realise a native implementation

Safely Speaking in Tongues: Statically Checking Domain Specific Languages in Haskell

Haskell makes it very easy to build and use Domain Specific Languages (DSLs). However, it is frequently the case that a DSL has invariants that can not be easily enforced statically, resulting in runtime checks. This is a great pity given HaskellÆs rich and powerful type system and leads to all the usual problems of dynamic checking. We believe that Domain Specific Languages are becoming more popular: the internet itself is a good example of many DSLs (HTML, CSS, JavaScript, Flash, etc), and more seem to be being added every day; most graphics cards already accept programs written in the DSL OpenGL Shading Language (GLSL); and the predicted growth of heterogeneous CPUs (for example IBMÆs Cell CPU) will demand many different DSLs for the various programming models and instruction sets that become available. We present a technique that allows invariants of any given DSL to be lifted into the Haskell type system. This removes the need for runtime checks of the DSL and prevents programs that violate the invariants of the DSL from ever being compiled or executed. As a result we avoid the pitfalls of dynamic checking and return the user of the DSL to the safety and tranquillity of the strongly statically typed Haskell world

Verificación estática de confidencialidad en un sistema de múltiples niveles de seguridad basado en Java bytecode

Debido al incremento en la cantidad e importancia de la información manejada por sistemas informáticos, también se incrementa la importancia de controlar la difusión de información privada de los usuarios. Los mecanismos de control del acceso y las técnicas criptográficas aseguran que la información sólo es accedida por entidades autorizadas, pero resultan insuficientes puesto que una vez que la información es accedida no existe control sobre su distribución. Extender el sistema de tipos de un lenguaje de programación agregando niveles de seguridad permite analizar estáticamente, antes de su ejecución, cómo un programa accede y utiliza la información confidencial. El creciente uso de código móvil –software obtenido de la red y ejecutado localmente, generalmente en Java bytecode– resalta la importancia de aplicar estos análisis de confidencialidad a lenguajes de bajo nivel. En este proyecto desarrollaremos un sistema de tipos para Java bytecode extendido con información de seguridad e implementaremos un chequeador de tipos que verifique la confidencialidad de la información local accedida por código móvil. También estudiaremos la desclasificación controlada de información, a fin de incluir en nuestro análisis a programas que inevitablemente revelan información confidencial, por ejemplo, al responder negativamente ante una contraseña inválida.Eje: Nuevas Tecnologías en desarrollo de Sistemas de SoftwareRed de Universidades con Carreras en Informática (RedUNCI