Consistency Models with Global Operation Sequencing and their Composition

Modern distributed systems often achieve availability and scalability by providing consistency guarantees about the data they manage weaker than linearizability. We consider a class of such consistency models that, despite this weakening, guarantee that clients eventually agree on a global sequence of operations, while seeing a subsequence of this final sequence at any given point of time. Examples of such models include the classical Total Store Order (TSO) and recently proposed dual TSO, Global Sequence Protocol (GSP) and Ordered Sequential Consistency. We define a unified model, called Global Sequence Consistency (GSC), that has the above models as its special cases, and investigate its key properties. First, we propose a condition under which multiple objects each satisfying GSC can be composed so that the whole set of objects satisfies GSC. Second, we prove an interesting relationship between special cases of GSC - GSP, TSO and dual TSO: we show that clients that do not communicate out-of-band cannot tell the difference between these models. To obtain these results, we propose a novel axiomatic specification of GSC and prove its equivalence to the operational definition of the model

Chainspace: A Sharded Smart Contracts Platform

Chainspace is a decentralized infrastructure, known as a distributed ledger, that supports user defined smart contracts and executes user-supplied transactions on their objects. The correct execution of smart contract transactions is verifiable by all. The system is scalable, by sharding state and the execution of transactions, and using S-BAC, a distributed commit protocol, to guarantee consistency. Chainspace is secure against subsets of nodes trying to compromise its integrity or availability properties through Byzantine Fault Tolerance (BFT), and extremely high-auditability, non-repudiation and `blockchain' techniques. Even when BFT fails, auditing mechanisms are in place to trace malicious participants. We present the design, rationale, and details of Chainspace; we argue through evaluating an implementation of the system about its scaling and other features; we illustrate a number of privacy-friendly smart contracts for smart metering, polling and banking and measure their performance

Language and tool support for event refinement structures in Event-B

Event-B is a formal method for modelling and verifying the consistency of chains of model refinements. The event refinement structure (ERS) approach augments Event-B with a graphical notation which is capable of explicit representation of control flows and refinement relationships. In previous work, the ERS approach has been evaluated manually in the development of two large case studies, a multimedia protocol and a spacecraft sub-system. The evaluation results helped us to extend the ERS constructors, to develop a systematic definition of ERS, and to develop a tool supporting ERS. We propose the ERS language which systematically defines the semantics of the ERS graphical notation including the constructors. The ERS tool supports automatic construction of the Event-B models in terms of control flows and refinement relationships. In this paper we outline the systematic definition of ERS including the presentation of constructors, the tool that supports it and evaluate the contribution that ERS and its tool make. Also we present how the systematic definition of ERS and the corresponding tool can ensure a consistent encoding of the ERS diagrams in the Event-B models

A systematic approach to atomicity decomposition in Event-B

Event-B is a state-based formal method that supports a refinement process in which an abstract model is elaborated towards an implementation in a step-wise manner. One weakness of Event-B is that control flow between events is typically modelled implicitly via variables and event guards. While this fits well with Event-B refinement, it can make models involving sequencing of events more difficult to specify and understand than if control flow was explicitly specified. New events may be introduced in Event-B refinement and these are often used to decompose the atomicity of an abstract event into a series of steps. A second weakness of Event-B is that there is no explicit link between such new events that represent a step in the decomposition of atomicity and the abstract event to which they contribute. To address these weaknesses, atomicity decomposition diagrams support the explicit modelling of control flow and refinement relationships for new events. In previous work,the atomicity decomposition approach has been evaluated manually in the development of two large case studies, a multi media protocol and a spacecraft sub-system. The evaluation results helped us to develop a systematic definition of the atomicity decomposition approach, and to develop a tool supporting the approach. In this paper we outline this systematic definition of the approach, the tool that supports it and evaluate the contribution that the tool makes

A multi-modal data resource for investigating topographic heterogeneity in patient-derived xenograft tumors.

Patient-derived xenografts (PDXs) are an essential pre-clinical resource for investigating tumor biology. However, cellular heterogeneity within and across PDX tumors can strongly impact the interpretation of PDX studies. Here, we generated a multi-modal, large-scale dataset to investigate PDX heterogeneity in metastatic colorectal cancer (CRC) across tumor models, spatial scales and genomic, transcriptomic, proteomic and imaging assay modalities. To showcase this dataset, we present analysis to assess sources of PDX variation, including anatomical orientation within the implanted tumor, mouse contribution, and differences between replicate PDX tumors. A unique aspect of our dataset is deep characterization of intra-tumor heterogeneity via immunofluorescence imaging, which enables investigation of variation across multiple spatial scales, from subcellular to whole tumor levels. Our study provides a benchmark data resource to investigate PDX models of metastatic CRC and serves as a template for future, quantitative investigations of spatial heterogeneity within and across PDX tumor models

Applying Atomicity and Model Decomposition to a Space Craft System in Event-B

Event-B is a formal method for modeling and verifying consistency of systems. In formal methods such as Event-B, refinement is the process of enriching or modifying an abstract model in a step-wise manner in order to manage the development of complex and large systems. To further alleviate the complexity of developing large systems, Event-B refinement can be augmented with two techniques, namely atomicity decomposition and model decomposition. Our main objective in this paper is to investigate and evaluate the application of these techniques when used in a refinement based development. These techniques have been applied to the formal development of a space craft system. The outcomes of this experimental work are presented as assessment results. The experience and assessment can form the basis for some guidelines in applying these techniques in future cases

TITER: predicting translation initiation sites by deep learning.

MotivationTranslation initiation is a key step in the regulation of gene expression. In addition to the annotated translation initiation sites (TISs), the translation process may also start at multiple alternative TISs (including both AUG and non-AUG codons), which makes it challenging to predict TISs and study the underlying regulatory mechanisms. Meanwhile, the advent of several high-throughput sequencing techniques for profiling initiating ribosomes at single-nucleotide resolution, e.g. GTI-seq and QTI-seq, provides abundant data for systematically studying the general principles of translation initiation and the development of computational method for TIS identification.MethodsWe have developed a deep learning-based framework, named TITER, for accurately predicting TISs on a genome-wide scale based on QTI-seq data. TITER extracts the sequence features of translation initiation from the surrounding sequence contexts of TISs using a hybrid neural network and further integrates the prior preference of TIS codon composition into a unified prediction framework.ResultsExtensive tests demonstrated that TITER can greatly outperform the state-of-the-art prediction methods in identifying TISs. In addition, TITER was able to identify important sequence signatures for individual types of TIS codons, including a Kozak-sequence-like motif for AUG start codon. Furthermore, the TITER prediction score can be related to the strength of translation initiation in various biological scenarios, including the repressive effect of the upstream open reading frames on gene expression and the mutational effects influencing translation initiation efficiency.Availability and implementationTITER is available as an open-source software and can be downloaded from https://github.com/zhangsaithu/titer [email protected] or [email protected] informationSupplementary data are available at Bioinformatics online

A compiler approach to scalable concurrent program design

The programmer's most powerful tool for controlling complexity in program design is abstraction. We seek to use abstraction in the design of concurrent programs, so as to separate design decisions concerned with decomposition, communication, synchronization, mapping, granularity, and load balancing. This paper describes programming and compiler techniques intended to facilitate this design strategy. The programming techniques are based on a core programming notation with two important properties: the ability to separate concurrent programming concerns, and extensibility with reusable programmer-defined abstractions. The compiler techniques are based on a simple transformation system together with a set of compilation transformations and portable run-time support. The transformation system allows programmer-defined abstractions to be defined as source-to-source transformations that convert abstractions into the core notation. The same transformation system is used to apply compilation transformations that incrementally transform the core notation toward an abstract concurrent machine. This machine can be implemented on a variety of concurrent architectures using simple run-time support. The transformation, compilation, and run-time system techniques have been implemented and are incorporated in a public-domain program development toolkit. This toolkit operates on a wide variety of networked workstations, multicomputers, and shared-memory multiprocessors. It includes a program transformer, concurrent compiler, syntax checker, debugger, performance analyzer, and execution animator. A variety of substantial applications have been developed using the toolkit, in areas such as climate modeling and fluid dynamics