The surprising success of cryptocurrencies has led to a surge of interest in deploying large scale, highly robust, Byzantine fault tolerant (BFT) protocols for mission-critical applications, such as financial transactions. Although the conventional wisdom is to build atop a (weakly) synchronous protocol such as PBFT (or a variation thereof), such protocols rely critically on network timing assumptions, and only guarantee liveness when the network behaves as expected. We argue these protocols are ill-suited for this deployment scenario.We present an alternative, HoneyBadgerBFT, the first practical asynchronous BFT protocol, which guarantees liveness without making any timing assumptions. We base our solution on a novel atomic broadcast protocol that achieves optimal asymptotic efficiency. We present an implementation and experimental results to show our system can achieve throughput of tens of thousands of transactions per second, and scales to over a hundred nodes on a wide area network. We even conduct BFT experiments over Tor, without needing to tune any parameters. Unlike the alternatives, HoneyBadgerBFT simply does not care about the underlying network.

Smart contracts are applications that execute on blockchains. Today they manage billions of dollars in value and motivate visionary plans for pervasive blockchain deployment. While smart contracts inherit the availability and other security assurances of blockchains, however, they are impeded by blockchains' lack of confidentiality and poor performance.We present Ekiden, a system that addresses these critical gaps by combining blockchains with Trusted Execution Environments (TEEs). Ekiden leverages a novel architecture that separates consensus from execution, enabling efficient TEE-backed confidentiality-preserving smart contracts and high scalability. Our prototype (with Tendermint as the consensus layer) achieves example performance of 600x more throughput and 400x less latency at 1000x less cost than the Ethereum mainnet.Another contribution of this paper is that we systematically identify and treat the pitfalls arising from harmonizing TEEs and blockchains. Treated separately, both TEEs and blockchains provide powerful guarantees, but hybridized, though, they engender new attacks. For example, in naïve designs, privacy in TEE-backed contracts can be jeopardized by forgery of blocks, a seemingly unrelated attack vector. We believe the insights learned from Ekiden will prove to be of broad importance in hybridized TEE-blockchain systems.

BackgroundThe increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools.ResultsIn this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions.ConclusionsWith SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined.

PMR2 is available under an open source license at http://www.cellml.org/tools/pmr/; a fully functional instance of this software can be accessed at http://models.physiomeproject.org/.

BackgroundWith the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been proposed that can be used to describe models, simulations, data or other essential information in a consistent fashion. These constitute various separate components required to reproduce a given published scientific result.ResultsWe describe the Open Modeling EXchange format (OMEX). Together with the use of other standard formats from the Computational Modeling in Biology Network (COMBINE), OMEX is the basis of the COMBINE Archive, a single file that supports the exchange of all the information necessary for a modeling and simulation experiment in biology. An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing the model. The content of a COMBINE Archive consists of files encoded in COMBINE standards whenever possible, but may include additional files defined by an Internet Media Type. Several tools that support the COMBINE Archive are available, either as independent libraries or embedded in modeling software.ConclusionsThe COMBINE Archive facilitates the reproduction of modeling and simulation experiments in biology by embedding all the relevant information in one file. Having all the information stored and exchanged at once also helps in building activity logs and audit trails. We anticipate that the COMBINE Archive will become a significant help for modellers, as the domain moves to larger, more complex experiments such as multi-scale models of organs, digital organisms, and bioengineering.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-014-0369-z) contains supplementary material, which is available to authorized users.