Donal Fellows

The Taverna workflow tool suite (http://www.taverna.org.uk) is designed to combine distributed Web Services and/or local tools into complex analysis pipelines. These pipelines can be executed on local desktop machines or through larger infrastructure (such as supercomputers, Grids or cloud environments), using the Taverna Server. In bioinformatics, Taverna workflows are typically used in the areas of high-throughput omics analyses (for example, proteomics or transcriptomics), or for evidence gathering methods involving text mining or data mining. Through Taverna, scientists have access to several thousand different tools and resources that are freely available from a large range of life science institutions. Once constructed, the workflows are reusable, executable bioinformatics protocols that can be shared, reused and repurposed. A repository of public workflows is available at http://www.myexperiment.org. This article provides an update to the Taverna tool suite, highlighting new features and developments in the workbench and the Taverna Server.

Abstract The microbial production of fine chemicals provides a promising biosustainable manufacturing solution that has led to the successful production of a growing catalog of natural products and high-value chemicals. However, development at industrial levels has been hindered by the large resource investments required. Here we present an integrated Design–Build-Test–Learn (DBTL) pipeline for the discovery and optimization of biosynthetic pathways, which is designed to be compound agnostic and automated throughout. We initially applied the pipeline for the production of the flavonoid (2 S )-pinocembrin in Escherichia coli , to demonstrate rapid iterative DBTL cycling with automation at every stage. In this case, application of two DBTL cycles successfully established a production pathway improved by 500-fold, with competitive titers up to 88 mg L −1 . The further application of the pipeline to optimize an alkaloids pathway demonstrates how it could facilitate the rapid optimization of microbial strains for production of any chemical compound of interest.

In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline 10 lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers. We also outline the important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.

The authors examined the magnetic resonance (MR) appearance of inverted papillomas to determine if this histologically benign lesion could be distinguished from malignancies of the sinonasal cavity. MR images in 10 patients with histologically proved inverted papilloma were retrospectively reviewed. The signal intensity of inverted papillomas on short repetition time (TR) images was iso- to slightly hypertintense to muscle in all 10 patients. Inverted papillomas had intermediate signal intensity on the long TR/echo time (TE) images. The tumors were iso- or slightly hypointense to fat on long TR/short TE images. In the seven patients who received gadopentetate dimeglumine, all inverted papillomas showed solid inhomogeneous enhancement. A review of eight sinonasal malignancies showed no distinctive signal intensity or enhancement characteristics to help differentiate inverted papillomas from various malignant tumors. The authors conclude that there is no signature MR appearance for the benign inverted papilloma. The main utility of MR imaging is in defining the extent of the lesion.

This work presents sPyNNaker 4.0.0, the latest version of the software package for simulating PyNN-defined spiking neural networks (SNNs) on the SpiNNaker neuromorphic platform. Operations underpinning realtime SNN execution are presented, including an event-based operating system facilitating efficient time-driven neuron state updates and pipelined event-driven spike processing. Preprocessing, realtime execution, and neuron/synapse model implementations are discussed, all in the context of a simple example SNN. Simulation results are demonstrated, together with performance profiling providing insights into how software interacts with the underlying hardware to achieve realtime execution. System performance is shown to be within a factor of 2 of the original design target of 10,000 synaptic events per millisecond, however SNN topology is shown to influence performance considerably. A cost model is therefore developed characterizing the effect of network connectivity and SNN partitioning. This model enables users to estimate SNN simulation performance, allows the SpiNNaker team to make predictions on the impact of performance improvements, and helps demonstrate the continued potential of the SpiNNaker neuromorphic hardware.