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16 Publications visible to you, out of a total of 16
MGnify: the microbiome analysis resource in 2020
MGnify

Abstract (Expand)

MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in … particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline with multiple analysis pipelines that are tailored according to the input data, and that are formally described using the Common Workflow Language, enabling greater provenance, reusability, and reproducibility. MGnify's new analysis pipelines offer additional approaches for taxonomic assertions based on ribosomal internal transcribed spacer regions (ITS1/2) and expanded protein functional annotations. Biochemical pathways and systems predictions have also been added for assembled contigs. MGnify's growing focus on the assembly of metagenomic data has also seen the number of datasets it has assembled and analysed increase six-fold. The non-redundant protein database constructed from the proteins encoded by these assemblies now exceeds 1 billion sequences. Meanwhile, a newly developed contig viewer provides fine-grained visualisation of the assembled contigs and their enriched annotations.

Authors: Alex L Mitchell, Alexandre Almeida, Martin Beracochea, Miguel Boland, Josephine Burgin, Guy Cochrane, Michael R Crusoe, Varsha Kale, Simon C Potter, Lorna J Richardson, Ekaterina Sakharova, Maxim Scheremetjew, Anton Korobeynikov, Alex Shlemov, Olga Kunyavskaya, Alla Lapidus, Robert D Finn

Date Published: 7th Nov 2019

Publication Type: Journal

MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction.
QCIF Bioinformatics

Abstract (Expand)

BACKGROUND: Oxford Nanopore Technology (ONT) long-read sequencing has become a popular platform for microbial researchers due to the accessibility and affordability of its devices. However, easy and … automated construction of high-quality bacterial genomes using nanopore reads remains challenging. Here we aimed to create a reproducible end-to-end bacterial genome assembly pipeline using ONT in combination with Illumina sequencing. RESULTS: We evaluated the performance of several popular tools used during genome reconstruction, including base-calling, filtering, assembly, and polishing. We also assessed overall genome accuracy using ONT both natively and with Illumina. All steps were validated using the high-quality complete reference genome for the Escherichia coli sequence type (ST)131 strain EC958. Software chosen at each stage were incorporated into our final pipeline, MicroPIPE. Further validation of MicroPIPE was carried out using 11 additional ST131 E. coli isolates, which demonstrated that complete circularised chromosomes and plasmids could be achieved without manual intervention. Twelve publicly available Gram-negative and Gram-positive bacterial genomes (with available raw ONT data and matched complete genomes) were also assembled using MicroPIPE. We found that revised basecalling and updated assembly of the majority of these genomes resulted in improved accuracy compared to the current publicly available complete genomes. CONCLUSIONS: MicroPIPE is built in modules using Singularity container images and the bioinformatics workflow manager Nextflow, allowing changes and adjustments to be made in response to future tool development. Overall, MicroPIPE provides an easy-access, end-to-end solution for attaining high-quality bacterial genomes. MicroPIPE is available at https://github.com/BeatsonLab-MicrobialGenomics/micropipe .

Authors: V. Murigneux, L. W. Roberts, B. M. Forde, M. D. Phan, N. T. K. Nhu, A. D. Irwin, P. N. A. Harris, D. L. Paterson, M. A. Schembri, D. M. Whiley, S. A. Beatson

Date Published: 25th Jun 2021

Publication Type: Journal

Perspectives on automated composition of workflows in the life sciences
FAIR Computational Workflows

Abstract (Expand)

Scientific data analyses often combine several computational tools in automated pipelines, or workflows. Thousands of such workflows have been used in the life sciences, though their composition has …mposition has remained a cumbersome manual process due to a lack of standards for annotation, assembly, and implementation. Recent technological advances have returned the long-standing vision of automated workflow composition into focus. This article summarizes a recent Lorentz Center workshop dedicated to automated composition of workflows in the life sciences. We survey previous initiatives to automate the composition process, and discuss the current state of the art and future perspectives. We start by drawing the “big picture” of the scientific workflow development life cycle, before surveying and discussing current methods, technologies and practices for semantic domain modelling, automation in workflow development, and workflow assessment. Finally, we derive a roadmap of individual and community-based actions to work toward the vision of automated workflow development in the forthcoming years. A central outcome of the workshop is a general description of the workflow life cycle in six stages: 1) scientific question or hypothesis, 2) conceptual workflow, 3) abstract workflow, 4) concrete workflow, 5) production workflow, and 6) scientific results. The transitions between stages are facilitated by diverse tools and methods, usually incorporating domain knowledge in some form. Formal semantic domain modelling is hard and often a bottleneck for the application of semantic technologies. However, life science communities have made considerable progress here in recent years and are continuously improving, renewing interest in the application of semantic technologies for workflow exploration, composition and instantiation. Combined with systematic benchmarking with reference data and large-scale deployment of production-stage workflows, such technologies enable a more systematic process of workflow development than we know today. We believe that this can lead to more robust, reusable, and sustainable workflows in the future.

Authors: Anna-Lena Lamprecht, Magnus Palmblad, Jon Ison, Veit Schwämmle, Mohammad Sadnan Al Manir, Ilkay Altintas, Christopher J. O. Baker, Ammar Ben Hadj Amor, Salvador Capella-Gutierrez, Paulos Charonyktakis, Michael R. Crusoe, Yolanda Gil, Carole Goble, Timothy J. Griffin, Paul Groth, Hans Ienasescu, Pratik Jagtap, Matúš Kalaš, Vedran Kasalica, Alireza Khanteymoori, Tobias Kuhn, Hailiang Mei, Hervé Ménager, Steffen Möller, Robin A. Richardson, Vincent Robert, Stian Soiland-Reyes, Robert Stevens, Szoke Szaniszlo, Suzan Verberne, Aswin Verhoeven, Katherine Wolstencroft

Date Published: 2021

Publication Type: Journal

Perspectives on automated composition of workflows in the life sciences
Testing

Abstract

Not specified

Authors: Anna-Lena Lamprecht, Magnus Palmblad, Jon Ison, Veit Schwämmle, Mohammad Sadnan Al Manir, Ilkay Altintas, Christopher J. O. Baker, Ammar Ben Hadj Amor, Salvador Capella-Gutierrez, Paulos Charonyktakis, Michael R. Crusoe, Yolanda Gil, Carole Goble, Timothy J. Griffin, Paul Groth, Hans Ienasescu, Pratik Jagtap, Matúš Kalaš, Vedran Kasalica, Alireza Khanteymoori, Tobias Kuhn, Hailiang Mei, Hervé Ménager, Steffen Möller, Robin A. Richardson, Vincent Robert, Stian Soiland-Reyes, Robert Stevens, Szoke Szaniszlo, Suzan Verberne, Aswin Verhoeven, Katherine Wolstencroft

Date Published: 2021

Publication Type: Journal

Ten simple rules for making a software tool workflow-ready
Specimen Data Refinery, FAIR Computational Workflows

Abstract (Expand)

Workflows have become a core part of computational scientific analysis in recent years. Automated computational workflows multiply the power of researchers, potentially turning “hand-cranked” data …data processing by informaticians into robust factories for complex research output. However, in order for a piece of software to be usable as a workflow-ready tool, it may require alteration from its likely origin as a standalone tool. Research software is often created in response to the need to answer a research question with the minimum expenditure of time and money in resource-constrained projects. The level of quality might range from “it works on my computer” to mature and robust projects with support across multiple operating systems. Despite significant increase in uptake of workflow tools, there is little specific guidance for writing software intended to slot in as a tool within a workflow; or on converting an existing standalone research-quality software tool into a reusable, composable, well-behaved citizen within a larger workflow. In this paper we present 10 simple rules for how a software tool can be prepared for workflow use.

Authors: Paul Brack, Peter Crowther, Stian Soiland-Reyes, Stuart Owen, Douglas Lowe, Alan R. Williams, Quentin Groom, Mathias Dillen, Frederik Coppens, Björn Grüning, Ignacio Eguinoa, Philip Ewels, Carole Goble

Date Published: 24th Mar 2022

Publication Type: Journal

The Specimen Data Refinery: A Canonical Workflow Framework and FAIR Digital Object Approach to Speeding up Digital Mobilisation of Natural History Collections
Specimen Data Refinery, FAIR Computational Workflows

Abstract (Expand)

A key limiting factor in organising and using information from physical specimens curated in natural science collections is making that information computable, with institutional digitization tending … to focus more on imaging the specimens themselves than on efficiently capturing computable data about them. Label data are traditionally manually transcribed today with high cost and low throughput, rendering such a task constrained for many collection-holding institutions at current funding levels. We show how computer vision, optical character recognition, handwriting recognition, named entity recognition and language translation technologies can be implemented into canonical workflow component libraries with findable, accessible, interoperable, and reusable (FAIR) characteristics. These libraries are being developed in a cloud- based workflow platform—the ‘Specimen Data Refinery’ (SDR)—founded on Galaxy workflow engine, Common Workflow Language, Research Object Crates (RO-Crate) and WorkflowHub technologies. The SDR can be applied to specimens’ labels and other artefacts, offering the prospect of greatly accelerated and more accurate data capture in computable form. Two kinds of FAIR Digital Objects (FDO) are created by packaging outputs of SDR workflows and workflow components as digital objects with metadata, a persistent identifier, and a specific type definition. The first kind of FDO are computable Digital Specimen (DS) objects that can be consumed/produced by workflows, and other applications. A single DS is the input data structure submitted to a workflow that is modified by each workflow component in turn to produce a refined DS at the end. The Specimen Data Refinery provides a library of such components that can be used individually, or in series. To cofunction, each library component describes the fields it requires from the DS and the fields it will in turn populate or enrich. The second kind of FDO, RO-Crates gather and archive the diverse set of digital and real-world resources, configurations, and actions (the provenance) contributing to a unit of research work, allowing that work to be faithfully recorded and reproduced. Here we describe the Specimen Data Refinery with its motivating requirements, focusing on what is essential in the creation of canonical workflow component libraries and its conformance with the requirements of an emerging FDO Core Specification being developed by the FDO Forum.

Authors: Alex Hardisty, Paul Brack, Carole Goble, Laurence Livermore, Ben Scott, Quentin Groom, Stuart Owen, Stian Soiland-Reyes

Date Published: 7th Mar 2022

Publication Type: Journal

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