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Article ; Online: Application of a bioinformatics training delivery method for reaching dispersed and distant trainees.

Hall, Christina R / Griffin, Philippa C / Lonie, Andrew J / Christiansen, Jeffrey H

2021 Volume 17, Issue 3, Page(s) e1008715

Abstract: Many initiatives have addressed the global need to upskill biologists in bioinformatics tools and techniques. Australia is not unique in its requirement for such training, but due to its large size and relatively small and geographically dispersed ... ...

Abstract	Many initiatives have addressed the global need to upskill biologists in bioinformatics tools and techniques. Australia is not unique in its requirement for such training, but due to its large size and relatively small and geographically dispersed population, Australia faces specific challenges. A combined training approach was implemented by the authors to overcome these challenges. The "hybrid" method combines guidance from experienced trainers with the benefits of both webinar-style delivery and concurrent face-to-face hands-on practical exercises in classrooms. Since 2017, the hybrid method has been used to conduct 9 hands-on bioinformatics training sessions at international scale in which over 800 researchers have been trained in diverse topics on a range of software platforms. The method has become a key tool to ensure scalable and more equitable delivery of short-course bioinformatics training across Australia and can be easily adapted to other locations, topics, or settings.
MeSH term(s)	Australia ; Biomedical Research/education ; Biomedical Research/methods ; Biomedical Research/organization & administration ; Computational Biology/education ; Computational Biology/methods ; Computational Biology/organization & administration ; Education, Distance/methods ; Humans
Language	English
Publishing date	2021-03-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1008715
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: CloudLaunch: Discover and Deploy Cloud Applications.

Afgan, Enis / Lonie, Andrew / Taylor, James / Goonasekera, Nuwan

Future generations computer systems : FGCS

2018 Volume 94, Page(s) 802–810

Abstract: Cloud computing is a common platform for delivering software to end users. However, the process of making complex-to-deploy applications available across different cloud providers requires isolated and uncoordinated application-specific solutions, often ... ...

Abstract	Cloud computing is a common platform for delivering software to end users. However, the process of making complex-to-deploy applications available across different cloud providers requires isolated and uncoordinated application-specific solutions, often locking-in developers to a particular cloud provider. Here, we present the CloudLaunch application as a uniform platform for discovering and deploying applications for different cloud providers. CloudLaunch allows arbitrary applications to be added to a catalog with each application having its own customizable user interface and control over the launch process, while preserving cloud-agnosticism so that authors can easily make their applications available on multiple clouds with minimal effort. It then provides a uniform interface for launching available applications by end users across different cloud providers. Architecture details are presented along with examples of different deployable applications that highlight architectural features.
Language	English
Publishing date	2018-06-15
Publishing country	Netherlands
Document type	Journal Article
ISSN	0167-739X
ISSN	0167-739X
DOI	10.1016/j.future.2018.04.037
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Article: CloudBridge: a Simple Cross-Cloud Python Library.

Goonasekera, Nuwan / Lonie, Andrew / Taylor, James / Afgan, Enis

Proceedings of XSEDE16 : Diversity, Big Data, and Science at Scale : July 17-21, 2016, Intercontinental Miami Hotel, Miami, Florida, USA. Conference on Extreme Science and Engineering Discovery Environment (5th : 2016 : Miami, Fla.)

2016 Volume 2016

Abstract: With clouds becoming a standard target for deploying applications, it is more important than ever to be able to seamlessly utilise resources and services from multiple providers. Proprietary vendor APIs make this challenging and lead to conditional code ... ...

Abstract	With clouds becoming a standard target for deploying applications, it is more important than ever to be able to seamlessly utilise resources and services from multiple providers. Proprietary vendor APIs make this challenging and lead to conditional code being written to accommodate various API differences, requiring application authors to deal with these complexities and to test their applications against each supported cloud. In this paper, we describe an open source Python library called CloudBridge that provides a simple, uniform, and extensible API for multiple clouds. The library defines a standard 'contract' that all supported providers must implement, and an extensive suite of conformance tests to ensure that any exposed behavior is uniform across cloud providers, thus allowing applications to confidently utilise any of the supported clouds without any cloud-specific code or testing.
Language	English
Publishing date	2016-07-17
Publishing country	United States
Document type	Journal Article
DOI	10.1145/2949550.2949648
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Article ; Online: Investigating reproducibility and tracking provenance - A genomic workflow case study.

Kanwal, Sehrish / Khan, Farah Zaib / Lonie, Andrew / Sinnott, Richard O

BMC bioinformatics

2017 Volume 18, Issue 1, Page(s) 337

Abstract: Background: Computational bioinformatics workflows are extensively used to analyse genomics data, with different approaches available to support implementation and execution of these workflows. Reproducibility is one of the core principles for any ... ...

Abstract	Background: Computational bioinformatics workflows are extensively used to analyse genomics data, with different approaches available to support implementation and execution of these workflows. Reproducibility is one of the core principles for any scientific workflow and remains a challenge, which is not fully addressed. This is due to incomplete understanding of reproducibility requirements and assumptions of workflow definition approaches. Provenance information should be tracked and used to capture all these requirements supporting reusability of existing workflows. Results: We have implemented a complex but widely deployed bioinformatics workflow using three representative approaches to workflow definition and execution. Through implementation, we identified assumptions implicit in these approaches that ultimately produce insufficient documentation of workflow requirements resulting in failed execution of the workflow. This study proposes a set of recommendations that aims to mitigate these assumptions and guides the scientific community to accomplish reproducible science, hence addressing reproducibility crisis. Conclusions: Reproducing, adapting or even repeating a bioinformatics workflow in any environment requires substantial technical knowledge of the workflow execution environment, resolving analysis assumptions and rigorous compliance with reproducibility requirements. Towards these goals, we propose conclusive recommendations that along with an explicit declaration of workflow specification would result in enhanced reproducibility of computational genomic analyses.
MeSH term(s)	Computational Biology/methods ; Genomics ; High-Throughput Nucleotide Sequencing ; Internet ; Reproducibility of Results ; Sequence Analysis, DNA ; User-Computer Interface
Language	English
Publishing date	2017-07-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-017-1747-0
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Conference proceedings ; Audio / Video ; Online: An online bioinformatics training method delivering practical and tailored workshops to distant trainees

Hall, Christina / Backhaus, Ann / De La Pierre, Marco / Christiansen, Jeffrey / Lonie, Andrew

2020

Abstract: This poster was presented at the eResearch Australasia 2020 virtual conference, 19-23 October 2020. It described the training methodology used by Australian BioCommons, documenting the move to purely online events in response to the COVID-19 pandemic. As ...

Abstract	This poster was presented at the eResearch Australasia 2020 virtual conference, 19-23 October 2020. It described the training methodology used by Australian BioCommons, documenting the move to purely online events in response to the COVID-19 pandemic. As part of our mission to help life scientists develop bioinformatics competencies, Australian BioCommons faces challenges relating to Australia’s large size and small, widely-dispersed population. Pre-COVID19, we developed a ‘hybrid’ training method to deliver hands-on bioinformatics workshops to large groups of researchers across the country. The method combined features and benefits of webinar-style delivery from an expert trainer with face-to-face hands-on practical exercises in a classroom setting. Workshops were held concurrently in classrooms at participating sites with trained local researchers acting as facilitators. Since the pandemic has made face-to-face training impossible, we now face different challenges when trying to reach researchers needing our training. When gathering together physically became restricted, we moved our training workshops completely online. In partnership with Pawsey Supercomputing Centre, we augmented the method to utilise ‘breakout rooms’ for personal interactions between small curated groups of trainees with trained facilitators. Despite the delivery of workshops as online presentations, we preserved what makes our training valuable - the provision of hands-on, interactive and tailored learning opportunities. The method has become a key tool for us to ensure scalable and more equitable delivery of short-course bioinformatics training nationally.
Keywords	covid19
Publishing date	2020-10-19
Publishing country	eu
Document type	Conference proceedings ; Audio / Video ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv.

Khan, Farah Zaib / Soiland-Reyes, Stian / Sinnott, Richard O / Lonie, Andrew / Goble, Carole / Crusoe, Michael R

GigaScience

2019 Volume 8, Issue 11

Abstract: Background: The automation of data analysis in the form of scientific workflows has become a widely adopted practice in many fields of research. Computationally driven data-intensive experiments using workflows enable automation, scaling, adaptation, ... ...

Abstract	Background: The automation of data analysis in the form of scientific workflows has become a widely adopted practice in many fields of research. Computationally driven data-intensive experiments using workflows enable automation, scaling, adaptation, and provenance support. However, there are still several challenges associated with the effective sharing, publication, and reproducibility of such workflows due to the incomplete capture of provenance and lack of interoperability between different technical (software) platforms. Results: Based on best-practice recommendations identified from the literature on workflow design, sharing, and publishing, we define a hierarchical provenance framework to achieve uniformity in provenance and support comprehensive and fully re-executable workflows equipped with domain-specific information. To realize this framework, we present CWLProv, a standard-based format to represent any workflow-based computational analysis to produce workflow output artefacts that satisfy the various levels of provenance. We use open source community-driven standards, interoperable workflow definitions in Common Workflow Language (CWL), structured provenance representation using the W3C PROV model, and resource aggregation and sharing as workflow-centric research objects generated along with the final outputs of a given workflow enactment. We demonstrate the utility of this approach through a practical implementation of CWLProv and evaluation using real-life genomic workflows developed by independent groups. Conclusions: The underlying principles of the standards utilized by CWLProv enable semantically rich and executable research objects that capture computational workflows with retrospective provenance such that any platform supporting CWL will be able to understand the analysis, reuse the methods for partial reruns, or reproduce the analysis to validate the published findings.
MeSH term(s)	Genomics ; Humans ; Models, Theoretical ; Software ; Workflow
Language	English
Publishing date	2019-11-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2708999-X
ISSN	2047-217X ; 2047-217X
ISSN (online)	2047-217X
ISSN	2047-217X
DOI	10.1093/gigascience/giz095
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Article ; Online: Ready-to-use public infrastructure for global SARS-CoV-2 monitoring.

Maier, Wolfgang / Bray, Simon / van den Beek, Marius / Bouvier, Dave / Coraor, Nathan / Miladi, Milad / Singh, Babita / De Argila, Jordi Rambla / Baker, Dannon / Roach, Nathan / Gladman, Simon / Coppens, Frederik / Martin, Darren P / Lonie, Andrew / Grüning, Björn / Kosakovsky Pond, Sergei L / Nekrutenko, Anton

Nature biotechnology

2021 Volume 39, Issue 10, Page(s) 1178–1179

MeSH term(s)	COVID-19/epidemiology ; COVID-19/virology ; Databases, Factual ; Genome, Viral/genetics ; Humans ; Pandemics ; SARS-CoV-2/pathogenicity
Language	English
Publishing date	2021-09-01
Publishing country	United States
Document type	Letter ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/s41587-021-01069-1
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Zs.A 2167: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 137: Show issues
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Article: Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring.

Maier, Wolfgang / Bray, Simon / van den Beek, Marius / Bouvier, Dave / Coraor, Nathaniel / Miladi, Milad / Singh, Babita / De Argila, Jordi Rambla / Baker, Dannon / Roach, Nathan / Gladman, Simon / Coppens, Frederik / Martin, Darren P / Lonie, Andrew / Grüning, Björn / Kosakovsky Pond, Sergei L / Nekrutenko, Anton

bioRxiv : the preprint server for biology

2021

Abstract: The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data.Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is ... ...

Abstract	The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data.Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is necessary to pull together global computational resources and deliver the best open source tools and analysis workflows within a ready to use, universally accessible resource. Such a resource should not be controlled by a single research group, institution, or country. Instead it should be maintained by a community of users and developers who ensure that the system remains operational and populated with current tools. A community is also essential for facilitating the types of discourse needed to establish best analytical practices. Bringing together public computational research infrastructure from the USA, Europe, and Australia, we developed a distributed data analysis platform that accomplishes these goals. It is immediately accessible to anyone in the world and is designed for the analysis of rapidly growing collections of deep sequencing datasets. We demonstrate its utility by detecting allelic variants in high-quality existing SARS-CoV-2 sequencing datasets and by continuous reanalysis of COG-UK data. All workflows, data, and documentation is available at https://covid19.galaxyproject.org .
Language	English
Publishing date	2021-03-25
Publishing country	United States
Document type	Preprint
DOI	10.1101/2021.03.25.437046
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Article: iSRAP - a one-touch research tool for rapid profiling of small RNA-seq data.

Quek, Camelia / Jung, Chol-Hee / Bellingham, Shayne A / Lonie, Andrew / Hill, Andrew F

Journal of extracellular vesicles

2015 Volume 4, Page(s) 29454

Abstract: Small non-coding RNAs have been significantly recognized as the key modulators in many biological processes, and are emerging as promising biomarkers for several diseases. These RNA species are transcribed in cells and can be packaged in extracellular ... ...

Abstract	Small non-coding RNAs have been significantly recognized as the key modulators in many biological processes, and are emerging as promising biomarkers for several diseases. These RNA species are transcribed in cells and can be packaged in extracellular vesicles, which are small vesicles released from many biotypes, and are involved in intercellular communication. Currently, the advent of next-generation sequencing (NGS) technology for high-throughput profiling has further advanced the biological insights of non-coding RNA on a genome-wide scale and has become the preferred approach for the discovery and quantification of non-coding RNA species. Despite the routine practice of NGS, the processing of large data sets poses difficulty for analysis before conducting downstream experiments. Often, the current analysis tools are designed for specific RNA species, such as microRNA, and are limited in flexibility for modifying parameters for optimization. An analysis tool that allows for maximum control of different software is essential for drawing concrete conclusions for differentially expressed transcripts. Here, we developed a one-touch integrated small RNA analysis pipeline (iSRAP) research tool that is composed of widely used tools for rapid profiling of small RNAs. The performance test of iSRAP using publicly and in-house available data sets shows its ability of comprehensive profiling of small RNAs of various classes, and analysis of differentially expressed small RNAs. iSRAP offers comprehensive analysis of small RNA sequencing data that leverage informed decisions on the downstream analyses of small RNA studies, including extracellular vesicles such as exosomes.
Language	English
Publishing date	2015-11-09
Publishing country	Sweden
Document type	Journal Article
ZDB-ID	2683797-3
ISSN	2001-3078
ISSN	2001-3078
DOI	10.3402/jev.v4.29454
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Article ; Online: Hi-Plex2: a simple and robust approach to targeted sequencing-based genetic screening.

Hammet, Fleur / Mahmood, Khalid / Green, Thomas R / Nguyen-Dumont, Tu / Southey, Melissa C / Buchanan, Daniel D / Lonie, Andrew / Nathanson, Katherine L / Couch, Fergus J / Pope, Bernard J / Park, Daniel J

BioTechniques

2019 Volume 67, Issue 3, Page(s) 118–122

Abstract: We have previously reported Hi-Plex, a multiplex PCR methodology for building targeted DNA sequencing libraries that offers a low-cost protocol compatible with high-throughput processing. Here, we detail an improved protocol, Hi-Plex2, that more ... ...

Abstract	We have previously reported Hi-Plex, a multiplex PCR methodology for building targeted DNA sequencing libraries that offers a low-cost protocol compatible with high-throughput processing. Here, we detail an improved protocol, Hi-Plex2, that more effectively enables the robust construction of small-to-medium panel-size libraries while maintaining low cost, simplicity and accuracy benefits of the Hi-Plex platform. Hi-Plex2 was applied to three panels, comprising 291, 740 and 1193 amplicons, targeting genes associated with risk for breast and/or colon cancer. We show substantial reduction of off-target amplification to enable library construction for small-to-medium-sized design panels not possible using the previous Hi-Plex chemistry.
MeSH term(s)	DNA Primers/genetics ; Electrophoresis, Agar Gel/methods ; Gene Library ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Multiplex Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/methods
Chemical Substances	DNA Primers
Language	English
Publishing date	2019-07-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	48453-2
ISSN	1940-9818 ; 0736-6205
ISSN (online)	1940-9818
ISSN	0736-6205
DOI	10.2144/btn-2019-0026
Database	MEDical Literature Analysis and Retrieval System OnLINE

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