Author

Simon L. Gladman

The University of MelbourneORCID 0000-0002-6100-4385Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Signature Assays, Organisms & Methods

Click to filter · or open tag

Research Focus:software / tool· 7 Research Focus:benchmarking· 6 Research Focus:database / resource· 6 Approach:experimental assay· 5 Assay:whole-genome sequencing· 2 Approach:statistical model· 1 Research Focus:variant calling· 1

Frequent Co-Authors

Björn Andreas GrüningiD· 6 shared Anthony BretaudeauiD· 4 shared Daniel J BlankenbergiD· 4 shared Dave BouvieriD· 4 shared Frederik CoppensiD· 4 shared Nicola SoranzoiD· 4 shared Anton NekrutenkoiD· 3 shared Bérénice BatutiD· 3 shared

Activity by Year

2017-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

6 shared papersBioinformatics

Björn Andreas GrüningORCID

Mutual co-authors in cluster

Author profile →

8 papers

Recent·Most cited

Galaxy Training: A Powerful Framework for Teaching!

Saskia Hiltemann, Helena Rasche, Simon L. Gladman, Hans-Rudolf Hotz, Delphine Larivière, Daniel J Blankenberg, Pratik Dilip Jagtap, Thomas Wollmann, Anthony Bretaudeau, Nadia Goué, Timothy J. Griffin, Coline Royaux, Yvan Le Bras, Subina Mehta, Anna Syme, , the Galaxy Training Network

The paper introduces Galaxy Training Network (GTN) as a framework for creating and sharing FAIR training materials for data analysis, with recent improvements to support educators and expand its use in various learning environments.

PLoS Computational Biology · Jan 9, 2023Peer-reviewedBioinformatics

Training Infrastructure as a Service

Helena Rasche, Cameron J. Hyde, John Davis, Simon L. Gladman, Nate Coraor, Anthony Bretaudeau, Gianmauro Cuccuru, Wendi Bacon, Beatriz Serrano‐Solano, Jennifer Hillman‐Jackson, Saskia Hiltemann, Miaomiao Zhou, Björn Andreas Grüning, Andrew Stubbs

TIaaS provides scalable infrastructure for efficient bioinformatics training, enabling remote and in-person classes with minimal delays and administrative overhead.

GigaScience · Dec 28, 2022Peer-reviewedBioinformatics

Expanding the Galaxy's reference data

VIJAY NAGAMPALLI, Jayadev Joshi, Nate Coraor, Jennifer Hillman‐Jackson, Dave Bouvier, Marius van den Beek, Ignacio Eguinoa, Frederik Coppens, John Davis, Michał Stolarczyk, Nathan C. Sheffield, Simon L. Gladman, Gianmauro Cuccuru, Björn Andreas Grüning, Nicola Soranzo, , Daniel J Blankenberg

The paper describes integrating refgenie into Galaxy to manage and share reference datasets, with tools for retrieval and a global repository for easy access.

Bioinformatics Advances · Jan 1, 2022Peer-reviewedBioinformatics

Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring

Wolfgang Maier, Simon A. Bray, Marius van den Beek, Dave Bouvier, Nathan Coraor, Milad Miladi, Babita Singh, Jordi Rambla, Dannon Baker, Nathan P. Roach, Simon L. Gladman, Frederik Coppens, Darren Patrick Martin, Andrew J. Lonie, Björn Andreas Grüning, , Anton Nekrutenko

The paper presents a global, community-maintained platform for analyzing SARS-CoV-2 genomic data, demonstrating its utility in variant detection and reanalysis of existing datasets.

bioRxiv · Mar 25, 2021 · PreprintBioinformatics

No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics

Dannon Baker, Marius van den Beek, Daniel J Blankenberg, Dave Bouvier, John M. Chilton, Nate Coraor, Frederik Coppens, Ignacio Eguinoa, Simon L. Gladman, Björn Andreas Grüning, Nicholas Keener, Delphine Larivière, Andrew J. Lonie, Sergei L. Kosakovsky Pond, Wolfgang Maier, , Steven Weaver

The paper highlights the importance of open data and analytics in responding to public health emergencies, using COVID-19 genomic data to demonstrate the effectiveness of community-driven software tools and infrastructure.

PLoS Pathogens · Aug 13, 2020Peer-reviewedGenomics

Bioconda: A sustainable and comprehensive software distribution for the life sciences

Björn Grüning, Ryan Dale, Andreas Sjödin, Brad Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, Adam Caprez, Bérénice Batut, Mathias Haudgaard, Thomas Cokelaer, Kyle A. Beauchamp, Brent S. Pedersen, Youri Hoogstrate, Anthony Bretaudeau, , Matthew L. Workentine

Bioconda provides a sustainable, comprehensive distribution of bioinformatics software using Conda for reproducible analysis across platforms.

Nature Methods · Jun 25, 2018Peer-reviewedBioinformatics

Community-driven data analysis training for biology

Bérénice Batut, Saskia Hiltemann, Andrea Bagnacani, Dannon Baker, Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, Martin Čech, John M. Chilton, Dave Clements, Olivia Doppelt‐Azeroual, Anika Erxleben, Mallory Freeberg, Simon L. Gladman, , Björn Andreas Grüning

The paper presents a community-driven framework for interactive data analytics training in life sciences, enabling researchers to learn through web-based computation without software installation.

Cell Systems · Jun 1, 2018Peer-reviewedBioinformatics

Best Practice Data Life Cycle Approaches for the Life Sciences

Philippa C. Griffin, Jyoti R. Khadake, Kate S. Lemay, Suzanna Lewis, Sandra E. Orchard, Andrew J. Pask, Bernard J. Pope, Ute Roessner, Keith Russell, Torsten Seemann, Andrew E. Treloar, Sonika Tyagi, Jeffrey H. Christiansen, Saravanan Dayalan, Simon L. Gladman, , Maria Victoria Schneider

The paper provides best practice data life cycle approaches for life sciences researchers focusing on omics datasets and computational data analysis.

F1000Research · Aug 31, 2017Peer-reviewedBioinformatics