The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update
2024/05/20 by The Galaxy Community, Linelle Ann L Abueg, Enis Afgan +97 · 52 citations
Computer Science · Decision Sciences · #Advanced Data Storage Technologies #Research Data Management Practices #Scientific Computing and Data Management
paper · pdf · doi:10.1093/nar/gkae410
openalex publication_date 2024/05/20 · openalex created_date 2024/05/22 · openalex updated_date 2026/07/31
Abstract
Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform stability, tool and reference dataset diversity, training, support and integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements in accessibility, tool discoverability through Galaxy Labs/subdomains, and a redesigned Galaxy ToolShed. Galaxy tool capabilities are progressing in two strategic directions: integrating general purpose graphical processing units (GPGPU) access for cutting-edge methods, and licensed tool support. Engagement with global research consortia is being increased by developing more workflows in Galaxy and by resourcing the public Galaxy services to run them. The Galaxy Training Network (GTN) portfolio has grown in both size, and accessibility, through learning paths and direct integration with Galaxy tools that feature in training courses. Code development continues in line with the Galaxy Project roadmap, with improvements to job scheduling and the user interface. Environmental impact assessment is also helping engage users and developers, reminding them of their role in sustainability, by displaying estimated CO2 emissions generated by each Galaxy job.
Citations
Cited by
- A novel planctomycetotal isolate from subsurface percolates belongs to the novel species Anatilimnocola aquadivae sp. nov. in the family Pirellulaceae
- Assessing the validity of leucine zipper constructs predicted by <scp>AlphaFold</scp>
- Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data
- Galaxy for accessible, reproducible, and collaborative data analyses: 2026 update
- Fungal ecology in the age of 'omics
- Ancestral <i>Wolbachia</i> lineages are likely donors of ribotoxin genes in <i>Aedes aegypti</i>
- Soil community structure across native and exotic forests is shaped by edaphoclimatic conditions and eukaryotic biomarkers
- A Nuclear Effector of <i>Magnaporthe oryzae</i> Targets a Mitogen-Activated Protein Kinase to Suppress Basal Plant Defense
- A Nanopore-Only Assembly of a Nuclear and Mitochondrial Genome of a Red Coachwhip (Masticophis flagellum piceus)
- Chd4 remodels chromatin to control retinal cell type specification and lineage termination
- Evidence supporting the first secondary chromosome in Actinobacteria as a hallmark of the <i>Embleya</i> genus.
- Harnessing Bulk‐Segregant Mapping to Identify Trait‐Associated Genes in the Allopolyploid Model Plant <i>Nicotiana benthamiana</i>
- Sulfur disproportionation occurs globally across anoxic habitats and has multiple mechanisms of independent evolutionary origin
- Hangover regulates gene expression by limiting NSL-mediated H4K16 acetylation
- Acidithiobacillus sibiricus sp. nov., a novel extremely acidophilic sulfur-oxidizing bacterium isolated from a magmatic sulfide-rich ore deposit
- Evolution of sexual systems and regressive evolution in <i>Riccia</i>
- CESA7 and microtubules pattern complex secondary cell walls in explosive fruit of <i>Cardamine hirsuta</i>
- SNiPgenie: a tool for microbial SNP site detection from whole-genome sequencing data
- Allele frequency selection and no age-related increase in human oocyte mitochondrial mutations
- Catalytic-dependent and independent functions of the histone acetyltransferase CBP promote pioneer factor-mediated zygotic genome activation
- A Non‐Metaproteomics Researchers’ View on Metaproteomics in Microbiome Research
- Guidance framework to apply best practices in ecological data analysis: lessons learned from building Galaxy-Ecology
- bio.tools: an expanded web service for research software in the life sciences
- Cancer epitope prediction tools and analysis pipelines in CEDAR
- Saccharibacteria deploy two distinct type IV pili, driving episymbiosis, host competition, and twitching motility
- Human gut strains of <i>Desulfovibrio piger</i> exhibit spontaneous induction of multiple prophages
- A catalog of metagenome-assembled genomes from Amazonian forest and pasture soils
- Nascent CUT&Tag captures transcription factor binding after chromatin duplication
- Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant
- RDMkit: A research data management toolkit for life sciences
- Genome assembly of the endangered Santa Marta Harlequin Toad, <i>Atelopus laetissimus</i> , endemic to the Sierra Nevada de Santa Marta of Colombia
- The microbiologist's guide to metaproteomics
- Re-description, systematics and complete mitochondrial genome of Philhelius coreanus (Shiraki, 1930) (Diptera, Syrphidae) in the Republic of Korea
- <i>Lactobacillus</i> and <i>Limosilactobacillus</i> MAGs from alcoholic fermentation in sugarcane biorefineries
- The segregase CDC48 integrates blue light and hormonal cues to regulate photomorphogenesis in Arabidopsis
- Atkinsonella hypoxylon virus capsid structure highlights the diversity of capsid proteins among the Partitiviridae
- piqtree: A Python Package for Seamless Phylogenetic Inference with IQ-TREE
- Replication-stress-induced chromatin loops protect fork stability
- GRHL and PGR control WNT4 expression via 3D looping of conserved and species-specific enhancers
- A highly contiguous genome assembly for the California vole, <i>Microtus californicus,</i> provides insight into phylogenetic relationships and patterns of synteny among voles
- Neural function of Netrin-1 in precancerous lesions of the pancreas
- Galaxy QCxMS for straightforward semi-empirical quantum mechanical EI-MS prediction
- Cryptic Kultarr: Integrative Taxonomy Reveals Unrecognized Species of Carnivorous Marsupial (Dasyuridae: <i>Antechinomys</i> ) in Arid Australia
- Exploring the microbial communities in coastal cenote and their hidden biotechnological potential
- Identification of a sex-determining locus potentially involved in a conflict over sex-ratio
- Characterization of a novel zebrafish model of <i>MTMR5</i>-associated Charcot-Marie-Tooth disease type 4B3
- Dual function of ERH in primary miRNA biogenesis
- Knowledge preservation in the era of big science and AI: strategies for sustainable scientific research
- Revisiting the Identification of <i>Xanthomonas arboricola</i> Strains Isolated from Cherry in Montenegro Through Genome Analysis and Pathogenicity Testing
- The Genome of <i>Pseudocercospora cladosporioides</i> : A Step Toward Understanding Olive Cercosporiosis
- piqtree: a python package for seamless phylogenetic inference with IQ-TREE
- Ten simple rules to follow when cleaning occurrence data in palaeobiology
Related