Journal article
CrustyBase v.2.0: new features and enhanced utilities to support open science
BMC Genomics, Vol.25, pp.1-12
2024
PMCID: PMC10823621
PMID: 38281926
Abstract
Transcriptomes present a rich, multi-dimensional subset of genomics data. They provide broad insights into genetic sequence, and more significantly gene expression, across biological samples. This technology is frequently employed for describing the genetic response to experimental conditions and has created vast libraries of datasets which shed light on gene function across different tissues, diseases, diets and developmental stages in many species. However, public accessibility of these data is impeded by a lack of suitable software interfaces and databases with which to locate and analyse them. BODY: Here we present an update on the status of CrustyBase.org, an online resource for analysing and sharing crustacean transcriptome datasets. Since its release in October 2020, the resource has provided many thousands of transcriptome sequences and expression profiles to its users and received 19 new dataset imports from researchers across the globe. In this article we discuss user analytics which point towards the utilization of this resource. The architecture of the application has proven robust with over 99.5% uptime and effective reporting of bugs through both user engagement and the error logging mechanism. We also introduce several new features that have been developed as part of a new release of CrustyBase.org. Two significant features are described in detail, which allow users to navigate through transcripts directly by submission of transcript identifiers, and then more broadly by searching for encoded protein domains by keyword. The latter is a novel and experimental feature, and grants users the ability to curate gene families from any dataset hosted on CrustyBase in a matter of minutes. We present case studies to demonstrate the utility of these features.
Community engagement with this resource has been very positive, and we hope that improvements to the service will further enable the research of users of the platform. Web-based platforms such as CrustyBase have many potential applications across life science domains, including the health sector, which are yet to be realised. This leads to a wider discussion around the role of web-based resources in facilitating an open and collaborative research community.
Details
- Title
- CrustyBase v.2.0: new features and enhanced utilities to support open science
- Authors
- Cameron Hyde (Author) - University of the Sunshine Coast, Queensland, Centre for BioinnovationTomer Ventura (Corresponding Author) - University of the Sunshine Coast, Queensland, Centre for Bioinnovation
- Publication details
- BMC Genomics, Vol.25, pp.1-12
- Publisher
- BioMed Central Ltd.
- Date published
- 2024
- DOI
- 10.1186/s12864-024-10033-7
- ISSN
- 1471-2164
- PMID
- 38281926; PMC10823621
- Copyright note
- This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
- Data Availability
- For security reasons, we do not intend to open-source the CrustyBase application code, but we encourage anyone wishing to collaborate on this project to contact us for access.
- Organisation Unit
- School of Science, Technology and Engineering; Centre for Bioinnovation
- Language
- English
- Record Identifier
- 991002598602621
- Output Type
- Journal article
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