Abstract
BackgroundImproving the availability and usability of data and analytical tools is a critical precondition for further advancing modern biological and biomedical research. For instance, one of the many ramifications of the COVID-19 global pandemic has been to make even more evident the importance of having bioinformatics tools and data readily actionable by researchers through convenient access points and supported by adequate IT infrastructures. One of the most successful efforts in improving the availability and usability of bioinformatics tools and data is represented by the Galaxy workflow manager and its thriving community. In 2020 we introduced Laniakea, a software platform conceived to streamline the configuration and deployment of “on-demand” Galaxy instances over the cloud. By facilitating the set-up and configuration of Galaxy web servers, Laniakea provides researchers with a powerful and highly customisable platform for executing complex bioinformatics analyses. The system can be accessed through a dedicated and user-friendly web interface that allows the Galaxy web server’s initial configuration and deployment.Results“Laniakea@ReCaS”, the first instance of a Laniakea-based service, is managed by ELIXIR-IT and was officially launched in February 2020, after about one year of development and testing that involved several users. Researchers can request access to Laniakea@ReCaS through an open-ended call for use-cases. Ten project proposals have been accepted since then, totalling 18 Galaxy on-demand virtual servers that employ ~ 100 CPUs, ~ 250 GB of RAM and ~ 5 TB of storage and serve several different communities and purposes. Herein, we present eight use cases demonstrating the versatility of the platform.ConclusionsDuring this first year of activity, the Laniakea-based service emerged as a flexible platform that facilitated the rapid development of bioinformatics tools, the efficient delivery of training activities, and the provision of public bioinformatics services in different settings, including food safety and clinical research. Laniakea@ReCaS provides a proof of concept of how enabling access to appropriate, reliable IT resources and ready-to-use bioinformatics tools can considerably streamline researchers’ work.
Highlights
Improving the availability and usability of data and analytical tools is a critical precondition for further advancing modern biological and biomedical research
During this first year of activity, the Laniakea-based service emerged as a flexible platform that facilitated the rapid development of bioinformatics tools, the efficient delivery of training activities, and the provision of public bioinformatics services in different settings, including food safety and clinical research
We focused our analysis on 91 samples with small insertion and deletion (INDELS) and multi-nucleotides variants (MNVs), since single nucleotide variants and splice-site single nucleotide variants did not require any modification of the CoVaCS pipeline
Summary
Improving the availability and usability of data and analytical tools is a critical precondition for further advancing modern biological and biomedical research. One of the most successful efforts in improving the availability and usability of bioinformatics tools and data is represented by the Galaxy workflow manager and its thriving community. The availability and accessibility of analytical software tools, standardised workflows and IT infrastructures are among the most critical enablers of data-driven science [1]. Similar considerations can be applied to bioinformatics workflows, which are an arrangement of software components that can be heterogeneous in their versioning, dependencies and environment requirements, limiting their portability, integration and, making it challenging to ensure an adequate level of analytical reproducibility [3]. The bioinformatics community in recent years has devoted considerable efforts to mitigate those barriers, for example, with the development of workflow managers (e.g., Taverna [4], Chipster [5], Galaxy [6]) as well as tools and workflow registries and repositories (e.g., bio.tools [7], myExperiment [8], Workflowhub [9])
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