The CSHQ-DE Questionnaire Uncovers Relevant Sleep Disorders in Children and Adolescents with Long COVID

Acute SARS-CoV-2 infections in children and adolescents are usually mild. However, they can suffer from ongoing symptoms, generally referred to as long COVID. Sleep disorders are one of the most frequent complaints in long COVID although precise data are missing. We assessed the sleep behavior of children and adolescents who presented at our outpatient clinic between January 2021 and May 2022 with the Children’s Sleep Habits Questionnaire (CSHQ-DE). We compared the sleep behavior at three different time points: pre-COVID-19; post-COVID-19 at the initial presentation; and post-COVID-19 at re-presentation. Data from 45 patients were analyzed. Of those, 64% were female and the median age was 10 years (range: 0–18 years). Asymptomatic or mild COVID-19 disease was experienced in 89% of patients; 11% experienced moderate disease. The initial presentation occurred at a median of 20.4 weeks (6 weeks–14 months) after the infection. The CSHQ-DE score increased significantly from pre-COVID-19 (45.82 ± 8.7 points) to post-COVID-19 (49.40 ± 8.3 points; p ≤ 0.01). The score then normalized at re-presentation (46.98 ± 7.8; p = 0.1). The greatest changes were seen in the CSHQ-DE subscale score “daytime sleepiness”. Our data showed that children and adolescents with long COVID often suffer from sleep disturbances. For most children and adolescents, these sleep disorders decreased over time without any further medical intervention aside from a basic sleep consultation

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

Galaxy (homepage: https://galaxyproject.org, main public server: https://usegalaxy.org) is a web-based scientific analysis platform used by tens of thousands of scientists across the world to analyze large biomedical datasets such as those found in genomics, proteomics, metabolomics and imaging. Started in 2005, Galaxy continues to focus on three key challenges of data-driven biomedical science: making analyses accessible to all researchers, ensuring analyses are completely reproducible, and making it simple to communicate analyses so that they can be reused and extended. During the last two years, the Galaxy team and the open-source community around Galaxy have made substantial improvements to Galaxy's core framework, user interface, tools, and training materials. Framework and user interface improvements now enable Galaxy to be used for analyzing tens of thousands of datasets, and >5500 tools are now available from the Galaxy ToolShed. The Galaxy community has led an effort to create numerous high-quality tutorials focused on common types of genomic analyses. The Galaxy developer and user communities continue to grow and be integral to Galaxy's development. The number of Galaxy public servers, developers contributing to the Galaxy framework and its tools, and users of the main Galaxy server have all increased substantially

The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond

There are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For more than a decade, the Galaxy Project has been providing computational infrastructure and a unified user interface for these tools to make them accessible to a wide range of researchers. To streamline the process of integrating tools and constructing workflows as much as possible, we have developed Planemo, a software development kit for tool and workflow developers and Galaxy power users. Here we outline Planemo’s implementation and describe its broad range of functionality for designing, testing, and executing Galaxy tools, workflows, and training material. In addition, we discuss the philosophy underlying Galaxy tool and workflow development, and how Planemo encourages the use of development best practices, such as test-driven development, by its users, including those who are not professional software developers

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

International audienceHigh-throughput data production technologies, particularly 'next-generation' DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods , as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible , transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication , or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale

Galaxy planemo 0.35.0

Command-line utilities to assist in developing tools for the Galaxy Project. http://galaxyproject.or

Expanding the Galaxy’s reference data

Properly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie is a reference asset management system that allows users to easily organize, retrieve and share such datasets. Here, we describe the integration of refgenie into the Galaxy platform. Server administrators are able to configure Galaxy to make use of reference datasets made available on a refgenie instance. In addition, a Galaxy Data Manager tool has been developed to provide a graphical interface to refgenie’s remote reference retrieval functionality. A large collection of reference datasets has also been made available using the CVMFS (CernVM File System) repository from GalaxyProject.org, with mirrors across the USA, Canada, Europe and Australia, enabling easy use outside of Galaxy. Availability and implementation The ability of Galaxy to use refgenie assets was added to the core Galaxy framework in version 22.01, which is available from https://github.com/galaxyproject/galaxy under the Academic Free License version 3.0. The refgenie Data Manager tool can be installed via the Galaxy ToolShed, with source code managed at https://github.com/BlankenbergLab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull and released using an MIT license. Access to existing data is also available through CVMFS, with instructions at https://galaxyproject.org/admin/reference-data-repo/. No new data were generated or analyzed in support of this research

bgruening/docker-galaxy-stable: Galaxy Docker Image 17.09

much improved documentation about using Galaxy Docker and an external cluster (@rhpvorderman) CVMFS support - mounting in 4TB of pre-build reference data (@chambm) Singularity support and tests (compose only) more work on K8s support and testing (@jmchilton) using .env files to configure the compose setup for SLURM, Condor, K8s, SLURM-Singularity, Condor-Docke