CRUMB: a shiny-based app to analyze rhythmic feeding in Drosophila using the FLIC system
| Autor: | Sergio Hidalgo, Joanna C Chiu |
|---|---|
| Rok vydání: | 2023 |
| Předmět: |
General Immunology and Microbiology
Shiny Clinical Sciences Oncology and Carcinogenesis chrononutrition Reproducibility of Results Health Promotion General Medicine Circadian clock Mobile Applications General Biochemistry Genetics and Molecular Biology Circadian Rhythm Food-Drug Interactions Feeding-fasting rhythm Animals Drosophila Biochemistry and Cell Biology FLIC time-restricted eating General Pharmacology Toxicology and Pharmaceutics Sleep Research Nutrition |
| Zdroj: | F1000Research. 12:374 |
| ISSN: | 2046-1402 |
| DOI: | 10.12688/f1000research.132587.1 |
| Popis: | Rhythmic feeding activity has become an important research area for circadian biologists as it is now clear that metabolic input is critical for regulating circadian rhythms, and chrononutrition has been shown to promote health span. In contrast to locomotor activity rhythm, studies conducting high throughput analysis of Drosophila rhythmic food intake have been limited and few monitoring system options are available. One monitoring system, the Fly Liquid-Food Interaction Counter (FLIC) has become popular, but there is a lack of efficient analysis toolkits to facilitate scalability and ensure reproducibility by using unified parameters for data analysis. Here, we developed Circadian Rhythm Using Mealtime Behavior (CRUMB), a user-friendly Shiny app to analyze data collected using the FLIC system. CRUMB leverages the ‘plotly’ and ‘DT’ packages to enable interactive raw data review as well as the generation of easily manipulable graphs and data tables. We used the main features of the FLIC master code provided with the system to retrieve feeding events and provide a simplified pipeline to conduct circadian analysis. We also replaced the use of base functions in time-consuming processes such as ‘rle’ and ‘read.csv’ with faster versions available from other packages to optimize computing time. We expect CRUMB to facilitate analysis of feeding-fasting rhythm as a robust output of the circadian clock. |
| Databáze: | OpenAIRE |
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