Toward collaborative open data science in metabolomics using Jupyter Notebooks and cloud computing

AbstractBackgroundA lack of transparency and reporting standards in the scientific community has led to increasing and widespread concerns relating to reproduction and integrity of results. As an omics science, which generates vast amounts of data and relies heavily on data science for deriving biological meaning, metabolomics is highly vulnerable to irreproducibility. The metabolomics community has made substantial efforts to align with FAIR data standards by promoting open data formats, data repositories, online spectral libraries, and metabolite databases. Open data analysis platforms also exist; however, they tend to be inflexible and rely on the user to adequately report their methods and results. To enable FAIR data science in metabolomics, methods and results need to be transparently disseminated in a manner that is rapid, reusable, and fully integrated with the published work. To ensure broad use within the community such a framework also needs to be inclusive and intuitive for both computational novices and experts alike.Aim of ReviewTo encourage metabolomics researchers from all backgrounds to take control of their own data science, mould it to their personal requirements, and enthusiastically share resources through open science.Key Scientific Concepts of ReviewThis tutorial introduces the concept of interactive web-based computational laboratory notebooks. The reader is guided through a set of experiential tutorials specifically targeted at metabolomics researcher...
Source: Metabolomics - Category: Biology Source Type: research

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Publication date: Available online 20 November 2019Source: Journal of Advanced ResearchAuthor(s): Sohail Mumtaz, Pradeep Bhartiya, Neha Kaushik, Manish Adhikari, Pradeep Lamichhane, Su-Jae Lee, Nagendra Kumar Kaushik, Eun Ha ChoiAbstractOver the past few decades, microwave (MW) radiation has been widely used, and its biological effects have been extensively investigated. However, the effect of MW radiation on human skin biology is not well understood. We study the effects of pulsed high-power microwaves (HPMs) on melanoma (G361 and SK-Mel-31) and normal human dermal fibroblast (NHDF) cells. A pulsed power generator (Chundo...
Source: Journal of Advanced Research - Category: Research Source Type: research
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Source: Medscape Pulmonary Medicine Headlines - Category: Respiratory Medicine Tags: Infectious Diseases News Source Type: news
Suresh K. Mukherji
Source: Neuroimaging Clinics - Category: Radiology Source Type: research
SURESH K. MUKHERJI, MD, MBA, FACR
Source: Neuroimaging Clinics - Category: Radiology Source Type: research
Magnetoencephalography
Source: Neuroimaging Clinics - Category: Radiology Source Type: research
ELSEVIER
Source: Neuroimaging Clinics - Category: Radiology Source Type: research
NEUROIMAGING CLINICS OF NORTH AMERICA
Source: Neuroimaging Clinics - Category: Radiology Authors: Source Type: research
Source: Neuroimaging Clinics - Category: Radiology Source Type: research
Resting state functional connectivity (RSFC) has been widely studied in functional magnetic resonance imaging (fMRI) and is observed by a significant temporal correlation of spontaneous low-frequency signal fluctuations (SLFs) both within and across hemispheres during rest. Different hypotheses of RSFC include the biophysical origin hypothesis and cognitive origin hypothesis, which show that the role of SLFs and RSFC is still not completely understood. Furthermore, RSFC and age studies have shown an “age-related compensation” phenomenon. RSFC data analysis methods include time domain analysis, seed-based correl...
Source: Neuroimaging Clinics - Category: Radiology Authors: Source Type: research
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Source: European Journal of Radiology - Category: Radiology Source Type: research
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