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

Abstract: Background

A 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 Review

To 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 Review

This 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 researchers, based around the Jupyter Notebook web application, GitHub data repository, and Binder cloud computing platform.

Breaking down the walls of scientific secrecy | CBC News

Getting scooped by a competing researcher is one of a scientist’s biggest fears. And some of the most important discoveries in medical history have been tainted by competitive controversy.

Back in 1952, before he co-discovered the structure of DNA, James Watson got access to Rosalind Franklin’s revolutionary X-ray image of DNA without her knowledge.

That image, known as Photo 51, was a major clue that helped Watson and Francis Crick complete their Nobel Prize-winning discovery. The lack of credit given to Franklin remains a stain on the story of their breakthrough.

But what if Franklin had been informally publishing her research notes all along?

“She would have gotten credit instantly for her contribution,” said Susan Lamb, a historian of medicine who holds the Hannah Chair in the History of Medicine at the University of Ottawa….”