Notebook Sharing: Scholarly Scribbles

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In the second guest blog post of our ‘Opening Science’ Series, Dr Rachel Harding talks to us about her Open lab notebook project, Lab Scribbles. Rachel is a Postdoctoral Fellow within the Structural Genomics Consortium (SGC), at the University of Toronto, and performs her work in a collaboration with the Cure for Huntington’s Disease Initiative (CHDI) Foundation. She blogs at labscribbles.com.
Contact: @LabScribbles, rachel.harding@utoronto.ca.

Huntington’s disease (HD) is a devastating inherited neurodegenerative disorder with limited therapies and no cures available to patients. HD symptoms are progressive in their severity throughout a patient’s lifetime and include a range of physical, psychiatric and cognitive manifestations. These are often likened to having Alzheimer’s, Parkinson’s and ALS simultaneously. All HD patients have a mutation in the huntingtin gene of their DNA, and was successfully mapped in the human genome more than 20 years ago. In the intervening time, however, our knowledge of the huntingtin protein, encoded by this gene, remains incomplete. Thus, how the HD mutation might affect the function of the protein is also poorly understood.

envelope

Electron microscopy allows calculation of a low resolution envelope of the huntingtin protein particles, revealing their overall shape

Using a technique called cryo-electron microscopy, I am working with a collaborative team of scientists in numerous labs around the world to image individual huntingtin protein molecules, in the hope that it might give insight into how huntingtin functions in the cells of our bodies. This is not a novel premise for a project in the field, with many labs already attempting similar experimental strategies. However, very little evidence of this research can be found in the published literature. This likely reflects the intrinsic bias of the traditional scientific publishing system to preferentially report complete research stories — and so-called ‘positive’ data. My hypothesis is that this progress would be faster if all scientists shared detailed methods and data, both positive and negative, more rapidly with the wider community.

“One of the greatest benefits has been the international collaborative network of scientists who have contributed ideas, materials and experimental data…”

In an effort to catalyse research efforts, I am releasing all of my methods and results for this project in close to real time using the data repository Zenodo and my blog Lab Scribbles. Using a CC-BY license, all output is available for anyone to read, use and critique. Since commencing this project, I have been fortunate to have had many great conversations about my research with academics also working on HD, patients and families affected by this disease, and many other persons interested in the research and this alternative ‘publication’ process. One of the greatest benefits has been the international collaborative network of scientists who have contributed ideas, materials and experimental data towards this project, pushing us towards our research goals more quickly. Following the first anniversary of this project, I am now looking to see how I can improve my data sharing to ensure the data is both discoverable and in a format useful to other scientists.

I have been fortunate to have the full support for the Open notebook project from both the SGC, and my funding agency, the CHDI. In particular, I have appreciated the mentorship of Aled Edwards, Cheryl Arrowsmith and Leticia Toledo-Sherman.

The text, figure and photograph are by Rachel Harding, and are distributed under the Creative Commons Attribution License (CC-BY). Illustration by Hindawi and is also CC-BY.

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