Promoting open notebook science in an institutional biotech lab

Speaker: Rahmi Lale

This is a presentation given on 20 January, 2016, at the Open Tools and Infrastructure for Biology 2016 held at Newcastle University.

PhotoSynLab: working with Mesophiles, psychrophiles (some of these can grow at -10 degrees) and eukaryotic algae. Built a plasmid pTA-Mob and published in PLoS One, which allows you to do conjugation – the host can work as a donor in conjugation. It has a broad host range, practically all gram negatives.

When discussing the openness aspect of his work, he begins with the four essential elements of the scientific method: characterization, hypotheses, predictions, experiments (and of course, publishing). He will be focussing on reproducibility. With respect to publishing, “you have to understand human nature”. In publishing and sharing, there is a tension between cooperation and competition. Many believe that those scientists who make the greatest contribution often behave the worst, and vice versa.

In a 2014 Nature Methods editorial where they tried to stress the importance of the methods section of papers, they say that an open implementation provides confidence in the performance of a method, but also increases the likelihood that other researchers can build upon it.

An article about computer science in a publication is not the scholarship, but merely the advertising of the scholarship (Jon Claerbout). The inability to reproduce experiments indicates the possible limits of big science, and that without verification there is no science (Garfield, 1990).

A researcher moves from experiment to publishing, while a reader moves in the opposite direction. Having your data free isn’t such a big deal, but having a standard method of how you got your data there is more of an issue.

On their lab website, they give access to the raw data and the analysis (using wordpress). The latest version uses (is?) Benchling. The idea behind all of this is to aid reproducibility by giving access to all data and analysis. They also wish people to publish negative as well as positive results. This should aid career development by involving students in scientific writing. It is important to teach students how to communicate their science.

Please note that this post is merely my notes on the presentation. I may have made mistakes: these notes are not guaranteed to be correct. Unless explicitly stated, they represent neither my opinions nor the opinions of my employers. Any errors you can assume to be mine and not the speaker’s. I’m happy to correct any errors you may spot – just let me know!

 

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