February 21, 2017

New Orthogonal Laboratory Methods

Lately I have been incorporating two new tools into my research program's [1] infrastructure. One is a software tool with community support, and the other is a development of my own. 

The first addition is the Jupyter Notebook (sometimes called the iPython Notebook, as it is based on this platform). The Jupyter Notebook allows us to build repositories of methods, notes, code, and data analyses in an integrated manner. Jupyter Notebooks can be rendered in Github, making them freely accessible and distributable. For example, the DevoWorm project already has several notebooks hosted at Github. The long-term goal is to create notebooks for typical research activities, and using them for a host of purposes, from a Wiki-like instructional manual to supplemental materials for publications [2].

Jupyter Notebooks (example)

The other is a pipeline for project management with the goal of increasing participation and success in research. The idea is one that I have been bouncing around in my head based on my involvement with the OpenWorm Foundation community committee and personal experience. This could be a way to encourage more underrepresented and "high-risk" researchers to advance their work [3]. It is based on two exceedingly obvious principles: failure is not a breaking point for any research trajectory, and projects themselves should be defined in a bottom-up fashion (building on previous successes and experiences) [4]. Hopefully, this pipeline works well in implementation.

Building a Research Group Philosophy

UPDATE (2/22): I failed to include a snapshot of the Orthogonal Laboratory Slack team (currently with an n of 1). Slack is fast becoming a popular tool for laboratory management [5, 6], particularly those that are partially or fully virtual.

[1] I am in the process of turning Orthogonal Research into Orthogonal Laboratory. Currently it is a group of one (and a few collaborators). I am currently looking for an academic home, so putting the tools needed to scale up is worth the investment in time. More on this initiative later.

[2] Brown, C.T. (2017). Topics and concepts I'm excited about (Paper of the Future). Living in an Ivory Basement blog, January 9.

[3] the very notion of "high-risk research" is biased toward a fear of failure. Considering what is usually thrown into that bucket, "high-risk research" is a statement of cultural values more than an inherent risk. Removing the industrial, one-size-fits-all aspect of research might be a way to mitigate risk.

[4] sometimes you get lucky and get to define a project right out of the box. But in doing so, projects often end up exhibiting a hodgepodge quality that makes them seem unfocused.

[5] Perkel, J.M. (2017). How Scientists Use Slack. Nature, 541, 123-124.

[6] Washietl, S. (2016). 6 Ways to Streamline Communication in Your Research Group Using Slack. Paperpile blog, April 12.

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