Open Notebook Series: Open Notebook Platforms

July 17, 2012 | Posted by Anthony in Research |

This is the third in a series of posts by Anthony Salvagno about open notebook science.

An open notebook is ideally an online representation of your standard lab notebook. Everyone has a different style and volume of notes though, and an open notebook is no different. Software engineers need to take notes in their code, biologists need to take pictures, and mathematicians need any medium that can contain pages of equations.

There are consequently an array of open notebook platforms to choose from, and some better suited for certain applications than others. Five such platforms are discussed below, all capable of supporting scientific disciplines in varying aspects.

WordPress

Originally developed as a blogging platform, WordPress has become much more than that. It is the go to Content Management System (CMS) in web design, and is used for online shopping, blogs, artistic portfolios, personal websites, and even open notebooks. Personally speaking, WordPress is the most versatile platform for open notebooks and should be the model that open notebook designers look toward.

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Open Notebook Series: Why You Should Be An Open Notebook Scientist

July 6, 2012 | Posted by Anthony in Research |

This is the second in a series of posts by Anthony Salvagno about open notebook science.

Any discussion of a new scientific technique should begin with “What? Why? and How?”. The “Why?” in the case of Open Notebook Science (ONS) is likely the most important aspect of the paradigm. It is the most frequent question I get asked when discussing ONS, and its answers represent the key to unlocking its merits.

With this in mind, there are three main facets to ONS I can describe, which give credence to why one should be an open notebook scientist.

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About a year ago I was working on a project that required me to tether micron sized spheres to glass with DNA. I had my own protocol for successful tethering that was having some issues, so I turned to the literature.

I read about 10 different papers, each describing a different protocol, and often unclearly. I attempted each version of the published protocols after spending a great deal of time “decoding” the publications, and ended up with a different result every time. By contrast, had I had access to the raw protocols of each lab, I would have saved a lot of time. So as an ONS scientist, I published my own protocol, hoping to save other scientists a great deal of time.

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Open Notebook Series: What is an Open Notebook?

June 22, 2012 | Posted by Anthony in Research |

This is the first in a series of posts by Anthony Salvagno about open notebook science.

Most scientific information is stored in countless journals, recorded in disparate articles produced by scientists from all over the world and across many decades. And in the digital age, this content is easily found all over the web. Journals have adapted to host .pdf versions articles, they host blogs to make the content more approachable, and there are some that are built on open access or have preprint hosting capabilities (also open access).

Despite the digital revolution though, science hasn’t changed. Even though information is right at our fingertips, it is still locked. Locked behind a paywall. Locked behind technical jargon. And locked behind interpretation.

If journals are the masterlock for science, then what’s the combination?

Enter open notebooks. Open notebook science is the practice of making your entire research project available online as it is recorded. This online location is known as an open notebook and is the online analog to the paper notebook most scientists keep in their lab. It is the storage center for project plans, experimental protocols and setups, raw data, and even unfiltered interpretations.

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